ROBERT STROUD
COMPLETE PUBLICATION LIST (* for most relevant 20) h index 104
Complete List of Published Work also in MyBibliography:
PDB COORDINATES OF PROTEIN STRUCTURES DETERMINED & DEPOSITED
369 coordinate sets of Protein structures determined by X-ray crystallography in the Protein Data Bank as of July1st 2018; 8 sets currently being processed
REFEREED PUBLICATIONS:
1. MacKay AL, Stroud RM. (l968). Journal of Perception and Psychophysics 4, 90. An optical illusion.
2. Stroud RM, Kay L, Stanford RH, Battfay O, Corey RB, Dickerson, RE. (l969). Acta Cryst. A25, S182. The Crystal Structure of DIP-Trypsin at 2.7 Å Resolution.
3. Stroud RM, Kay LM, Dickerson RE. (l971). Cold Spring Harbor Symposia on Quantitative Biology 36, 125-140. The Crystal and Molecular Structure of DIP-inhibited Bovine Trypsin at 2.7 Å Resolution. (PMID: 4508129)
4. Stroud RM, Carlisle CH. (1972). Acta Cryst. B28, 304-307. A Single-Crystal Structure Determination of DL-6-Thioctic Acid, C8H14O2S2.
5. Stroud RM. (1973). Acta Cryst. B29, 690-696. The Crystal and Molecular Structure of Tubercidin, C11H14N4O4.
6. Stroud RM. (1973). Stockholm Symposium on Structure of Biological Molecules. The High Resolution Structure of Trypsin.
7. Stroud RM, Kay LM, Dickerson RE. (1974). J. Mol. Biol. 83, 185-208. The Structure of Bovine Trypsin: Electron Density Maps of the Inhibited Enzyme at 5 Å and at 2.7 Å Resolution. (PMID: 4821870)
8. Krieger M, Kay LM, Stroud RM. (1974). J. Mol. Biol. 83, 209-230. Structure and Specific Binding of Trypsin: Comparison of Inhibited Derivatives and a Model for Substrate Binding. (PMID: 4821871)
9. Chambers JL, Christoph GG, Krieger M, Kay L and Stroud RM. (1974). Bioch. Bioph. Res. Commun. 59, 70-74. Silver Ion Inhibition of Serine Proteases: Crystallographic Study of Silver-Trypsin. (PMID: 4842294)
10. Raftery MA, Bode J, Vandlen R, Michaelson D, Deutsch J, Moody T, Ross MJ, Stroud RM. (1974). FEBS Proc. 9, 9. Molecular Properties of Torpedo californica Acetylcholine Receptors.
11. Stroud RM. (1974). Scientific American 231, 74-88. A Family of Protein-Cutting Proteins.
12. Krieger M, Chambers JL, Christoph GG, Stroud RM, Trus BL. (1974). Acta Cryst. A30, 740-748. Data Collection in Protein Crystallography: Capillary Effects, and Background Corrections.
13. Stroud RM, Krieger M, Koeppe RE II, Kossiakoff AA, Chambers JL. (1975). In Proteases and Biological Control, pp. 13-32, Cold Spring Harbor Laboratory. Structure-Function Relationships in the Serine Proteases.
14. Raftery MA, Bode J, Vandlen R, Michaelson D, Deutsch J, Moody T, Ross MJ, Stroud RM. (1975). In Protein-Ligand Interactions, pp. 328-355, Walter de Gruyter & Co, Berlin, Germany. Structural and Functional Studies of an Acetylcholine Receptor.
15. Koeppe RE II, Stroud RM, Pena VA, Santi DV. (1975). J. Mol. Biol. 98, 155-160. A Pulsed Diffusion Technique for the Growth of Protein Crystals for X-ray Diffraction. (PMID: 1195375)
16. Koeppe RE II, Stroud RM. (1976). Biochemistry 15, 3450-3458. Mechanism of Hydrolysis by Serine Proteases: Direct Determination of the pKa's of Aspartyl-102 and Aspartyl-194 in Bovine Trypsin Using Difference Infrared Spectroscopy. (PMID: 986162)
17. Krieger M, Koeppe RE II, Stroud RM. (1976). Biochemistry 15, 3458-3464. pH Depend- ence of Tritium Exchange with the C-2 Protons of the Histidines in Bovine Trypsin. (PMID: 8090)
18. Krieger M, Stroud RM. (1976). Acta Cryst. A32, 653-656. Data Collection in Protein Crystallography: Experimental Methods for Reducing Background Radiation.
19. Webb NG, Samson S, Stroud RM, Gamble RC, Baldeschwieler JD. (1976). Rev. Sci. Instrum. 47, 836-839. Remotely controlled mirror of variable geometry for small-angle x-ray diffraction with synchrotron radiation.
20. Levitski A, Dodson GG, Henderson R, Palm D, Sheppard H, Stroud RM, Tanford C, Wright P, Zatz M. (1976). Dahlem Workshop on Hormone and Antihormone Action at the Target Cell. Catecholamine Receptors Group Report.
21. Webb NG, Samson S, Stroud RM, Gamble RC, Baldeschwieler JD. (l977). J. Appl. Cryst. 10, 104-110. A Focusing Monochromator for Small-Angle Diffraction Studies with Synchrotron Radiation.
22. Koeppe RE II, Krieger M, Stroud RM. (1977). Biochimica et Biophysica Acta 481, 617-621. The Effect of Pre-Incubation on Trypsin Kinetics at Low pH. (PMID: 15615)
23. Kossiakoff AA, Chambers JL, Kay LM, Stroud RM. (1977). Biochemistry 16, 654-664. Structure of Bovine Trypsinogen at 1.9 Å Resolution. (PMID: 556951)
24. Chambers JL, Stroud RM. (1977). Acta Cryst. B33, 1824-1837. Difference Fourier Refinement of the Structure of DIP-Trypsin at 1.5 Å with a Minicomputer Technique.
25. Ross MJ, Stroud RM. (1977). Acta Cryst. A33, 500-508. Error Analysis in the Biophysical Applications of a Flatbed Autodensitometer.
26. Ross MJ, Klymkowsky MW, Agard DA, Stroud RM. (1977). J. Mol. Biol. 116, 635-659. Structural Studies of a Membrane-bound Acetylcholine Receptor from Torpedo californica. (PMID: 563472)
27. Stroud RM, Kossiakoff AA, Chambers JL. (1977). Ann. Rev. Bioph. Bioeng. 6, 177-193. Mechanisms of Zymogen Activation. (PMID: 17350)
28. McKay DB, Kay LM, Stroud RM. (1977). In Chemistry and Biology of Thrombin, Lundblad RL, Fenton JW II, Mann KG eds. pp. 113-121, Ann Arbor Science Publishers, Inc, Ann Arbor, Michigan. Preliminary Crystallization and X-Ray Diffraction Studies of Human Thrombin.
29. Stroud RM, Agard DA. (1979). Biophys. J. 25, 495-512. Structure Determination of Asymmetric Membrane Profiles Using An Iterative Fourier Method. (PMID: 318062)
30. Chambers JL, Stroud RM. (1979). Acta. Cryst. B35, 1861-1874. The Accuracy of Refined Protein Structures: Comparison of Two Independently Refined Models of Bovine Trypsin.
31. Klymkowsky MW, Stroud RM. (1979). J. Mol. Biol. 128, 319-334. Immunospecific Identification and Three-dimensional Structure of a Membrane-bound Acetylcholine Receptor from Torpedo californica. (PMID: 439138)
32. Klymkowsky MW, Heuser JE, Stroud RM. (1980). J. Cell Biol. 85, 823-838. Protease Effects on the Structure of Acetylcholine Receptor Membranes from Torpedo californica. (PMID: 6993498)
33. Tobler J, Krieger M, Stroud RM. (1981). J. Cellular Physiology 108, 277-290. The Binding and Processing of Plasminogen by Balb/c 3T3 and SV3T3 Cells. (PMID: 6267086)
* 34. Kistler J, Stroud RM. (1981). Proc. Natl Acad. Sci. USA 78, 3678-3682. Crystalline arrays of membrane-bound acetylcholine receptor. (PMID: 6943572)
35. Katre NV, Wolber PK, Stoeckenius W, Stroud RM. (1981). Proc. Natl. Acad. Sci. USA 78, 4068-4072. Attachment site(s) of retinal in bacteriorhodopsin. (PMID: 6794028)
36. Agard DA, Steinberg RA, Stroud RM. (1981). Analyt. Biochem. 111, 257-268. Quantitative Analyses of Electrophoretograms: A Mathematical Approach to Super-Resolution. (PMID: 7247021)
37. Hayward SB, Stroud RM. (1981). J. Mol. Biol. 151, 491-517. Projected Structure of Purple Membrane Determined to 3.7 Å Resolution by Low Temperature Electron Microscopy. (PMID: 7338903)
38. Stroud RM, Serwer P, Ross MJ. (1981). Biophys. J. 36, 743-757. Assembly of Bacteriophage T7: Dimensions of the Bacteriophage and its Capsids. (PMID: 7326332)
39. Stroud RM. (1981). In Biomolecular Stereodynamics 1, 55-73, R.H. Sarma, ed. Adenine Press, New York. Proceedings of the Second SUNYA Conversation in the Discipline Biomolecular Stereodynamics, Vol. II. Structure of an Acetylcholine Receptor, A Hypothesis for a Dynamic Mechanism of its Action.
40. Katre NV, Stroud RM. (1981). FEBS Letters. 136, 170-174. A Probable Linking Sequence Between Two Transmembrane Components of Bacteriorhodopsin.
41. Kistler J, Stroud RM, Klymkowsky MW, Lalancette RA, Fairclough RH. (1982). Biophys. J. 37, 371-383. Structure and Function of an Acetylcholine Receptor. (PMID: 7055628)
42. Agard DA, Stroud RM. (1982). Acta Cryst. A38, 186-194. α-Bungarotoxin Structure Revealed by a Rapid Method for Averaging Electron Density of Non-crystallographically, Translationally Related Molecules.
43. Agard DA, Stroud RM. (1982). Biophys. J. 37, 589-602. Linking Regions Between Helices in Bacteriorhodopsin Revealed. (PMID: 7074187)
44. Wetzel R, Levine HL, Estell DA, Shire S, Finer-Moore JS, Stroud RM, Bewley TA. (1982). In Interferons, Academic Press, New York, N.Y. pp. 365-376. Structure-Function Studies on Human Alpha Interferon.
45. Stroud RM. (1983). In Frontiers in Biochemical and Biophysical Studies of Proteins and Membranes, Liu TY, et al, ed Elsevier Science Publishing Co. Inc, New York, N.Y., pp. 331-349. The Structure of Acetylcholine Receptor and of Bacteriorhodopsin
46. Stroud RM. (1983). Neuroscience Commentaries 1, 124-138. Acetylcholine Receptor Structure.
47. Fairclough RH, Finer-Moore J, Love RA, Kristofferson D, Desmeules PJ, Stroud RM. (1983). Cold Spring Harbor Symposia on Quantitative Biology 48, 9-20. Subunit Organization and Structure of an Acetylcholine Receptor. (PMID: 6586365)
* 48. Finer-Moore J, Stroud RM (1984) Amphipathic analysis and possible formation of the ion channel in an acetylcholine receptor. Proc Natl Acad Sci U S A. 81: 155-159 (PMID: 6320162 PMC344629)
49. Stroud RM. (1984). In Biological Membranes 5 (6), 221-239, Chapman, D., ed., Academic Press Inc. (London) Ltd, London. Acetylcholine Receptor Structure and Function.
50. Katre NV, Finer-Moore J, Stroud RM, Hayward SB. (1984). Biophys. J. 46, 195-203. Location of an Extrinsic Label in the Primary and Tertiary Structure of Bacteriorhodopsin. (PMID: 6478034)
51. Finer-Moore J, Stroud RM, Prescott B, Thomas GJ, Jr. (1984). J. Biomolec. Struc. Dynam. 2 (1), 93-100. Subunit Secondary Structure in Filamentous Viruses: Predictions and Observations. (PMID: 6400935)
52. Liscum L, Finer-Moore J, Stroud RM, Luskey KL, Brown MS, Goldstein JL. (1985). J. Biol. Chem. 260, 522-530. Domain Structure of 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase, A Glycoprotein of the Endoplasmic Reticulum. (PMID: 3965461)
53. Young EF, Ralston E, Blake J, Ramachandran J, Hall ZW, Stroud RM. (1985). Proc. Natl. Acad. Sci. USA 82, 626-630. Topological mapping of acetylcholine receptor: Evidence for a model with five transmembrane segments and a cytoplasmic COOH-terminal peptide. (PMID: 3881770)
54. Stroud RM, Finer-Moore J, (1985). Ann. Rev. Cell Biol. 1, 317-351. Acetylcholine Receptor Structure, Function, and Evolution.
55. Fairclough RH, Miake-Lye RC, Stroud RM, Hodgson KO, Doniach S. (1986). J. Mol. Biol. 189, 673-680. Location of Terbium Binding Sites on Acetylcholine Receptor-enriched Membranes. (PMID: 3783687)
56. McCarthy MP, Earnest JP, Young EF, Choe S, Stroud RM. (1986). Ann. Rev. Neurosci. 9, 383-413. The Molecular Neurobiology of the Acetylcholine Receptor. (PMID: 2423008)
57. Hershenson S, Helmers N, Desmueles P, Stroud RM. (1986). J. Biol. Chem. 261, 3732-3736. Purification and Crystallization of Creatine Kinase from Rabbit Skeletal Muscle. (PMID: 3949787)
58. Stroud RM. (1986). In Proteins of Excitable Membranes, Hille B., Fambrough, D. eds., Society of General Physiologists Series Vol. 41, pp. 67-75. Topological Mapping and the Ionic Channel in an Acetylcholine Receptor. (PMID: 2436314)
59. Katre NV, Kimura Y, Stroud RM. (1986). Biophys. J. 50, 277-284. Cation Binding Sites on the Projected Structure of Bacteriorhodopsin. (PMID: 3741984)
60. Thomas GJ Jr, Prescott B, Love R, Stroud RM. (1986). Spectrochimica Acta 42A, 215-222. Evidence for conformational differences in aqueous and crystalline structures of α-bungarotoxin and cobratoxin.
61. Love RA, Stroud RM. (1986). Protein Engineering 1, 37-46. The crystal structure of α-bungarotoxin at 2.5 Å resolution: relation to solution structure and binding to acetylcholine receptor. (PMID: 3507686)
62. Masters SB, Stroud RM, Bourne HR. (1986). Protein Engineering 1, 47-54. Family of G protein α chains: amphipathic analysis and predicted structure of functional domains. (PMID: 3148932)
63. Stroud RM, Finer-Moore J. (1987). In Biological Organization: Macromolecular Interactions at High Resolution, Burnett, R.M., Vogel, H.J., eds., Academic Press Inc, Orlando, pp. 307-318. The Acetylcholine Receptor: What the Three-Dimensional Structure Tells Us about Ion Conductance.
64. Vassarotti A, Stroud RM, Douglas M. (1987). EMBO J. 6, 705-711. Independent mutationsat the amino terminus of a protein act as surrogate signals for mitochondrial import. (PMID: 2884105)
* 65. Hardy LW, Finer-Moore JS, Montfort WR, Jones MO, Santi DV, Stroud RM. (1987). Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design. Science 235, 448-455. (PMID: 3099389)
66. Earnest JP, Stroud RM, McNamee MG. (1987). In Membrane Proteins: Proceedings of the Membrane Protein Symposium, Goheen, S.C., ed., Bio-Rad Laboratories, Richmond, California, 117-130. Effects of the Functional State of the Acetylcholine Receptor on Reconstitution into Lipid Vesicles.
67. Stroud RM. (1987). In Molecular Neurobiology in Neurology and Psychiatry, E. Kandel, ed., Raven Press, N.Y. 65, 51-63. An Archetypal Molecular Transducer of the Nervous System: The Acetylcholine Receptor. (PMID: 2455312)
68. Sprang S, Standing T, Fletterick RJ, Stroud RM, Finer-Moore J, Xuong N-H, Hamlin R, Rutter WJ, Craik CS. (1987). Science 237, 905-909. The Three-Dimensional Structure of Asn102 Mutant of Trypsin: Role of Asp102 in Serine Protease Catalysis. (PMID: 3112942)
69. Fairclough RH, Stroud RM, Miake-Lye RC, Hodgson KO, Doniach S. (1988). In Myasthenia Gravis: Biology and Treatment. Annals of the New York Academy of Sciences 505, 752-755. Terbium-Calcium Binding Sites on the Acetylcholine Receptor.
70. Basus VJ, Billeter M, Love RA, Stroud RM, Kuntz ID. (1988). Biochemistry 27, 2763-2771. Structural Studies of α-Bungarotoxin. 1. Sequence-Specific 1H NMR Resonance Assignments. (PMID: 3401447)
71. Basson ME, Thorsness M, Finer-Moore J, Stroud RM, Rine J. (1988). Molecular and Cellular Biology 8, 3797-3808. Structural and Functional Conservation between Yeast and Human 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductases, the Rate-Limiting. (PMID: 3065625)
72. Falick AM, Mel SF, Stroud RM, Burlingame AL. (1988). In Techniques in Protein Chemistry, Academic Press pp 152-159. A New Strategy for Mapping the Topography of a Transmembrane Protein Using Mass Spectrometry.
73. Poulter L, Earnest JP, Stroud RM, Burlingame AL. (1988). Biomed. and Environ. Mass. Spectrom. 16, 25-30. Cesium Ion Liquid Secondary Ion Mass Spectometry of Membrane-bound Glycoproteins: Structural and Topological Considerations of Acetylcholine Receptor from Torpedo californica. (PMID: 3242677)
74. McCarthy MP, Stroud RM. (1989). Biochemistry 28, 40-48. Conformational States ofthe Nicotinic Acetylcholine Receptor from Torpedo californica Induced by the Binding of Agonists, Antagonists and Local Anaesthetics. Equilibrium Measurements Using Tritium-Hydrogen Exchange.
75. Finer-Moore J, Bazan JF, Rubin J, Stroud RM. (1989). In Prediction of Protein Structure and the Principles of Protein Conformation, G. Fasman, ed., Plenum Press, New York, 719-759. Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis.
76. Stroud RM, McCarthy MP, Earnest JP, Shuster M, Ghosh P, Mitra AR. (1989). In Fernstrom Series on Neuromuscular Junction, L.C. Sellin, R. Libelius, S. Thesleff, eds., Elsevier Science Publishers, The Netherlands, pp 209-216. Molecular Biology of the Acetylcholine Receptor. (PMID: 2423008)
77. Miercke LJW, Ross PE, Stroud RM, Dratz EA. (1989). J. Biol. Chem. 264, 7531-7535. Purification of Bacteriorhodopsin and Characterization of Mature and Partially Processed Forms. (PMID: 2708376)
78. McCarthy MP, Stroud RM. (1989). J. Biol. Chem. 264, 10911-10916. Changes in Conformation upon Agonist Binding, and Nonequivalent Labeling, of the Membrane-spanning Regions of the Nicotinic Acetylcholine Receptor Subunits. (PMID: 2732250)
79. Mitra AK, McCarthy MP, Stroud RM. (1989). J. Cell Biol. 109, 755-774. Three-Dimensional Structure of Nicotinic Acetylcholine Receptor and Location of the Major Associated 43-kD Cytoskeletal Protein, Determined at 22 Å by Low Dose Electron Microscopy and X-Ray Diffraction to 12.5Å. (PMID: 2760111 / PMCID: PMC2115713)
80. Poulter L, Earnest JP, Stroud RM, Burlingame AL. (1989). Proc. Natl. Acad. Sci. (USA) 86, 6645-6649. Structure, oligosaccharide structures, and posttranslationally modified sites of the nicotinic acetylcholine receptor. (PMID: 2771948)
81. Hurley JH, Thorsness PE, Ramalingam V, Helmers NH, Koshland DE, Stroud RM. (1989). Proc. Natl. Acad. Sci. (USA) 86, 8635-8639. Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase. (PMID: 2682654)
82. Miercke LJW, Stroud RM, Dratz EA. (1989). J. of Chromatography 483, 331-340. Preparative Purification of Functional Bacteriorhodopsin by High-Performance Size-Exclusion Chromatography. (PMID: 2560474)
83. Mitra AK, Stroud RM. (1990). Biophysical Journal 57, 301-311. High sensitivity electron diffraction analysis: A study of divalent cation binding to purple membrane. (PMID: 2317552)
84. Hurley JH, Dean AM, Thorsness PE, Koshland DE, Stroud RM. (1990). J. Biol.Chem. 265, 3599-3602. Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-range Conformational Change in the Free Enzyme. (PMID: 2406256)
85. Montfort WR, Fauman EB, Perry KM, Stroud RM. (1990). In Current Research in Protein Chemistry: Techniques, Structure and Function, J.J. Villafranca, ed., Academic Press, San Diego, pp 367-382. Segmental Accommodation: A Novel Conformational Change Induced Upon Ligand Binding by Thymidylate Synthase.
86. Shuster MJ, Mitra AK, Stroud RM. (1990). In Protein and Pharmaceutical Engineering (UCLA Symposia on Molecular and Cellular Biology), 110 C.W. Craik, R.J. Fletterick, eds, Alan R. Liss, New York, NY, pp. 55-70. The Acetylcholine Receptor.
87. Schiffer CA, Caldwell JW, Kollman PA, Stroud RM. (1990). Proteins 8, 30-43. Prediction of Homologous Protein Structures Based on Conformational Searches and Energetics. (PMID: 2217162)
88. Montfort WR, Perry KM, Fauman EB, Finer-Moore JS, Maley GF, Hardy L, Maley F, Stroud RM. (1990). Biochemistry 29, 6964-6977. Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding dUMP and an Anti-Folate (PMID: 2223754)
89. Finer-Moore JS, Montfort WR, Stroud RM. (1990). Biochemistry 29, 6977-6986. Pairwise Specificity and Sequential Binding in Enzyme Catalysis: Thymidylate Synthase. (PMID: 2223755)
90. Stroud RM. (1990). In Progress in Cell Research, Vol.1, J.M. Ritchie, P.J. Magistretti, L. Bolis, eds, Elsevier Science Publishers, New York, Chapt. 11, pp 123-138. What the structure of the acetylcholine receptor tells us about function of the ligand gated ion channel family.
91. Perry KM, Fauman EB, Finer-Moore JS, Montfort WR, Maley GF, Maley F, Stroud RM. (1990). Proteins 8, 315-333. Plastic Adaptation Toward Mutations in Proteins: Structural Comparison of Thymidylate Synthases. (PMID: 2128651)
* 92. Hurley JH, Dean AM, Sohl JL, Koshland DE Jr., Stroud RM. (1990). Regulation of an Enzyme by Phosphorylation at the Active Site. Science 249, 1012-1016. (PMID: 2204109)
93. Mangel WF, Singer PT, Cyr DM, Umland TC, Toledo DL, Stroud RM, Pflugrath JW, Sweet RM. (1990). Biochemistry 29, 8351-8357. Structure of an Acyl-Enzyme Intermediate during Catalysis: (Guanidinobenzoyl) trypsin. (PMID: 2252895)
94. Stroud RM, McCarthy MP, Shuster M. (1990). Biochemistry 29, 11009-11023. Nicotinic Acetylcholine Receptor Superfamily of Ligand-Gated Ion Channels. (PMID: 1703009)
95. Climie S, Ruiz-Perez L, Gonzalez-Pacanowska D, Prapunwattana P, Cho S-W, Stroud RM, Santi DV. (1990). J. Biol. Chemistry 265, 18776-18779. Saturation Site-directed Mutagenesis of Thymidylate Synthase. (PMID: 2229040)
96. Stroud R M. (1990). In Biological Mass Spectrometry, A.L. Burlingame, J.A. McCloskey, eds, Elsevier Science Publishers, New York, pp 653-670. Proceedings of the Second International Symposium on Mass Spectrometry in the Health and Life Sciences. Cellular Signalling - What the Structure of Neuroreceptors Tells Us About Function.
97. Milder SJ, Thorgeirsson TE, Miercke LJW, Stroud RM, Kliger DS. (1991). Biochemistry 30, 1751-1761. Effects of Detergent Environments on the Photocycle of Purified Monomeric Bacteriorhodopsin. (PMID: 1993191)
98. Shand RF, Miercke LJW, Mitra AK, Fong SK, Stroud RM, Betlach MC. (1991). Biochemistry 30, 3082-3088. Wild-Type and Mutant Bacterioopsins D85N, D96N, and R82Q: High-Level Expression in Escherichia coli. (PMID: 2007142)
99. Miercke LJW, Betlach MC, Mitra AK, Shand RF, Fong SK, Stroud RM. (1991). Biochemistry 30, 3088-3098. Wild-Type and Mutant Bacteriorhodopsins D85N, D96N and R82Q: Purification to Homogeneity, pH Dependence of Pumping, and Electron Diffraction. (PMID: 1848786)
100. Lin SW, Fodor SPA, Miercke LJW, Shand RF, Betlach MC, Stroud RM, Mathies RA. (1991). Photochemistry and Photobiology 53, 341-346. Resonance Raman Spectra of Bacteriorhodopsin Mutants with Substitutions at Asp-85, Asp-96 and Arg-82. (PMID: 2062880)
101. Ghosh P and Stroud RM. (1991). Biochemistry 30, 3551-3557. Ion Channels Formed by a Highly Charged Peptide. (PMID: 1707312)
102. Schiffer CA, Davisson VJ, Santi DV, Stroud RM. (1991). J. Mol. Biol. 219, 161-163. Crystallization of Human Thymidylate Synthase. (PMID: 2038053)
103. Earnest T, Fauman E, Craik CS, Stroud R. (1991). Proteins 10, 171-187. 1.59 Å Structure of Trypsin at 120 K: Comparison of Low Temperature and Room Temperature Structures. (PMID: 1881877)
104. Lax I, Mitra AK, Ravera C, Hurwitz DR, Rubinstein M, Ullrich A, Stroud RM, Schlessinger J. (1991). J. Biol. Chem. 266, 13828-13833. Epidermal Growth Factor (EGF) Induces Oligomerization of Soluble, Extracellular, Ligand-binding Domain of EGF Receptor. A Low Resolution Projection Structure of the Ligand-binding Domain. (PMID: 1856216)
105. Hurley JH, Dean AM, Koshland DE Jr., Stroud RM. (1991). Biochemistry 30, 8671-8678. Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-Isocitrate and NADP Complexes. (PMID: 1888729)
106. Stroud RM. (1991). Science 253, 685-686. Molecular Biology in Three Dimensions. Review of Introduction to Protein Structure by Carl Branden, John Tooze, Garland, New York.
107. Thorgeirsson TE, Milder SJ, Miercke LJW, Betlach MC, Shand RF, Stroud RM, Kliger DS. (1991). Biochemistry 30, 9133-9142. Effects of Asp-96 → Asn, Asp-85 → Asn, and Arg-82 → Gln Single-Site Substitutions on the Photocycle of Bacteriorhodopsin. (PMID: 1892824)
108. Stroud RM. (1991). In Molecular Conformation and Biological Interactions, P. Balaram, S. Ramaseshan, eds., Indian Academy of Sciences Press, Bangalore, India, pp 627-644. Structure and Function of Transmembrane Ion Channels.
109. Stroud RM. (1991). Current Opinion in Structural Biology 1, 826-835. Mechanisms of biological control by phosphorylation.
110. Finer-Moore JS, Kossiakoff AA, Hurley JH, Earnest T, Stroud RM. (1992). Proteins 12, 203-222. Solvent Structure in Crystals of Trypsin Determined by X-Ray and Neutron Diffraction. (PMID: 1557349)
111. Schiffer CA, Caldwell JW, Stroud RM, Kollman PA. (1992). Protein Science 1, 396-400. Inclusion of solvation free energy with molecular mechanics energy: Alanyl dipeptide as a test case. (PMID: 1304346)
112. Perry KM, Pookanjanatavip M, Zhao J, Santi DV, Stroud RM. (1992). ProteinScience 1, 796-800. Reversible dissociation and unfolding of the dimeric protein thymidylate synthase. (PMID: 1304920)
113. Kamb A, Finer-Moore JS, Stroud RM. (1992). Biochemistry 31, 12876-12884. Cofactor Triggers the Conformational Change in Thymidylate Synthase: Implications for an Ordered Binding Mechanism. (PMID: 1281428)
114. Kamb A, Finer-Moore J, Calvert AH, Stroud RM. (1992). Biochemistry 31, 9883-9890. Structural Basis for Recognition of Polyglutamyl Folates by Thymidylate Synthase. (PMID: 1390771)
115. Shoichet BK, Stroud RM, Santi DV, Kuntz ID, Perry KM. (1993). Science 259, 1445-1450. Structure-Based Discovery of Inhibitors of Thymidylate Synthase. (PMID: 8451640)
116. Turner, G.J, Miercke, L.J.W, Thorgeirsson, T.E, Kliger, D.S, Betlach, M.C., Stroud, R.M. (1993). Biochemistry 32, 1332-1337. Bacteriorhodopsin D85N: Three Spectroscopic Species in Equilibrium. (PMID: 8448142)
117. Mel SF, Stroud RM. (1993). Biochemistry 32, 2082-2089. Colicin Ia Inserts into Negatively Charged Membranes at Low pH with a Tertiary but Little Secondary Structural Change. (PMID: 8448167)
118. Stroud RM, Finer-Moore JS. (1993). FASEB J. 7, 671-677. Stereochemistry of a multistep/bipartite methyl transfer reaction: thymidylate synthase. (PMID: 8500692)
119. Ghosh P, Mel SF, Stroud RM. (1993). J. Membrane Biol. 134, 85-92. A Carboxy-Terminal Fragment of Colicin Ia Forms Ion Channels. (PMID: 7692058)
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122. Mitra AK, Miercke LJW, Turner GJ, Shand RF, Betlach MC, Stroud RM. (1993). Biophys. J. 65, 1295-1306. Two-dimensional Crystallization of Escherichia coli-expressed Bacteriorhodopsin and Its D96N Variant: High Resolution Structural Studies in Projection. (PMID: 8241409)
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124. Mel SF, Falick AM, Burlingame AL, Stroud RM. (1993). Biochemistry 32, 9473-9479. Mapping a Membrane-Associated Conformation of Colicin Ia. (PMID: 7690252)
125. Finer-Moore J, Fauman EB, Foster PG, Perry KM, Santi DV, Stroud RM. (1993). J. Mol. Biol. 232, 1101-1116. Refined Structures of Substrate-bound and Phosphate-bound Thymidylate Synthase from Lactobacillus casei. (PMID: 8371269)
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127. Rose RB, Rosé JR, Salto R, Craik CS, Stroud RM. (1993). Biochemistry 32, 12498-12507. Structure of the Protease from Simian Immunodeficiency Virus: Complex with an Irreversible Nonpeptide Inhibitor. (PMID: 8241141)
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132. Finer-Moore JS, Maley GF, Maley F, Montfort WR, Stroud RM. (1994). Biochemistry 33, 15459-15468. Crystal Structure of Thymidylate Synthase from T4 Phage: Component of a Deoxynucleoside Triphosphate-Synthesizing Complex. (PMID: 7803410)
133. Katz BA, Finer-Moore J, Mortezaei R, Rich DH, Stroud RM. (1995). Biochemistry 34, 8264-8280. Episelection: Novel Ki~Nanomolar Inhibitors of Serine Proteases Selected by Binding or Chemistry on an Enzyme Surface. (PMID: 7599119)
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137. Schiffer CA, Clifton IJ, Davisson VJ, Santi DV, Stroud RM. (1995). Biochemistry 34, 16279-16287. Crystal Structure of Human Thymidylate Synthase: A Structural Mechanism for Guiding Substrates into the Active Site. (PMID: 8845352)
138. Katz BA, Stroud RM, Collins N, Liu B, Arze R. (1995). Chemistry & Biology 2, 591-600. Topochemistry for preparing ligands that dimerize receptors. (PMID: 9383463)
139. Stout TJ, Stroud RM. (1996). Structure 4, 67-77. The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 Å resolution: implications for a new mode of inhibition. (PMID: 8805515)
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144. Costi PM, Liu L, Finer-Moore JS, Stroud RM, Santi DV. (1996). Biochemistry 35, 3944-3949. Asparagine 229 Mutants of Thymidylate Synthase Catalyze the Methylation of 3-Methyl-2’-deoxyuridine 5’-Monophosphate. (PMID: 8672425)
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146. Rose RB, Craik CS, Douglas NL, Stroud RM. (1996). Biochemistry 35, 12933-12944. Three-Dimensional Structures of HIV-1 and SIV Protease Product Complexes. (PMID: 8841139)
147. Rutenber EE, Stroud RM. (1996). Structure 4, 1317-1324. Binding of the anti-cancer drug ZD1694 to E. coli thymidylate synthase: assessing specificity and affinity. (PMID: 8939755)
148. Sage CR, Rutenber EE, Stout TJ, Stroud RM. (1996). Biochemistry 35, 16270-16281. An Essential Role for Water in an Enzyme Reaction Mechanism: The Crystal Structure of the Thymidylate Synthase Mutant E58Q. (PMID: 8973201)
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150. Fremann DM, Keenan RJ, Stroud RM, Walter P. (1997). Nature 385, 361-364. Structure of the conserved GTPase domain of the signal recognition particle. (PMID: 9002524)
151. Schafmeister CE, LaPorte SL, Miercke LJW, Stroud RM. (1997). Nature Struct. Biol. 4, 1039-1046. A designed four helix bundle protein with native-like structure. (PMID: 9406555)
152. Agarwalla S, LaPorte S, Liu L, Finer-Moore J, Stroud RM, Santi DV. (1997). Biochemistry 36, 15909-15917. A Novel dCMP Methylase by Engineering Thymidylate Synthase. (PMID: 9398324)
153. Finer-Moore JS, Liu L, Birdsall DL, Brem R, Apfeld J, Santi DV, Stroud RM. (1998). J. Mol. Biol. 276, 113-129. Contributions of Orientation and Hydrogen Bonding to Catalysis in Asn229 Mutants of Thymidylate Synthase. (PMID: 9514716)
154. Finer-Moore J, Tsutakawa SE, Cherbavaz DB, LaPorte DC,Koshland DE Jr, Stroud RM. (1998). Biochemistry 36, 13890-13896. Access to Phosphorylation in Isocitrate Dehydrogenase May Occur by Domain Shifting. (PMID: 9374867)
155. Rose RB, Craik CS, Stroud RM. (1998). Biochemistry 37, 2607-2621. Domain Flexibility in Retroviral Proteases: Structural Implications for Drug Resistant Mutations. (PMID: 9485411)
156. Katz BA, Clark JM, Finer-Moore JS, Jenkins TE, Johnson CR, Ross MJ, Luong C, Moore WR, Stroud RM. (1998). Design of potent selective zinc-mediated serine protease inhibitors. Nature 391: 608-612. (PMID: 9468142)
157. Costi MP, Barlocco D, Rinaldi M, Tondi D, Pecorari P, Ghelli S, Sciunto F, Musiu C, Congeddu E, Loi AG, Stroud RM, Santi DV, Kuntz ID, Stout TJ, Schoichet BK, La Colla P. (1997). Journal of Medicinal Chemistry, Vol. 42, No. 12, 2115-2124. Design, Synthesis and Biological Evaluation of Phthalein Derivatives as a New Class of Species Specific Inhibitors of Thymidylate Synthase.
158. Chen C-H, Miercke LJW, Krucinski J, Starr JR, Saenz G, Wang X, Spilburg CA, Lange LG, Ellsworth JL, Stroud RM. (1998). Biochemistry 37, 5107-5117. Structure of Bovine Pancreatic Cholesterol Esterase at 1.6 Å: Novel Structural Features Involved in Lipase Activation. (PMID: 9548741)
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160. Birdsall DL, Huang W, Santi DV, Stroud RM, Finer-Moore J. (1998). Protein Engineering 11, 171-183. The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis. (PMID: 9613841)
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163. Sheppeck J, Schneider H, Stroud B, Matthews D, Carr G, Gosink L, Ly C, Chaovapong W, Collins N, Hopkins T, Zhan H. (1998). Submitted to Biochemistry. Identification of a class of small molecule in vitro antagonists of Erythropoietin (EPO). Structure-activity relationships and progress towards small molecule agonists of EPO activity.
164. Zhan H, Liu B, Reid SW, Aoki KH, Li C, Syed RS, Karkaria C, Koe G, Sitney K, Hayenga K, Mistry F, Savel L, Dreyer M, Katz BA, Schreurs J, Matthews DJ, Cheetham JC, Egrie J, Giebel LB and Stroud RM. (1999). Protein Engineering 12, 505-513. Engineering a soluble extracellular erythropoietin receptor (EPObp)in Pichia pastoris to eliminate microheterogeneity, and its complex with erythropoietin. (PMID: 10388848)
165. Stout TJ, Sage CR, Stroud RM. (1998). Structure 6, 839-848. The additivity of substrate fragments in enzyme-ligand binding. (PMID: 9687366)
166. Stout TJ, Schellenberger U, Santi DV, Stroud RM. (1998). Biochemistry 37, 14736-14747. Crystal Structures of a Unique Thermal-Stable Thymidylate Synthase from Bacillus subtilis. (PMID: 9778348)
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170. Sage CR, Michelitsch MD, Stout TJ, Biermann D, Nissen R, Finer-Moore J, Stroud RM. (1998). Biochemistry 37, 13893-13901. D221 in Thymidylate Synthase Controls Conformation Change, and Thereby Opening of the Imidazolidine. (PMID: 9753479)
171. Schafmeister CE, Stroud RM. (1998). Current Opinion in Biotechnology 9, 350-353.Helical protein design. (PMID: 9720261)
172. Stroud RM, Reiling K, Wiener M, Freymann D. (1998). Current Opinion in Structural Biology 8, 525-533. Ion-channel-forming colicins. (PMID: 9729746)
173. Rutenber EE, De Voss JJ, Hoffman L, Stroud RM, Lee KH, Alvarez J, McPhee F, Craik C, Ortiz de Montellano PR. (1997). Bioorganic & Medicinal Chemistry 5, 1311-1320. The Discovery, Characterization and Crystallographically Determined Binding Mode of an FMOC-Containing Inhibitor of HIV-1 Protease. (PMID: 9377091)
174. Anderson AC, O’Neil RH, DeLano WL, Santi DV, Stroud RM. (1999). Biochemistry 38, 13829-13836. A Structural Mechanism for Half-the-Sites Reactivity. (PMID: 10529228)
175. Foster PG, Huang L, Santi DV, Stroud RM. (2000). Nature Structural Biology vol 7, 23-27. The Structural Basis for Pseudouridine Formation in tRNA: Pseudouridine Synthase I at 1.5 Å Resolution.
176. Freymann D, Keenan R, Stroud RM, Walter P (1999). Nature Struct. Biol. Vol 6. No 8. 793-801. April 1999). Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP.
177. Morse RJ, Kawase S, Santi DV, Finer-Moore J, Stroud R. (2000). Biochemistry 39, 1011-1020. Energetic Contributions of Four Arginines to Phosphate-Binding in Thymidylate Synthase Are More than Additive and Depend on Optimization of “Effective Charge Balance.”
178. Costi PM, Rinaldi M, Tondi D, Pecorari P, Barlocco D, Shelli S, Stroud RM, Santi DV, Stout TJ, Musiu C, Marangiu EM, Pani A, Congiu D, Loi GA, LaColla P. (1999). Journal of Medicinal Chemistry 42, 2112-2124. Phthalein Derivatives asa New Tool for Selectivity in Thymidylate Synthase Inhibition.
179. Turner GJ, Miercke LJW, Mitra AK, Stroud RM, Betlach MC, Winter-Vann A. (1999). Protein Expression and Purification 17, 324-338. Expression, Purification, andStructural Characterization of the Bacteriorphodopsin Aspartyl Transcarbamylase Fusion Protein.
180. Anderson AC, Perry KM, Freymann DM, Stroud RM (2000). Journal of Molecular Biology 297, 645-657. The Crystal Structure of Thymidylate Synthase from Pneumocystis carinii Reveals a Fungal Insert Important for Drug Design.
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182. Lackey DB, Groziak MP, Sergeeva M, Beryt M, Boyer C, Stroud RM, Sayre P, Park JW, Johnston P, Slamon D, Shepard HM, Pegram M. (2001) Biochemical Pharmacology 61, 179-198. Enzyme-catalyzed therapeutic agent (ECTA) design: activation of the antitumor ECTA compound NB1011 by thymidylate synthase.
183. Stroud RM, Walter P. (1999). Current Opinion in Structural Biology 9, 754-759. Signal Sequence Recognition and Protein Targeting.
184. Stroud RM, Wells JA. (2004). Mechanisms of receptor signaling across cell membranes. Science. Signal Transduction Knowledge Environment 2004 pp. Re7, May 2004
185. Reiling KK, Pray TR, Craik CS, Stroud RM. (2000) Functional Consequences of the Kaposi’s Sarcoma-Associated Herpesviral Protease Structure: Regulation of Activity and Dimerization by Conserved Structural Elements. Biochemistry. 39: 12796-803 (PMID: 11041844)
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188. Kawase S, Cho SW, Rozelle J, Stroud RM, Finer-Moore J, Santi D. (2000). Protein Engineering. 13, 557-563. Replacement Set Mutagenesis of the Four Phosphate-Binding Arginine Residues of Thymidylate Synthase. (PMID: 10964985)
189. Erlanson DA, Braisted AC, Raphael DR, Randal M, Stroud RM, Gordon EM, Wells JA. (2000). Proc. Natl Acad Sci USA 97: 9367-72. Site-directed Ligand Discovery. (PMID: 10944209)
190. Variath P, Yaoquan Liu, Lee TT, Stroud RM, Santi DV. (2000). Biochemistry 39: 2429-2435. Effects of Subunit Occupancy on Partitioning of an Intermediate in Thymidylate Synthase Mutants. (PMID: 10704192)
191. Wiener MC, Verkman AS, Stroud RM, van Hoek AN. (2000). Protein Sci 9: 1407-9. Mesoscopic Surfactant Organization, and Membrane Protein Crystallization. (PMID: 10933509)
192. Keenan RJ, Freymann DM, Stroud RM, Walter P. (2001). Ann. Rev. of Biochemistry 70: 755-75. The Signal Recognition Particle. (PMID: 11395422)
193. Morse RJ, Yamamoto T, Stroud RM. (2001). Structure 9: 409-417. Structure of Cry2Aa Suggests an Unexpected Receptor-Binding Epitope. (PMID: 11377201)
194. Fritz TA, Tondi D, Finer-Moore JS, Costi, M.P, Stroud, R.M. (2001). Chemistry & Biology. 8: 981-995. Predicting and Harnessing Protein Flexibility in the Design of Species-Specific Inhibitors of Thymidylate Synthase. (PMID: 11590022)
195. Nollert P, Harries WEC, Fu D, Miercke LJW, Stroud RM. (2001). FEBS Letters 504: 112-7. Atomic Structure of a Glycerol Channel and Implications for Substrate Permeation in Aqua(glyero)porins. (PMID: 11532442)
196. Sayre PH, Finer-Moore JS, Fritz TA, Biermann D, Gates SB, MacKellar WC, Patel VF, Stroud RM. (2001). Journal of Molecular Biology. 313: 813-829 Multi-Targeted Antifolates Aimed at Avoiding Drug Resistance Form Covalent Closed Inhibitory Complexes with Human and Escherichia coli Thymidylate Synthase. (PMID: 11697906)
197. Tsai S-C, Miercke LJW, Krucinski J, Gokhale R, Chen Julian C-H, Foster PG, Cane DE, Khosla C, Stroud RM. (2001). Proc Nat. Acad Sci. 98: 14808-14813. Crystal Structure of the Macrocycle-Forming Thioesterase Domain of the Erythromycin Polyketide Synthase: Versatility from a Unique Substrate Channel. (PMID: 11752428)
198. Katz BA, Stroud RM, Clark JM, Jenkins TE, Janc JW, Moore WR, Venuti MC. (2001). In Medicinal Chemistry into the Millennium, Delta Technology for Protease Inhibition 211-222.
199. Pan H, Tsai S, Meadows ES, Miercke LJW, Keatinge-Clay AT, O’Connell J, Khosla C, Stroud RM. (2002) Structure 10: 1559-1568. Crystal Structure of the Priming bKetosynthase from the R1128 Biosynthetic Pathway: Implications for the Design of Novel Estrogen Receptor Antagonists. Proteins. (PMID: 12429097)
200. Anderson AC, O’Neil RH, Surti TS, Stroud RM. (2001). Chemistry & Biology 8: 445-57. Approaches to Solving the Rigid Receptor Problem by Identifying a Minimal Set of Flexible Residues during Ligand Docking. (PMID: 11358692)
201. Reiling KK, Endres N, Dauber DS, Craik CS, Stroud RM. (2002). Biochemistry. 41: 4582 –4594. Anistropic Dynamics of the JE-2147-HIV Protease Complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09 Å Structure. (PMID: 11926820)
202. Fritz TA, Liu L, Finer-Moore JS, Stroud RM. (2002). Biochemistry. 41: 7021-7025 Tryptophan 80 and leucine 143 are critical for the hydride transfer step of thymidylate synthase by controlling active site access. (PMID: 12033935)
203. Birdsall DL, Bencal J, Santi DV, Stroud RM, Finer-Moore J. (2003). Protein Engineering 16: 229-240. The Only Active Mutant of Thymidylate Synthase D169, a Residue Far from the Site of Methyl Transfer, Demonstrates the Exquisite Nature of Catalysis in Enzymology.
204. Agarwalla S, Kealey JT, Santi DV, Stroud RM. (2002). J. Biol. Chem. 277: 8835-8840. Chemistry Characterization of the 23S rRNA m5U1939 Methyltransferase from E. coli. (PMID: 11779873)
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206. Fu D, Libson A, Stroud R. (2002). Novartis Found Symp 245: 51-61. The structure of GlpF, a glycerol conducting channel. (PMID: 12027015)
207. Ramirez UD, Minasov G, Focia PJ, Stroud RM, Walter P, Kuhn P, Freymann DM. (2002). J Mol Biol 320: 783-99. Structural basis for mobility in the 1.1 Å crystal structure of the NG domain of Thermus aquaticus Ffh. (PMID: 12095255)
208. Stroud RM, Nollert P, Miercke LMJ. (2003) The Glycerol Facilitator GlpF, its Aquaporin Family of Channels and their Selectivity. Advances in Protein Chemistry Membrane Proteins. Ed. Doug Rees. 63: 291-316. (PMID: 12629974)
209. Reiling KK, Krucinski J, Miercke LJ, Raymond WW, Caughey GH, Stroud RM. (2003). Biochemistry 42: 2616-2624. Structure of Human Pro-Chymase: A Model for the Activating Transition of Granule-Associated Proteases. (PMID: 12614156)
210. Tsai SC, Lu H, Cane DE, Khosla C, Stroud RM. (2002). Biochemistry 41: 12598-12606. Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases.
211. Costi MP, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Soragni F, Venturelli A, Stroud RM. Biochim Biophys Acta 1587: 206-214 Structure-based studies on species-specific inhibition of thymidylate synthase. (PMID: 12084462)
212. Finer-Moore JS, Santi DV, Stroud RM. (2003). Biochemistry 42: 248-256. Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure. (PMID: 1252515)
213. Stroud RM, Finer-Moore JS. (2003). Biochemistry 42: 239-247. Conformational Dynamics along an Enzymatic Reaction Pathway: Thymidylate Synthase, "the Movie". (PMID: 12525150)
214. Stroud RM, Miercke LJW, O'Connell J, Khademi S, Lee JK, Remis J, Harries W, Robles Y, Akhavan D. (2003). Curr Opin Struct Biol 13: 424-431. Glycerol facilitator GlpF and the associated aquaporin family of channels. (PMID: 12948772)
215. Gonzalez-Pacanowska D, Ruiz-Perez LM, Carreras-Gomez MA, Costi MP, Stroud RM, Finer-Moore JS, Santi DV. (2003) Protein Engineering, 16: 229-240. The structural roles of conserved Pro-196, Pro-197 and His-199 in the mechanism of thymidylate synthase. (PMID: 12968078)
216. Jez JM, Chen JC, Rastelli G, Stroud RM, Santi DV. (2003) Chem Biol 10: 361-368. Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90. (PMID: 12725864)
217. O’Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. (2003) J Eukaryot Microbiol 50: Suppl 555-556. The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme. (PMID: 14736160)
218. Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJW, O’Connell JD 3rd, Khosla C, Stroud RM. Structure 11: 147-154. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA: ACP transacylase. (PMID: 12575934)
219. Pan H, Agarwalla S, Moustakas DT, Finer-Moore JS, Stroud RM. (2003) Proc Nat. Acad. Sci 100: 12648-12653. Crystal Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA-protein recognition through a combination of rigid docking and induced fit. (PMID: 14566049)
220. Lee T L, Agarwalla S, Stroud RM. (2003) Structure 12: 397-407. The first structure of an RNA 5-methyluridine methyltransferase contains an iron-sulfur cluster
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222. O’Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. (2003). J Biol Chem 278: 52980-52987. Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. (PMID: 14555647)
223. Stroud RM, Savage D, Miercke LJ, Lee JK, Khademi S, Harries W. (2003). FEBS Lett 555: 79-84. Selectivity and conductance among the glycerol and water conducting aquaporin family of channels. (PMID: 14630323)
224. Agarwalla S, Stroud RM, Gaffney BJ. (2004). J Biol Chem 279: 34123-34129. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. (PMID: 15181002)
225. Foster PG, Nunes CR, Greene P, Moustakas D, Stroud RM. (2003). Structure (Camb) 11: 1609-1620. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. (PMID: 14656444)
226. Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell J, Khosla C, Stroud RM. (2003). Structure (Camb) 11: 147-154. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. (PMID: 12575934)
227. Lee JK, Khademi S, Harries W, Savage D, Miercke L, Stroud RM. (2004). J Synchrotron Radiat 11: 86-88. Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family. (PMID: 14646142)
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[News and Views: Nature Chem Biol (2009) 5: 146. News and Views: Nature Structural and Molecular Biology 11, 115-116. Reviewed by Cross et al., Nature Reviews Molecular Cell Biology (2009) 10, 255-264]
229. Stroud RM, Wells JA. (2004). Science STKE 2004, re7. May 4th. Mechanistic diversity of cytokine receptor signaling across cell membranes. (PMID: 15126678)
230. Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Alma L, Burlingame AL. (2004) Proc. Nat Acad Sci 101: 16454-9 Unraveling the interface of signal recognition particle and its receptor using chemical cross-linking and tandem mass spectrometry. (PMID: 15546976)
* 231. Harries WEC, Akhavan D, Miercke LJW, Khademi S, Stroud RM. (2004) The Channel Architecture of Aquaporin 0 At 2.2 Å Resolution. Proc Nat Acad Sci 101: 14045-14050. (PMID: 15377788 PMCID: PMC521118)
* 232. Khademi S, O'Connell III J, Remis J, Robles-Colmenares Y, Miercke LJW, Stroud RM. (2004) Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A Science 305: 1587-1594. (PMID: 15361618) [Cover Article, with Perspective by Knepper, Agre. p1573-1574] Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A. Highlighted: Recognized as one of the 4 discoveries of the year in Chemistry of C&E News.
233. Keatinge-Clay AT, Maltby DA, Medzihradszky KF, Khosla C, Stroud RM. (2004) Nature Struct Mol Biol 11: 888-893. An antibiotic factory caught in action. (PMID: 15286722)
234. Shan SO, Stroud RM, Walter P. (2004) PLoS Biol 2, e320 Mechanism of association and reciprocal activation of two GTPases. (PMID: 15383838 / PMCID: PMC517823)
235. Laporte SL, Forsyth CM, Cunningham BC, Miercke L J, Akhavan D, Stroud RM. (2005). Proc Natl Acad Sci U S A 102: 1889-1894. De novo design of an IL-4 antagonist and its structure at 1.9 Å. (PMID: 15684085 / PMCID: PMC548554)
236. Lee TT, Agarwalla S, Stroud RM. (2005). Cell 120: 599-611. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. (PMID: 15766524)
237. Egea PF, Stroud RM, Walter P. (2005). Curr Opin Struct Biol 15: 213-220. Targeting proteins to membranes: structure of the signal recognition particle. (PMID: 15837181)
238. Finer-Moore JS, Anderson AC, O’Neil RH, Costi MP, Stroud RM. (2005) The Structure of Cryptococcus neoformans Thymidylate Synthase Suggests Strategies for Using Target Dynamics for Species-Specific Inhibition, Acta Crystallogr. Sect. D, D61: 1320-1334.
239. Credle JJ, Finer-Moore JS, Papa FR, Stroud RM, Walter P. (2005) Proc Nat Acad Sci 102: 18773-18784 On the Mechanism of Sensing Unfolded Protein in the Endoplasmic Reticulum. (PMID: 16365312 / PMCID: PMC1316886)
240. Lee JK, Kozono D, Remis J, Kitagawa Y, Agre P, Stroud RM. (2005) Proc. Nat Acad Sci USA 102: 18932-7. Structural Basis for Conductance by the Archaeal Aquaporin AqpM at 1.68 Å. (PMID: 16361443 / PMCID: PMC1323191)
241. Stroud RM, Harries WEC, Lee J, Khademi S, Savage D. (2006). Chapter in Royal Society of Chemistry: Structural Biology of Membrane Proteins, ed., Reinhard Grisshammer and Susan K. Buchanan. Chapter 11: 195-211. Aquaporins: Integral Membrane Channel Proteins
242. Khademi S, Stroud RM. (2006), Chapter in Royal Society of Chemistry: Structural Biology of Membrane Proteins, ed., Reinhard Grisshammer, Susan K. Buchanan. Chapter 12: 212-234 Gas Channels for Ammonia
243. Khademi S, Stroud RM. (2006) The Amt/MEP/Rh family: structure of AmtB and the mechanism of ammonia gas conduction. Physiology (Bethesda) 21: 419-429. (PMID: 17119155)
244. Keatinge-Clay AT, Stroud RM. (2006) Structure 14: 737-748. The Structure of a Ketoreductase Determines the Organization of the beta-Carbon Processing Enzymes of Modular Polyketide Synthases. (PMID: 16564177)
245. Newby Z, Lee TT, Morse RJ, Liu Y, Liu L, Venkatraman P, Santi DV, Finer-Moore JS, Stroud RM. (2006). The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261. Biochemistry 45: 7415-7428. (PMID: 16768437 / PMCID: PMC2556892)
246. Hur S, Stroud RM, Finer-Moore J. (2006). Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective. J Biol Chem 281: 38969-38973. (PMID: 17085441)
247. Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL. (2007). X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2, Rna 13: 1043-1051. (PMCID: PMC1894928)
248. He X, Alian A, Stroud R, Ortiz de Montellano PR. (2006). Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis, J Med Chem 49: 6308-6323. (PMID: 17034137 / PMCID: PMC2517584)
249. Hur S, Stroud RM. (2007). How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA. Mol Cell 26:189-203. (PMID: 17466622 / PMCID: PMC3562137)
250. Menuz K, Stroud RM, Nicoll RA, Hays FA. (2007). TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists, Science 318, 815-817. (PMID: 17975069)
251. Pan H, Ho JD, Stroud RM, Finer-Moore J. (2007). The crystal structure of E. coli rRNA pseudouridine synthase RluE, J Mol Biol 367: 1459-1470252. (PMID: 17320904 / PMCID: PMC1876706)
252. Reyes CL, Rutenber E, Walter P, Stroud RM. (2007). X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates, PLoS ONE 2: e607. (PMID: 17622352 / PMCID: PMC1904258)
253. Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM. (2007). Cell-free complements in vivo expression of the E. coli membrane proteome, Protein Sci 16: 966-976. (PMID: 17456747 / PMCID: PMC2206641)
254. Savage DF, Stroud RM. (2007). Structural basis of aquaporin inhibition by mercury, J Mol Biol 368: 607-617. (PMID: 17376483)
255. Stroud RM. (2007). Transmembrane transporters: an open and closed case, Proc Natl Acad Sci USA 104: 1445-1446. (PMID: 17251354 / PMCID: PMC1785277)
256. Gruswitz F, O'Connell J, 3rd, Stroud RM. (2007). Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A. Proc Natl Acad Sci USA 104: 42-47. (PMID: 17190799 / PMCID: PMC1765473).
257. Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL. (2007). X-ray crystallographic and NMR studies of protein-protein and protein-nucleic acid interactions involving the KH domains from human poly(C)-binding protein-2. Rna 13: 1043 (PMID: 17526645 / PMCID: PMC1894928)
258. Du Z, Lee JK, Tjhen R, Stroud RM, James TL. 2008. Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage. Proc Natl Acad Sci USA 105: 2391. (PMID: 18268334 / PMCID: PMC2268147)
259. Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James TL. (2007). Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 A resolution. Nucleic Acids Res 35: 2651. (PMID: 17426136 / PMCID: PMC1885661)
260. Newby ZE, O'Connell J, 3rd, Robles-Colmenares Y, Khademi S, Miercke LJ, Stroud RM. (2008). Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum. Nature Struct Mol Biol 15: 619-625. (PMID: 18500352 / PMCID: PMC2568999)
261. Lee JK, Belogrudov GI, Stroud RM. (2008) Crystal structure of bovine mitochondrial factor B at 0.96-A resolution. Proc Natl Acad Sci USA. 105: 13381-13384. (PMID: 18768789)
262. Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J. (2008). Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci USA 105: 6876. (PMID: 18451029 / PMCID: PMC2383949)
263. Egea PF, Napetschnig J, Walter P, Stroud RM. (2008). Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus. PLoS ONE 3: e3528. (PMID: 18953414 / PMCID: PMC2568955)
264. Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM. (2008). Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane. PLoS ONE 3: e3619. (PMID: 18978942 / PMCID: PMC2572998)
265. Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, et al. (2009). Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. J Struct Funct Genomics 10, (1): 9-16. (PMID: 19031011 / PMCID: PMC2756966)
* 266. Korennykh AV, Egea PF, Korostelev AA, Finer-Moore J, Zhang C, Shokat KM, Stroud RM, Walter,P (2009). The unfolded protein response signals through high-order assembly of Ire1. Nature 457: 687. (PMID: 19079236 / PMCID: PMC2846394)
267. Alian A, Griner SL, Chiang V, Tsiang M, Jones G, Birkus G, Geleziunas R, Leavitt AD, & Stroud RM. (2009) Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs. Proc Natl Acad Sci USA 106: 8192-8197. (PMID: 19416821 / PMCID: PMC2688900)
268. Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, & Harries W. (2009) 2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins. Journal of structural and functional genomics 10: 193-208. (PMID: 19148774 / PMCID: PMC2705707)
269. Newby ZE, O'Connell JD, 3rd, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM. (2009) A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nature protocols 4: 619-637. (PMID: 19360018)
270. Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD 3rd, Miercke LJ, Giacomini KM, Sali A, Stroud RM. (2009) Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 385: 820-830. (PMID: 19061901 / PMCID: PMC2659619)
* 271. Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WE, Robbins RA, Miercke LJ, & Stroud RM. (2009) Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance. Proc Natl Acad Sci USA. 106: 7437-7442. (PMID: 19383790 / PMCID: PMC2678640)
272. Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, & Stroud RM. (2009) Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J Mol Biol 388: 785-800. (PMID: 19298824 / PMC2796871)
273. Stroud RM. Transmembrane transporters: an open and closed case. Proc Natl Acad Sci USA 104, 1445-1446, 2007.
274. Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A. (2009) A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics Sep 17. (PMID: 19760129 / PMCID: PMC2780624)
275. Gruswitz F, Chaudhary S, Ho, JD, Schlessinger, A, Pezeshki, B, Ho, C-M, Sali, A, Westhoff, C.M, Stroud, R.M. (2010) Function of human Rh based on structure of RhCG at 2.1 Å. Proc Natl Acad Sci USA. 107: 9638-43. (PMID: 20457942 / PMCID: PMC2906887)
276. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee Sw, Kelly L, Stroud RM, Ferrin TTE, Giacomini KM, Sali A. (2010) Comparison of human solute carriers. Protein Sci. 19: 412-28. (PMID: 20052679 / PMCID: PMC2866268)
277. De Angelis F, Lee JK, O'Connell JD 3rd, Miercke LJ, Verschueren KH, Srinivasan V, Bauvois C, Govaerts C, Robbins RA, Ruysschaert JM, Stroud RM, Vandenbussche G. (2010). Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems. Proc Natl Acad Sci USA 107:11038-43. (PMID: 20534468 / PMCID: PMC2890744)
278. Hays FA, Roe-Zurz Z, Stroud RM. (2010) Overexpression and purification of integral membrane proteins in yeast. Methods Enzymol. 470: 695-707. (PMID: 20946832)
* 279. Egea PF, Stroud RM. (2010) Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes. Proc Natl Acad Sci U S A. 107: 17182-17187 (PMID: 20855604 / PMCID: 2951439)
280. Chae PS,Gotfryd K, Pacyna J, Miercke LJ, Rasmussen SG, Robbins RA, Rana RR, Loland CJ, Kobilka B, Stroud R, Byrne B, Gether U, Gellman SH. Tandem facial amphiphiles for membrane protein stabilization. J Am Chem Soc 132: 16750-2, 2010. (PMCID: PMC3050673 / NIHMS250722)
281. Savage DF, O’Connell JD 3rd, Miercke LJ, Finer-Moore J, Stroud RM. Structural context shapes the aquaporin selectivity filter. Proc Natl Acad Sci USA. 40: 17164-9, 2010. (PMCID: PMC2951435)
282. Lee JK, Stroud RM. Unlocking the eukaryotic membrane protein structural proteome. Curr Opin Struct Biol. 4: 464-70, 2010. (PMID: 20739007/PMCID: PMC3530418)
283. Korennykh AV, Korostelev AA, Egea PF, Finer-Moore J, Stroud RM, Zhang, C, Shokat, KM, Walter, P. (2011) Structural and functional basis for RNA cleavage by Ire1. BMC Biol 9: 47. (PMCID: PMC3149027)
284. Korennykh AV, Egea PF, Korostelev AA, Finer-Moore J, Stroud RM, Zhang, C. Shokat, KM, Walter, P. (2011) Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1. BMC Biol 9: 48. (PMCID: PMC3158555)
285. Rosenberg, OS, Dovey, C, Tempesta, M, Robbins, RA, Finer-Moore, JS, Stroud, RM, Cox, JS. (2011) EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure among helix-turn-helix proteins. Proc Natl Acad Sci U S A. 108: 13450-13455 (PMID: 21795602 / PMCID:3158157)
286. Chaudhary S, Pak JE, Pedersen BP, Bang LJ, Zhang LB, Ngaw SM, Green RG, Sharma, V, Stroud RM (2011) Efficient expression screening of human membrane proteins in transiently transfected Human Embryonic Kidney 293S cells. Methods. 55: 273-280 (PMID: 21925269 / NIHMS430465)
287. Stroud RM, Schertler GF. Membranes. Curr Opin Struct Biol. (2011) 21: 495-6. (PMID: 21875531)
288. Stroud RM. New tools in membrane protein determination. F1000 Biol Rep. (2011) 3:8. (PMID: 21655333 / PMCID: PMC3100781).
289. Kim J, Stroud RM, Craik CS (2011) Rapid identification of recombinant Fabs that bind to membrane proteins. Methods, 55: 303-9. (PMCID: PMC3264787)
290. Pozzi C, Ferrari S, Cortesi D, Luciani R, Stroud RM, Catalano A, Costi MP, Mangani S. (2012). The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism. Acta Crystallogr D Biol Crystallogr 68: 1232-41. (PMID: 22948925/PMCID: in process)
291. Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F. (2012). Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its michaelis complex and covalently-trapped intermediates. PLoS One 7(4): e34918. (PMCID: PMC3329556)
292. Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampe R, Edwards RH, Stroud RM, Craik CS, Cheng Y. (2012) Fabs enable single particle cryoEM studies of small proteins. Structure 20: 582-92. (PMCID: PMC3322386)
293. Chaudhary S, Pak JE, Gruswitz F, Sharma V, Stroud RM. (2012). Overexpressing human membrane proteins in stably transfected and clonal human embryonic kidney 293S cells. Nat Protoc 7: 453-66. (PMID: 22322218 / PMCID: PMC3613139)
294. Varrin-Doyer M, Spencer CM, Schulze-Topphoff U, Nelson PA, Stroud RM, Cree BA, Zamvil SS. (2012). Aquaporin 4-specific T cells in neuromyelitis optica exhibit a Th17 bias and recognize Clostridium ABC transporter. Ann Neurol 72: 53-64. (PMCID: PMC3405197)
295. Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A. (2012). A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase. J Am Chem Soc 134: 17722-30. (PMID: 23611499 / PMCID: PMC3490427)
296. Metzger LE, Lee JK, Finer-Moore JS, Raetz CR, Stroud RM. (2012). LpxI structures reveal how a lipid A precursor is synthesized. Nat Struct Mol Biol 19: 1132-1138. (PMCID: PMC3562136)
297. Carosati E, Tochowicz A, Marverti G, Guaitoli G, Benedetti P, Ferrari S, Stroud RM, Finer-Moore JS, Luciani R, Farina D, Cruciani G, Costi MP. (2012). Inhibitor of ovarian cancer cells growth by virtual screening: a new thiazole derivative targeting human thymidylate synthase. J Med Chem 55: 10272-6. (PMID: 23075414 / PMCID).
298. Wu S, Avila-Sakar A, Kim J, Booth DS, Greenberg CH, Rossi A, Liao M, Li X, Alian A, Griner SL, Juge N, Yu Y, Mergel CM, Chaparro-Riggers J, Strop P, Tampe R, Edwards RH, Stroud RM, Craik CS, Cheng Y (2012) Fabs enable single particle cryoEM studies of small proteins. Structure. 20: 582-92. (PMCID: PMC3322386).
299. Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A. (2013). Coordinating the impact of structural genomics on the human α-helical transmembrane proteome. Nat Struct Mol Biol 20: 135-8. (PMCID: PMC3645303).
300. Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A (2013) Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J Am Chem Soc. 135: 7583-92. (PMID: 23611499 / PMCID: PMC3674108)
301. Tochowicz A, Dalziel S, Eidam O, O'Connell JD, 3rd, Griner S, Finer-Moore JS, Stroud RM (2013) Development and Binding Mode Assessment of N-[4-[2-Propyn-1-yl[(6S)-4,6,7,8-tetrahydro-2-(hydroxymethyl)-4-oxo-3H-cyclopenta [g]quinazolin-6-yl]amino]benzoyl]-l-gamma-glutamyl-d-glutamic Acid (BGC 945), a Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells. J Med Chem. 56: 5446-5455 (PMID: 23710599)
302. Czudnochowski N, Wang AL, Finer-Moore J, Stroud RM (2013) In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA, Consistent with Their Different Target Selectivities. J Mol Biol. 425: 3875-3887 (PMID: 24214967.)
* 303. Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM (2013) Crystal structure of a eukaryotic phosphate transporter. Nature 496: 533-536. (PMID: 23542591 / PMCID: PMC3678552)
* 304. Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM (2013) Structural basis for alternating access of a eukaryotic calcium/proton exchanger. Nature 499: 107-110. (PMID: 23685453 / PMCID: PMC3702627)
305. Pak JE, Ekende EN, Kifle EG, O'Connell JD, 3rd, De Angelis F, Tessema MB, Derfoufi KM, Robles-Colmenares Y, Robbins RA, Goormaghtigh E, Vandenbussche G, Stroud RM. Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter. Proc Natl Acad Sci U S A. (2013) 110:18484-18489. PubMed (PMID: 24173033; PMCID: PMC3832018).
306. Johri A, Oelmüller R, Dua M, Yadav V, Kumar M, Tuteja N, Varma A, Saha S, Bonfante P, Persson BL, Stroud RM. (2014) Fungal Association and utilization of phosphate by plants: success, limitations, and future prospects Front Microbiol. 6: 984 (PMID: 26528243 PMC4608361)
307. Kumar H, Kasho V, Smirnova I, Finer-Moore J, Kaback RH, Stroud RM. (2014) Structure of Sugar-Bound LacY Proc Natl Acad Sci U S A. 111: 1784-1788 (PMID: 24453216 / PMID: PMC3918835)
308. Monk BC, Tomasiak TM, Mikhail V, Keniya MV, Franziska U, Huschmann FU, Tyndall JDA, O’Connell III JD, Cannon RD, McDonald JG, Rodriguez A, Finer-Moore J, Stroud RM. (2014) Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Proc Natl Acad Sci U S A. 111: 3865-3870 (PMID: 24994900 PMC4115540)
309. Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM (2014) The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs. Nucleic Acids Res. 42: 2037-2048 (PMID: 24214967 PMC3919597)
310. Miercke LJ, Robbins RA, and Stroud RM, 2014. Tetra Detector Analysis of Membrane Proteins. Curr. Protoc. Protein Sci. 77:29.10:29.10.1–29.10.30. (PMID: 25081744 PMC4178957)
311. Tomasiak TM, Pedersen BP, Chaudhary S, Rodriguez A, Colmanares YR, Roe-Zurz Z, Thamminana S, Tessema M, Stroud RM (2014) General qPCR and Plate Reader Methods for Rapid Optimization of Membrane Protein Purification and Crystallization Using Thermostability Assays. Curr Protoc Protein Sci. 77: 29 11 1-29 11 4 (PMID: 25081745)
312. Lohse MB, Rosenberg OS, Cox JS, Stroud RM, Finer-Moore JS, Johnson AD (2014) Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi. Proc Natl Acad Sci U S A. 111: 10404-10410 (PMID: 24994900 / PMCID: PMC4115540)
313. Kumar H, Finer-Moore JS, Kaback HR, Stroud RM. Structure of LacY with an alpha-substituted galactoside: Connecting the binding site to the protonation site. (2015) Proc Natl Acad Sci U S A. 2015;112: 9004-9009. doi: 10.1073/pnas.1509854112. PubMed (PMID: 26157133 / PMCID: PMC4517220)
314. Salo-Ahen OM, Tochowicz A, Pozzi C, Cardinale D, Ferrari S, Boum Y, Mangani S, Stroud RM, Saxena P, Myllykallio H, Costi MP, Ponterini G, Wade RC. Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase. J Med Chem. 2015;58: 3572-3581. doi: 10.1021/acs.jmedchem.5b00137. (PMID: 25798950)
315. Tochowicz A, Santucci M, Saxena P, Guaitoli G, Trande M, Finer-Moore J, Stroud RM, Costi MP. (2015) Alanine mutants of the interface residues of human thymidylate synthase decode key features of the binding mode of allosteric anticancer peptides. J Med Chem. 58:1012-8. doi: 10.1021/jm5011176. (PMID: 25427005).
316. Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampe R, Craik CS, Cheng Y (2015) Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter. Nature. 517: 396-400 (PMID: 25363761 / PMCID: PMC4372080)
317. Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS (2015) Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion. Cell. 161: 501-512 (PMID: 25865481 / PMCID: PMC4409929)
318. Finer-Moore JS, Czudnochowski N, O’Connell JD IIIrd, Wang AL, Stroud RM (2015) Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target J Mol Biol 427: 3862-3876 (PMID: 26470919 / PMCID: PMC4663122)
* 319. Kintzer A, Stroud RM (2016) Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana. Nature. 531: 258-62 (PMID: 26961658 / PMCID: PMC4863712)
[It was highlighted in a ‘spotlight’ by Patel, S., Penny, C. J. & Rahman, T. “Two-pore Channels Enter the Atomic Era: Structure of Plant TPC Revealed.” Trends Biochem. Sci. 41, 475–477 (2016). It was covered in press releases: “X-ray Studies at SLAC and Berkeley Lab Aid Search for Ebola Cure” by SLAC National Accelerator Laboratory, in “Shutting Out Ebola And Other Viruses” by Lawrence Berkeley National Laboratory YouTube https://www.youtube.com/watch?v=NraaRsCtsQo, and recommended by Faculty of 1000]
320. Kapoor K, Finer-Moore J, Pedersen BP, Waight, Caboni L, Hillig R, Bringmann P, Heisler I, Mülle T, Siebeneicher H, Stroud RM (2016) Mechanism of inhibition of human glucose transporter GLUT1 is conserved between cytochalasin B and phenylalanine amides. Proc Natl Acad Sci U S A. 113: 4711-4716 (PMID: 27078104 / PMC4855560)
321. Thurtle-Schmidt BH, Stroud RM (2016) Structure of Bor1 supports an elevator transport mechanism for SLC4 anion exchangers. Proc Natl Acad Sci U S A. 113: 10542-10546 (PMID: 27601653 / PMCID: PMC5035872)
322. Chaudhary S, Saha S, Thamminana S, Stroud RM (2016) Small-Scale Screening to Large-Scale Over-Expression of Human Membrane Proteins for Structural Studies. Methods Mol Biol. 1432: 203-221 (PMID: 27485338)
323. Boswell-Casteel RC, Johnson JM, Stroud RM, Hays FA (2016) Integral Membrane Protein Expression in Saccharomyces cerevisiae. Methods Mol Biol. 1432: 163-86
324. Galilee M, Britan-Rosich E, Griner SL, Uysal S, Baumgartel V, Lamb DC, Kossiakoff AA, Kotler M, Stroud RM, Marx A, Alian A (2016) The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical. Structure. 24: 1936-1946 (PMID: 27692964 / PMCID: PMC5093063)
325. R.W. Schoenlein et al. Stroud RM et al. Zwart P. "New Science Opportunities Enabled by LCLS-II X-ray Lasers" SLAC Report SLAC-R-1053 (2015) https://portal.slac.stanford.edu/sites/lcls_public/Documents/LCLS-IIScienceOpportunities_final.pdf
326. Kintzer AF, Stroud RM. On the structure and mechanism of two-pore channels. FEBS J. (2017). 285: 233-243 DOI 10.1111/febs. 14154 (PMID: 28656706 / PMCID: PMC5745306
327. Noll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Bruchert S, Joseph B, Abele R, Olieric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, Tampe R (2017) Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP. Proc Natl Acad Sci U S A. 114: E438-E447 (PMID: 28069938 /PMCID: PMC5278451)
328. Finer-Moore JS, Lee TT, Stroud RM (2018) A Single Mutation Traps a Half-Sites Reactive Enzyme in Midstream, Explaining Asymmetry in Hydride Transfer. Biochemistry. 57: 2786-2795 (PMID: 29717875) PDF
329. Kumar H, Finer-Moore JS, Jiang X, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM. (2018) Crystal Structure of a ligand bound LacY/Nanobody Complex. Proc Natl Acad Sci U S A. –in press. PDF
330. Kintzer AF, Green EM,Dominik PK, Bridges M,Armache J-P,Deneka D, Kim SS, Hubbell W, Kossiakoff, AA, Cheng Y, Stroud RM. (2018) The structural basis for activation of voltage sensor domains in an ion channel TPC1. Proc Natl Acad Sci U S A. https://www.biorxiv.org/content/early/2018/07/21/373860 & Proc Natl Acad Sci U S A. –in press.
Complete List of Published Work in MyBibliography:
PATENTS
U.S. Patent 5,693,515 - Metal Complexed Serine Protease Inhibitors. Issued on December 2nd 1997.
U.S. Patent 5,900,371 - Metal Complexed Serine Protease Inhibitors. Issued on May 4th 1999.
U.S. Patent 08815885 – Methods and compositions for modulating IRE1, SRC, and ABL Published August 26 2014.
NON-REFEREED ARTICLES
1. Levitski A, Dodson GG, Henderson R, Palm D, Sheppard H, Stroud RM, Tanford C, Wright P., Zatz M. (1976). Dahlem Workshop on Hormone and Antihormone Action at the Target Cell. Catecholamine Receptors Group Report.
2. Stroud RM. (1991). Science 253, 685-686. Molecular Biology in Three Dimensions. Review of Introduction to Protein Structure by Carl Branden and John Tooze, Garland, New York.
3. Stroud RM. (1993). Science 262, 443-444. Practical Proteins. Review of Protein Structure. New Approaches to Disease and Therapy by Max Perutz, Freeman, New York, 1992.
4. Stroud RM. (1994). Nature Struct. Biol. 1 (3), 131-134. An electrostatic highway.
5. Stroud RM. (1994). Annual Review of Biophysics and Biomolecular Structure 23:v. Preface.
6. Stroud RM. (1995). Nature Structural Biology 2, 619-620. An inducement to collaboration. Review of Crystal Structure Analysis for Chemists and Biologists by J. Glusker with M. Lewis M, Rossi, UCH Publishers, New York, 1994.
7. Stroud RM. (1995). Annual Review of Biophysics and Biomolecular Structure 24:v. Preface.
8. Stroud RM. (1996). Nature Struct. Biol. 3, 567-569. Balancing ATP in the cell.
9. Stroud RM. (1996). Annual Review of Biophysics and Biomolecular Structure 25:v. Preface.
10. Stroud RM. (1997). Annual Review of Biophysics and Biomolecular Structure 26:v. Preface.
11. Stroud RM. (1998). Annual Review of Biophysics and Biomolecular Structure 27:v. Preface.
12. Stroud RM. (1998). In Structure-Based Drug Design – Experimental and Computational Approaches, P.W. Codding, Ed., Series E: Applied Sciences – Vol. 352, pp 233-237. Exploring Drug Design Methods with Thymidylate Synthase. Kluwer Academic Publishers, The Netherlands.
13. Stroud RM. (2000). Annual Review of Biophysics and Biomolecular Structure 29:v. Preface.
14. Stroud RM. (2001). Annual Review of Biophysics and Biomolecular Structure 30:v. Preface.
15. Stroud RM. (2002). Annual Review of Biophysics and Biomolecular Structure 31:v. Preface.
16. Stroud RM. (2003). Annual Review of Biophysics and Biomolecular Structure 32:v. Preface.
17. Stroud RM. (2004). Annual Review of Biophysics and Biomolecular Structure 33:v. Preface.
18. Stroud RM. (1994). Nature Struct. Biol. 1 (3), 131-134. An electrostatic highway.
19. Stroud RM. (1996). Nature Struct. Biol. 3, 567-569. Balancing ATP in the cell.
20. Stroud RM. (2008) Protein Science 17, 1864-1866 Michael A. Raftery (1936-2007)--the first enzyme mechanism, sequential cooperativity, and the nicotinic acetylcholine receptor defined
21 Stroud RM. (2008). Michael A. Raftery (1936-2007)--the first enzyme mechanism, sequential cooperativity, and the nicotinic acetylcholine receptor defined. Protein Sci 17: 1864263.
BOOK CHAPTERS:
14. Raftery MA, Bode J, Vandlen R, Michaelson D, Deutsch J, Moody T, Ross MJ, Stroud, RM (1975). In Protein-Ligand Interactions, pp 328-355, Walter de Gruyter & Co, Berlin, Germany. Structural and Functional Studies of an Acetylcholine Receptor.
28. McKay DB, Kay LM, Stroud RM. (1977). In Chemistry and Biology of Thrombin,
Lundblad, RL, Fenton, JW. II, Mann, KG. eds., pp. 113-121, Ann Arbor Science Publishers, Inc, Ann Arbor, Michigan. Preliminary Crystallization and X-Ray Diffraction Studies of Human Thrombin.
39. Stroud RM. (1981). In Biomolecular Stereodynamics 1, 55-73, RH. Sarma, ed., Adenine Press, New York. Proceedings of the Second SUNYA Conversation in the Discipline Biomolecular Stereodynamics, Vol. II. Structure of an Acetylcholine Receptor, A Hypothesis for a Dynamic Mechanism of its Action.
44. Wetzel R, Levine HL, Estell DA, Shire S, Finer-Moore JS, Stroud RM, Bewley TA. (1982). In Interferons, Academic Press, New York, N.Y, pp. 365-376. Structure-Function Studies on Human Alpha Interferon.
45. Stroud RM. (1983). In Frontiers in Biochemical and Biophysical Studies of Proteins and Membranes, Liu, T.Y, et al, ed., Elsevier Science Publishing Co. Inc, New York, N.Y.,
pp. 331-349. The Structure of Acetylcholine Receptor and of Bacteriorhodopsin.
49. Stroud RM. (1984). In Biological Membranes 5 (6), 221-239, Chapman, D, ed., Academic
Press Inc. (London) Ltd, London. Acetylcholine Receptor Structure and Function.
58. Stroud RM. (1986). In Proteins of Excitable Membranes, Hille B. and Fambrough, D. eds.,
Society of General Physiologists Series Vol. 41, pp. 67-75. Topological Mapping and the Ionic Channel in an Acetylcholine Receptor.
63. Stroud RM., Finer-Moore JS. (1987). In Biological Organization: Macromolecular Interactions at High Resolution, Burnett, RM., Vogel, HJ., eds., Academic Press Inc, Orlando, pp. 307-318. The Acetylcholine Receptor: What the Three-Dimensional Structure Tells Us about Ion Conductance.
66. Earnest JP, Stroud RM., McNamee MG. (1987). In Membrane Proteins: Proceedings
of the Membrane Protein Symposium, Goheen, S.C, ed., Bio-Rad Laboratories, Richmond, California, 117-130. Effects of the Functional State of the Acetylcholine Receptor on Reconstitution into Lipid Vesicles.
67. Stroud RM. (1987). In Molecular Neurobiology in Neurology and Psychiatry, E. Kandel, ed.,
Raven Press, N.Y. 65, 51-63. An Archetypal Molecular Transducer of the Nervous System:
The Acetylcholine Receptor.
69. Fairclough RH, Stroud RM, Miake-Lye, RC Hodgson KO, Doniach S. (1988).
In Myasthenia Gravis: Biology and Treatment. Annals of the New York Academy of
Sciences 505, 752-755. Terbium-Calcium Binding Sites on the Acetylcholine Receptor.
72. Falick AM, Mel SF, Stroud RM, Burlingame AL. (1988). In Techniques in Protein Chemistry, Academic Press pp 152-159. A New Strategy for Mapping the Topography of
a Transmembrane Protein Using Mass Spectrometry.
75. Finer-Moore JS, Bazan JF, Rubin J., Stroud RM. (1989). In Prediction of Protein Structure and the Principles of Protein Conformation, G. Fasman, ed., Plenum Press, New York, 719-759. Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis.
76. Stroud RM, McCarthy MP, Earnest JP, Shuster M, Ghosh P, Mitra AR. (1989).
In Fernstrom Series on Neuromuscular Junction, L.C. Sellin, R. Libelius, S. Thesleff, eds., Elsevier Science Publishers, The Netherlands, 209-216. Molecular Biology of the Acetylcholine Receptor.
85. Montfort WR, Fauman EB, Perry KM, Stroud RM. (1990). In Current Research in
Protein Chemistry: Techniques, Structure and Function, J.J. Villafranca, ed, Academic Press, San Diego, 367-382. Segmental Accommodation: A Novel Conformational Change Induced Upon Ligand Binding by Thymidylate Synthase.
86. Shuster MJ, Mitra AK, Stroud RM. (1990). In Protein and Pharmaceutical Engineering (UCLA Symposia on Molecular and Cellular Biology, Vol. 110), C.W. Craik, R.J. Fletterick, eds, Alan R. Liss, New York, NY, 55-70. The Acetylcholine Receptor.
90. Stroud RM. (1990). In Progress in Cell Research, Vol.1, J.M. Ritchie, P.J. Magistretti,and L.
Bolis, eds, Elsevier Science Publishers, New York, Chapt. 11, pp 123-138. What the structure
of the acetylcholine receptor tells us about function of the ligand gated ion channel family.
96. Stroud RM. (1990). In Biological Mass Spectrometry, A.L. Burlingame, J.A. McCloskey,
eds, Elsevier Science Publishers, New York, pp 653-670. Proceedings of the Second International Symposium on Mass Spectrometry in the Health and Life Sciences.
Cellular Signalling - What the Structure of Neuroreceptors Tells Us About Function.
108. Stroud RM. (1991). In Molecular Conformation and Biological Interactions, P.Balaram
and S. Ramaseshan, eds., Indian Academy of Sciences Press, Bangalore, India, 627-644. Structure and Function of Transmembrane Ion Channels.
240. Stroud RM. Harries W. Lee JK, Khademi S, Savage D. Chapter 11 Aquaporins;
Integral Membrane Protein Channels. Structural Biology of Membrane Proteins, Royal Society of Chemistry
241. Khademi S, Stroud RM. Chapter 12 Gas Channels for Ammonia. Structural Biology
of Membrane Proteins, Royal Society of Chemistry
999. Stroud RM., Finer-Moore JS. The editors; ‘Computational and Structural Approaches to
Drug Discovery; (2007) Royal Society of Chemistry UK; Also The preface, and Chapter 1 Facing the Wall in Computationally Based Approaches to Drug Discsovery.
PDB COORDINATES OF PROTEIN STRUCTURES DEPOSITED
369 coordinate sets of Protein structures; 44 are integral membrane proteins. determined by X-ray crystallography/CryoEM in the Protein Data Bank as of July 2018; 8 sets currently being processed.
updated 06/10/2018 rs