Robert Stroud, MA, PhD

Kinetic Network Modeling with Molecular Simulation Inputs: A Proton-Coupled Phosphate Symporter.

Biophysical journal

Liu Y, Li C, Gupta M, Stroud RM, Voth GA

Structural basis of prostaglandin efflux by MRP4.

Nature structural & molecular biology

Pourmal S, Green E, Bajaj R, Chemmama IE, Knudsen GM, Gupta M, Sali A, Cheng Y, Craik CS, Kroetz DL, Stroud RM

Vicia faba SV channel VfTPC1 is a hyperexcitable variant of plant vacuole Two Pore Channels.

eLife

Lu J, Dreyer I, Dickinson MS, Panzer S, Jaslan D, Navarro-Retamal C, Geiger D, Terpitz U, Becker D, Stroud RM, Marten I, Hedrich R

Substrate recognition and proton coupling by a bacterial member of solute carrier family 17.

The Journal of biological chemistry

Batarni S, Nayak N, Chang A, Li F, Hareendranath S, Zhou L, Xu H, Stroud R, Eriksen J, Edwards RH

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.

Nature structural & molecular biology

Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM

Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13.

bioRxiv : the preprint server for biology

Kim SK, Dickinson MS, Finer-Moore J, Guan Z, Kaake RM, Echeverria I, Chen J, Pulido EH, Sali A, Krogan NJ, Rosenberg OS, Stroud RM

Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth.

eLife

Costantino L, Ferrari S, Santucci M, Salo-Ahen OMH, Carosati E, Franchini S, Lauriola A, Pozzi C, Trande M, Gozzi G, Saxena P, Cannazza G, Losi L, Cardinale D, Venturelli A, Quotadamo A, Linciano P, Tagliazucchi L, Moschella MG, Guerrini R, Pacifico S, Luciani R, Genovese F, Henrich S, Alboni S, Santarem N, da Silva Cordeiro A, Giovannetti E, Peters GJ, Pinton P, Rimessi A, Cruciani G, Stroud RM, Wade RC, Mangani S, Marverti G, D'Arca D, Ponterini G, Costi MP

Diversity of function and mechanism in a family of organic anion transporters.

Current opinion in structural biology

Li F, Eriksen J, Finer-Moore J, Stroud RM, Edwards RH

Molecular basis of multistep voltage activation in plant two-pore channel 1.

Proceedings of the National Academy of Sciences of the United States of America

Dickinson MS, Lu J, Gupta M, Marten I, Hedrich R, Stroud RM

Symmetry Reduction in a Hyperpolarization-Activated Homotetrameric Ion Channel.

Biochemistry

Dickinson MS, Pourmal S, Gupta M, Bi M, Stroud RM

Allosteric Inhibition of a Vesicular Glutamate Transporter by an Isoform-Specific Antibody.

Biochemistry

Eriksen J, Li F, Stroud RM, Edwards RH

Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT.

Proceedings of the National Academy of Sciences of the United States of America

Liu Y, Li C, Gupta M, Verma N, Johri AK, Stroud RM, Voth GA

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Research square

Verba K, Gupta M, Azumaya C, Moritz M, Pourmal S, Diallo A, Merz G, Jang G, Bouhaddou M, Fossati A, Brilot A, Diwanji D, Hernandez E, Herrera N, Kratochvil H, Lam V, Li F, Li Y, Nguyen H, Nowotny C, Owens T, Peters J, Rizo A, Schulze-Gahmen U, Smith A, Young I, Yu Z, Asarnow D, Billesbølle C, Campbell M, Chen J, Chen KH, Chio US, Dickinson M, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez K, Mancino A, Iii FM, Paul M, Pawar K, Pelin A, Pospiech T, Puchades C, Remesh S, Safari M, Schaefer K, Sun M, Tabios M, Thwin A, Titus E, Trenker R, Tse E, Tsui TKM, Feng F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, Agard D, Cheng Y, Fraser J, Jura N, Kortemme T, Manglik A, Southworth D, Stroud R, Swaney D, Krogan N, Frost A, Rosenberg O

CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

bioRxiv : the preprint server for biology

Gupta M, Azumaya CM, Moritz M, Pourmal S, Diallo A, Merz GE, Jang G, Bouhaddou M, Fossati A, Brilot AF, Diwanji D, Hernandez E, Herrera N, Kratochvil HT, Lam VL, Li F, Li Y, Nguyen HC, Nowotny C, Owens TW, Peters JK, Rizo AN, Schulze-Gahmen U, Smith AM, Young ID, Yu Z, Asarnow D, Billesbølle C, Campbell MG, Chen J, Chen KH, Chio US, Dickinson MS, Doan L, Jin M, Kim K, Li J, Li YL, Linossi E, Liu Y, Lo M, Lopez J, Lopez KE, Mancino A, Moss FR, Paul MD, Pawar KI, Pelin A, Pospiech TH, Puchades C, Remesh SG, Safari M, Schaefer K, Sun M, Tabios MC, Thwin AC, Titus EW, Trenker R, Tse E, Tsui TKM, Wang F, Zhang K, Zhang Y, Zhao J, Zhou F, Zhou Y, Zuliani-Alvarez L, QCRG Structural Biology Consortium , Agard DA, Cheng Y, Fraser JS, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Swaney DL, Krogan NJ, Frost A, Rosenberg OS, Verba KA

Structural basis for Clostridium perfringens enterotoxin targeting of claudins at tight junctions in mammalian gut.

Proceedings of the National Academy of Sciences of the United States of America

Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog.

Biochemistry

Highlighting membrane protein structure and function: A celebration of the Protein Data Bank.

The Journal of biological chemistry

Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM

Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients.

eLife

Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS

Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.

Science (New York, N.Y.)

Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D

Ion transport and regulation in a synaptic vesicle glutamate transporter.

Science (New York, N.Y.)

Li F, Eriksen J, Finer-Moore J, Chang R, Nguyen P, Bowen A, Myasnikov A, Yu Z, Bulkley D, Cheng Y, Edwards RH, Stroud RM

Diversity in kinetics correlated with structure in nano body-stabilized LacY.

PloS one

Kumar H, Finer-Moore J, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Nature

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, O'Meara MJ, Rezelj VV, Guo JZ, Swaney DL, Tummino TA, Huettenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Meyer B, Roesch F, Vallet T, Mac Kain A, Miorin L, Moreno E, Naing ZZC, Zhou Y, Peng S, Shi Y, Zhang Z, Shen W, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Lyu J, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Rakesh R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Liboy-Lugo J, Lin Y, Huang XP, Liu Y, Wankowicz SA, Bohn M, Safari M, Ugur FS, Koh C, Savar NS, Tran QD, Shengjuler D, Fletcher SJ, O'Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, Sharp PP, Wenzell NA, Kuzuoglu D, Wang HY, Trenker R, Young JM, Cavero DA, Hiatt J, Roth TL, Rathore U, Subramanian A, Noack J, Hubert M, Stroud RM, Frankel AD, Rosenberg OS, Verba KA, Agard DA, Ott M, Emerman M, Jura N, von Zastrow M, Verdin E, Ashworth A, Schwartz O, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor SN, Fraser JS, Gross JD, Sali A, Roth BL, Ruggero D, Taunton J, Kortemme T, Beltrao P, Vignuzzi M, García-Sastre A, Shokat KM, Shoichet BK, Krogan NJ

Resting state structure of the hyperdepolarization activated two-pore channel 3.

Proceedings of the National Academy of Sciences of the United States of America

Dickinson MS, Myasnikov A, Eriksen J, Poweleit N, Stroud RM

Claudin-9 structures reveal mechanism for toxin-induced gut barrier breakdown.

Proceedings of the National Academy of Sciences of the United States of America

Vecchio AJ, Stroud RM

Ceapins block the unfolded protein response sensor ATF6a by inducing a neomorphic inter-organelle tether.

eLife

Torres SE, Gallagher CM, Plate L, Gupta M, Liem CR, Guo X, Tian R, Stroud RM, Kampmann M, Weissman JS, Walter P

Structures suggest a mechanism for energy coupling by a family of organic anion transporters.

PLoS biology

Leano JB, Batarni S, Eriksen J, Juge N, Pak JE, Kimura-Someya T, Robles-Colmenares Y, Moriyama Y, Stroud RM, Edwards RH

High-pressure, high-temperature molecular doping of nanodiamond.

Science advances

Crane MJ, Petrone A, Beck RA, Lim MB, Zhou X, Li X, Stroud RM, Pauzauskie PJ

High-Throughput Nano-Scale Characterization of Membrane Proteins Using Fluorescence-Detection Size-Exclusion Chromatography.

Methods in molecular biology (Clifton, N.J.)

Vecchio AJ, Stroud RM

Structural basis for activation of voltage sensor domains in an ion channel TPC1.

Proceedings of the National Academy of Sciences of the United States of America

Kintzer AF, Green EM, Dominik PK, Bridges M, Armache JP, Deneka D, Kim SS, Hubbell W, Kossiakoff AA, Cheng Y, Stroud RM

CRL4AMBRA1 targets Elongin C for ubiquitination and degradation to modulate CRL5 signaling.

The EMBO journal

Chen SH, Jang GM, HÃ¼ttenhain R, Gordon DE, Du D, Newton BW, Johnson JR, Hiatt J, Hultquist JF, Johnson TL, Liu YL, Burton LA, Ye J, Reichermeier KM, Stroud RM, Marson A, Debnath J, Gross JD, Krogan NJ

Crystal Structure of a ligand-bound LacY-Nanobody Complex.

Proceedings of the National Academy of Sciences of the United States of America

Kumar H, Finer-Moore JS, Jiang X, Smirnova I, Kasho V, Pardon E, Steyaert J, Kaback HR, Stroud RM

A Single Mutation Traps a Half-Sites Reactive Enzyme in Midstream, Explaining Asymmetry in Hydride Transfer.

Biochemistry

Finer-Moore JS, Lee TT, Stroud RM

On the structure and mechanism of two-pore channels.

The FEBS journal

Kintzer AF, Stroud RM

Crystal structure and mechanistic basis of a functional homolog of the antigen transporter TAP.

Proceedings of the National Academy of Sciences of the United States of America

Nöll A, Thomas C, Herbring V, Zollmann T, Barth K, Mehdipour AR, Tomasiak TM, Brüchert S, Joseph B, Abele R, Oliéric V, Wang M, Diederichs K, Hummer G, Stroud RM, Pos KM, Tampé R

The Preserved HTH-Docking Cleft of HIV-1 Integrase Is Functionally Critical.

Structure (London, England : 1993)

Galilee M, Britan-Rosich E, Griner SL, Uysal S, Baumgärtel V, Lamb DC, Kossiakoff AA, Kotler M, Stroud RM, Marx A, Alian A

Structure of Bor1 supports an elevator transport mechanism for SLC4 anion exchangers.

Proceedings of the National Academy of Sciences of the United States of America

Thurtle-Schmidt BH, Stroud RM

Mechanism of inhibition of human glucose transporter GLUT1 is conserved between cytochalasin B and phenylalanine amides.

Proceedings of the National Academy of Sciences of the United States of America

Kapoor K, Finer-Moore JS, Pedersen BP, Caboni L, Waight A, Hillig RC, Bringmann P, Heisler I, Müller T, Siebeneicher H, Stroud RM

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana.

Nature

Kintzer AF, Stroud RM

Integral Membrane Protein Expression in Saccharomyces cerevisiae.

Methods in molecular biology (Clifton, N.J.)

Boswell-Casteel RC, Johnson JM, Stroud RM, Hays FA

Small-Scale Screening to Large-Scale Over-Expression of Human Membrane Proteins for Structural Studies.

Methods in molecular biology (Clifton, N.J.)

Chaudhary S, Saha S, Thamminana S, Stroud RM

Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA(3)(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.

Journal of molecular biology

Finer-Moore J, Czudnochowski N, O'Connell JD, Wang AL, Stroud RM

Fungal association and utilization of phosphate by plants: success, limitations, and future prospects.

Frontiers in microbiology

Johri AK, Oelmüller R, Dua M, Yadav V, Kumar M, Tuteja N, Varma A, Bonfante P, Persson BL, Stroud RM

Structure of LacY with an a-substituted galactoside: Connecting the binding site to the protonation site.

Proceedings of the National Academy of Sciences of the United States of America

Kumar H, Finer-Moore JS, Kaback HR, Stroud RM

Substrates Control Multimerization and Activation of the Multi-Domain ATPase Motor of Type VII Secretion.

Cell

Rosenberg OS, Dovala D, Li X, Connolly L, Bendebury A, Finer-Moore J, Holton J, Cheng Y, Stroud RM, Cox JS

Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.

Journal of medicinal chemistry

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

Alanine mutants of the interface residues of human thymidylate synthase decode key features of the binding mode of allosteric anticancer peptides.

Journal of medicinal chemistry

Tochowicz A, Santucci M, Saxena P, Guaitoli G, Trande M, Finer-Moore J, Stroud RM, Costi MP

Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter.

Nature

Kim J, Wu S, Tomasiak TM, Mergel C, Winter MB, Stiller SB, Robles-Colmanares Y, Stroud RM, Tampé R, Craik CS, Cheng Y

General qPCR and Plate Reader Methods for Rapid Optimization of Membrane Protein Purification and Crystallization Using Thermostability Assays.

Current protocols in protein science

Tomasiak TM, Pedersen BP, Chaudhary S, Rodriguez A, Colmanares YR, Roe-Zurz Z, Thamminana S, Tessema M, Stroud RM

Tetra detector analysis of membrane proteins.

Current protocols in protein science

Miercke LJ, Robbins RA, Stroud RM

Structure of a new DNA-binding domain which regulates pathogenesis in a wide variety of fungi.

Proceedings of the National Academy of Sciences of the United States of America

Lohse MB, Rosenberg OS, Cox JS, Stroud RM, Finer-Moore JS, Johnson AD

Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer.

Proceedings of the National Academy of Sciences of the United States of America

Monk BC, Tomasiak TM, Keniya MV, Huschmann FU, Tyndall JD, O'Connell JD, Cannon RD, McDonald JG, Rodriguez A, Finer-Moore JS, Stroud RM

Structure of sugar-bound LacY.

Proceedings of the National Academy of Sciences of the United States of America

Kumar H, Kasho V, Smirnova I, Finer-Moore JS, Kaback HR, Stroud RM

The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs.

Nucleic acids research

Czudnochowski N, Ashley GW, Santi DV, Alian A, Finer-Moore J, Stroud RM

Structures of intermediate transport states of ZneA, a Zn(II)/proton antiporter.

Proceedings of the National Academy of Sciences of the United States of America

Pak JE, Ekendé EN, Kifle EG, O'Connell JD, De Angelis F, Tessema MB, Derfoufi KM, Robles-Colmenares Y, Robbins RA, Goormaghtigh E, Vandenbussche G, Stroud RM

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-?-glutamyl-D-glutamic acid (BGC 945), a novel thymidylate synthase inhibitor that targets tumor

Journal of medicinal chemistry

Tochowicz A, Dalziel S, Eidam O, O'Connell JD, Griner S, Finer-Moore JS, Stroud RM

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.

Journal of molecular biology

Czudnochowski N, Wang AL, Finer-Moore J, Stroud RM

Structural basis for alternating access of a eukaryotic calcium/proton exchanger.

Nature

Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM

Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.

Journal of the American Chemical Society

Wang Z, Sapienza PJ, Abeysinghe T, Luzum C, Lee AL, Finer-Moore JS, Stroud RM, Kohen A

Crystal structure of a eukaryotic phosphate transporter.

Nature

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

Coordinating the impact of structural genomics on the human a-helical transmembrane proteome.

Nature structural & molecular biology

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

Inhibitor of ovarian cancer cells growth by virtual screening: a new thiazole derivative targeting human thymidylate synthase.

Journal of medicinal chemistry

Carosati E, Tochowicz A, Marverti G, Guaitoli G, Benedetti P, Ferrari S, Stroud RM, Finer-Moore J, Luciani R, Farina D, Cruciani G, Costi MP

A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.

Journal of the American Chemical Society

Wang Z, Abeysinghe T, Finer-Moore JS, Stroud RM, Kohen A

LpxI structures reveal how a lipid A precursor is synthesized.

Nature structural & molecular biology

Metzger LE, Lee JK, Finer-Moore JS, Raetz CR, Stroud RM

The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism.

Acta crystallographica. Section D, Biological crystallography

Pozzi C, Ferrari S, Cortesi D, Luciani R, Stroud RM, Catalano A, Costi MP, Mangani S

Aquaporin 4-specific T cells in neuromyelitis optica exhibit a Th17 bias and recognize Clostridium ABC transporter.

Annals of neurology

Varrin-Doyer M, Spencer CM, Schulze-Topphoff U, Nelson PA, Stroud RM, Cree BA, Zamvil SS

Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.

PloS one

Egea PF, Muller-Steffner H, Kuhn I, Cakir-Kiefer C, Oppenheimer NJ, Stroud RM, Kellenberger E, Schuber F

Fabs enable single particle cryoEM studies of small proteins.

Structure (London, England : 1993)

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, Tampé R, Edwards RH, Stroud RM, Craik CS, Cheng Y

Overexpressing human membrane proteins in stably transfected and clonal human embryonic kidney 293S cells.

Nature protocols

Chaudhary S, Pak JE, Gruswitz F, Sharma V, Stroud RM

Rapid identification of recombinant Fabs that bind to membrane proteins.

Methods (San Diego, Calif.)

Kim J, Stroud RM, Craik CS

Efficient expression screening of human membrane proteins in transiently transfected Human Embryonic Kidney 293S cells.

Methods (San Diego, Calif.)

Chaudhary S, Pak JE, Pedersen BP, Bang LJ, Zhang LB, Ngaw SM, Green RG, Sharma V, Stroud RM

Membranes.

Current opinion in structural biology

Stroud RM, Schertler GF

EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure among helix-turn-helix proteins.

Proceedings of the National Academy of Sciences of the United States of America

Rosenberg OS, Dovey C, Tempesta M, Robbins RA, Finer-Moore JS, Stroud RM, Cox JS

Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1.

BMC biology

Korennykh AV, Egea PF, Korostelev AA, Finer-Moore J, Stroud RM, Zhang C, Shokat KM, Walter P

Structural and functional basis for RNA cleavage by Ire1.

BMC biology

Korennykh AV, Korostelev AA, Egea PF, Finer-Moore J, Stroud RM, Zhang C, Shokat KM, Walter P

New tools in membrane protein determination.

F1000 biology reports

Stroud RM

Immunodominant T cell determinants of aquaporin-4, the autoantigen associated with neuromyelitis optica.

PloS one

Nelson PA, Khodadoust M, Prodhomme T, Spencer C, Patarroyo JC, Varrin-Doyer M, Ho JD, Stroud RM, Zamvil SS

Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes.

Proceedings of the National Academy of Sciences of the United States of America

Egea PF, Stroud RM

Structural context shapes the aquaporin selectivity filter.

Proceedings of the National Academy of Sciences of the United States of America

Savage DF, O'Connell JD, Miercke LJ, Finer-Moore J, Stroud RM

Unlocking the eukaryotic membrane protein structural proteome.

Current opinion in structural biology

Lee JK, Stroud RM

Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.

Proceedings of the National Academy of Sciences of the United States of America

De Angelis F, Lee JK, O'Connell JD, Miercke LJ, Verschueren KH, Srinivasan V, Bauvois C, Govaerts C, Robbins RA, Ruysschaert JM, Stroud RM, Vandenbussche G

Function of human Rh based on structure of RhCG at 2.1 A.

Proceedings of the National Academy of Sciences of the United States of America

Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM

Comparison of human solute carriers.

Protein science : a publication of the Protein Society

Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A

Overexpression and purification of integral membrane proteins in yeast.

Methods in enzymology

Hays FA, Roe-Zurz Z, Stroud RM

A survey of integral alpha-helical membrane proteins.

Journal of structural and functional genomics

Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A

Catalytically-active complex of HIV-1 integrase with a viral DNA substrate binds anti-integrase drugs.

Proceedings of the National Academy of Sciences of the United States of America

Alian A, Griner SL, Chiang V, Tsiang M, Jones G, Birkus G, Geleziunas R, Leavitt AD, Stroud RM

Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance.

Proceedings of the National Academy of Sciences of the United States of America

Ho JD, Yeh R, Sandstrom A, Chorny I, Harries WE, Robbins RA, Miercke LJ, Stroud RM

Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.

Journal of molecular biology

Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM

2007 annual progress report synopsis of the Center for Structures of Membrane Proteins.

Journal of structural and functional genomics

Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W

A general protocol for the crystallization of membrane proteins for X-ray structural investigation.

Nature protocols

Newby ZE, O'Connell JD, Gruswitz F, Hays FA, Harries WE, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJ, Stroud RM

The unfolded protein response signals through high-order assembly of Ire1.

Nature

Korennykh AV, Egea PF, Korostelev AA, Finer-Moore J, Zhang C, Shokat KM, Stroud RM, Walter P

Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening.

Journal of molecular biology

Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM

Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

Journal of structural and functional genomics

Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM

Structures of the signal recognition particle receptor from the archaeon Pyrococcus furiosus: implications for the targeting step at the membrane.

PloS one

Egea PF, Tsuruta H, de Leon GP, Napetschnig J, Walter P, Stroud RM

Structures of SRP54 and SRP19, the two proteins that organize the ribonucleic core of the signal recognition particle from Pyrococcus furiosus.

PloS one

Egea PF, Napetschnig J, Walter P, Stroud RM

Michael A. Raftery (1936-2007)--the first enzyme mechanism, sequential cooperativity, and the nicotinic acetylcholine receptor defined.

Protein science : a publication of the Protein Society

Stroud RM

Crystal structure of bovine mitochondrial factor B at 0.96-A resolution.

Proceedings of the National Academy of Sciences of the United States of America

Lee JK, Belogrudov GI, Stroud RM

Crystal structure of the aquaglyceroporin PfAQP from the malarial parasite Plasmodium falciparum.

Nature structural & molecular biology

Newby ZE, O'Connell J, Robles-Colmenares Y, Khademi S, Miercke LJ, Stroud RM

Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.

Proceedings of the National Academy of Sciences of the United States of America

Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J

Structural and biochemical insights into the dicing mechanism of mouse Dicer: a conserved lysine is critical for dsRNA cleavage.

Proceedings of the National Academy of Sciences of the United States of America

Du Z, Lee JK, Tjhen R, Stroud RM, James TL

TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists.

Science (New York, N.Y.)

Menuz K, Stroud RM, Nicoll RA, Hays FA

X-ray structures of the signal recognition particle receptor reveal targeting cycle intermediates.

PloS one

Reyes CL, Rutenber E, Walter P, Stroud RM

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 (New York, N.Y.)

Du Z, Lee JK, Fenn S, Tjhen R, Stroud RM, James TL

Cell-free complements in vivo expression of the E. coli membrane proteome.

Protein science : a publication of the Protein Society

Savage DF, Anderson CL, Robles-Colmenares Y, Newby ZE, Stroud RM

How U38, 39, and 40 of many tRNAs become the targets for pseudouridylation by TruA.

Molecular cell

Hur S, Stroud RM

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 research

Fenn S, Du Z, Lee JK, Tjhen R, Stroud RM, James TL

Structural basis of aquaporin inhibition by mercury.

Journal of molecular biology

Savage DF, Stroud RM

The crystal structure of E. coli rRNA pseudouridine synthase RluE.

Journal of molecular biology

Pan H, Ho JD, Stroud RM, Finer-Moore J

Transmembrane transporters: an open and closed case.

Proceedings of the National Academy of Sciences of the United States of America

Stroud RM

Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96 A.

Proceedings of the National Academy of Sciences of the United States of America

Gruswitz F, O'Connell J, Stroud RM

The Amt/MEP/Rh family: structure of AmtB and the mechanism of ammonia gas conduction.

Physiology (Bethesda, Md.)

Khademi S, Stroud RM

Substrate recognition by RNA 5-methyluridine methyltransferases and pseudouridine synthases: a structural perspective.

The Journal of biological chemistry

Hur S, Stroud RM, Finer-Moore J

Pyrrolidine carboxamides as a novel class of inhibitors of enoyl acyl carrier protein reductase from Mycobacterium tuberculosis.

Journal of medicinal chemistry

He X, Alian A, Stroud R, Ortiz de Montellano PR

The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261.

Biochemistry

Newby Z, Lee TT, Morse RJ, Liu Y, Liu L, Venkatraman P, Santi DV, Finer-Moore JS, Stroud RM

The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases.

Structure (London, England : 1993)

Keatinge-Clay AT, Stroud RM

On the mechanism of sensing unfolded protein in the endoplasmic reticulum.

Proceedings of the National Academy of Sciences of the United States of America

Credle JJ, Finer-Moore JS, Papa FR, Stroud RM, Walter P

Structural basis for conductance by the archaeal aquaporin AqpM at 1.68 A.

Proceedings of the National Academy of Sciences of the United States of America

Lee JK, Kozono D, Remis J, Kitagawa Y, Agre P, Stroud RM

The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition.

Acta crystallographica. Section D, Biological crystallography

Finer-Moore JS, Anderson AC, O'Neil RH, Costi MP, Ferrari S, Krucinski J, Stroud RM

Crystal structure of the first KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.7 A.

The Journal of biological chemistry

Du Z, Lee JK, Tjhen R, Li S, Pan H, Stroud RM, James TL

Targeting proteins to membranes: structure of the signal recognition particle.

Current opinion in structural biology

Egea PF, Stroud RM, Walter P

A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.

Cell

Lee TT, Agarwalla S, Stroud RM

De novo design of an IL-4 antagonist and its structure at 1.9 A.

Proceedings of the National Academy of Sciences of the United States of America

Laporte SL, Forsyth CM, Cunningham BC, Miercke LJ, Akhavan D, Stroud RM

Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.

Proceedings of the National Academy of Sciences of the United States of America

Chu F, Shan SO, Moustakas DT, Alber F, Egea PF, Stroud RM, Walter P, Burlingame AL

Mechanism of association and reciprocal activation of two GTPases.

PLoS biology

Shan SO, Stroud RM, Walter P

The channel architecture of aquaporin 0 at a 2.2-A resolution.

Proceedings of the National Academy of Sciences of the United States of America

Harries WE, Akhavan D, Miercke LJ, Khademi S, Stroud RM

Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A.

Science (New York, N.Y.)

Khademi S, O'Connell J, Remis J, Robles-Colmenares Y, Miercke LJ, Stroud RM

An antibiotic factory caught in action.

Nature structural & molecular biology

Keatinge-Clay AT, Maltby DA, Medzihradszky KF, Khosla C, Stroud RM

Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies.

The Journal of biological chemistry

Agarwalla S, Stroud RM, Gaffney BJ

Mechanistic diversity of cytokine receptor signaling across cell membranes.

Science's STKE : signal transduction knowledge environment

Stroud RM, Wells JA

Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase.

Structure (London, England : 1993)

Lee TT, Agarwalla S, Stroud RM

Substrate twinning activates the signal recognition particle and its receptor.

Nature

Egea PF, Shan SO, Napetschnig J, Savage DF, Walter P, Stroud RM

Architecture and selectivity in aquaporins: 2.5 a X-ray structure of aquaporin Z.

PLoS biology

Savage DF, Egea PF, Robles-Colmenares Y, O'Connell JD, Stroud RM

The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate.

Structure (London, England : 1993)

Foster PG, Nunes CR, Greene P, Moustakas D, Stroud RM

Crystal structure of an Acyl-ACP dehydrogenase from the FK520 polyketide biosynthetic pathway: insights into extender unit biosynthesis.

Journal of molecular biology

Watanabe K, Khosla C, Stroud RM, Tsai SC

Water and glycerol permeation through the glycerol channel GlpF and the aquaporin family.

Journal of synchrotron radiation

Lee JK, Khademi S, Harries W, Savage D, Miercke L, Stroud RM

Selectivity and conductance among the glycerol and water conducting aquaporin family of channels.

FEBS letters

Stroud RM, Savage D, Miercke LJ, Lee JK, Khademi S, Harries W

Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

Proceedings of the National Academy of Sciences of the United States of America

Pan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM

Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase.

The Journal of biological chemistry

O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC

Glycerol facilitator GlpF and the associated aquaporin family of channels.

Current opinion in structural biology

Stroud RM, Miercke LJ, O'Connell J, Khademi S, Lee JK, Remis J, Harries W, Robles Y, Akhavan D

The structural roles of conserved Pro196, Pro197 and His199 in the mechanism of thymidylate synthase.

Protein engineering

Gonzalez-Pacanowska D, Ruiz-Perez LM, Carreras-Gómez MA, Costi MP, Stroud RM, Finer-Moore J, Santi DV

Crystal structure and molecular modeling of 17-DMAG in complex with human Hsp90.

Chemistry & biology

Jez JM, Chen JC, Rastelli G, Stroud RM, Santi DV

Structure of human pro-chymase: a model for the activating transition of granule-associated proteases.

Biochemistry

Reiling KK, Krucinski J, Miercke LJ, Raymond WW, Caughey GH, Stroud RM

The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity.

Protein engineering

Birdsall DL, Finer-Moore J, Stroud RM

Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase.

Structure (London, England : 1993)

Keatinge-Clay AT, Shelat AA, Savage DF, Tsai SC, Miercke LJ, O'Connell JD, Khosla C, Stroud RM

Conformational dynamics along an enzymatic reaction pathway: thymidylate synthase, "the movie".

Biochemistry

Stroud RM, Finer-Moore JS

Lessons and conclusions from dissecting the mechanism of a bisubstrate enzyme: thymidylate synthase mutagenesis, function, and structure.

Biochemistry

Finer-Moore JS, Santi DV, Stroud RM

The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme.

The Journal of eukaryotic microbiology

O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC

The glycerol facilitator GlpF its aquaporin family of channels, and their selectivity.

Advances in protein chemistry

Stroud RM, Nollert P, Miercke L

Structural basis for mobility in the 1.1 A crystal structure of the NG domain of Thermus aquaticus Ffh.

Journal of molecular biology

Ramirez UD, Minasov G, Focia PJ, Stroud RM, Walter P, Kuhn P, Freymann DM

Structure-based studies on species-specific inhibition of thymidylate synthase.

Biochimica et biophysica acta

Costi MP, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Soragni F, Venturelli A, Stroud RM

Tryptophan 80 and leucine 143 are critical for the hydride transfer step of thymidylate synthase by controlling active site access.

Biochemistry

Fritz TA, Liu L, Finer-Moore JS, Stroud RM

Encoding Selectivity of a Transmembrane Channel.

TheScientificWorldJournal

Stroud RM, Nollert P, Miercke LJW, Harries WEC, O'Connell J

Anisotropic dynamics of the JE-2147-HIV protease complex: drug resistance and thermodynamic binding mode examined in a 1.09 A structure.

Biochemistry

Reiling KK, Endres NF, Dauber DS, Craik CS, Stroud RM

Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli.

The Journal of biological chemistry

Agarwalla S, Kealey JT, Santi DV, Stroud RM

The structure of GlpF, a glycerol conducting channel.

Novartis Foundation symposium

Fu D, Libson A, Stroud R

Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel.

Proceedings of the National Academy of Sciences of the United States of America

Tsai SC, Miercke LJ, Krucinski J, Gokhale R, Chen JC, Foster PG, Cane DE, Khosla C, Stroud RM

Multi-targeted antifolates aimed at avoiding drug resistance form covalent closed inhibitory complexes with human and Escherichia coli thymidylate synthases.

Journal of molecular biology

Sayre PH, Finer-Moore JS, Fritz TA, Biermann D, Gates SB, MacKellar WC, Patel VF, Stroud RM

Structure of Cry2Aa suggests an unexpected receptor binding epitope.

Structure (London, England : 1993)

Morse RJ, Yamamoto T, Stroud RM

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking.

Chemistry & biology

Anderson AC, O'Neil RH, Surti TS, Stroud RM

Enzyme-catalyzed therapeutic agent (ECTA) design: activation of the antitumor ECTA compound NB1011 by thymidylate synthase.

Biochemical pharmacology

Lackey DB, Groziak MP, Sergeeva M, Beryt M, Boyer C, Stroud RM, Sayre P, Park JW, Johnston P, Slamon D, Shepard HM, Pegram M

Functional consequences of the Kaposi's sarcoma-associated herpesvirus protease structure: regulation of activity and dimerization by conserved structural elements.

Biochemistry

Reiling KK, Pray TR, Craik CS, Stroud RM

Structure of a glycerol-conducting channel and the basis for its selectivity.

Science (New York, N.Y.)

Fu D, Libson A, Miercke LJ, Weitzman C, Nollert P, Krucinski J, Stroud RM

Site-directed ligand discovery.

Proceedings of the National Academy of Sciences of the United States of America

Erlanson DA, Braisted AC, Raphael DR, Randal M, Stroud RM, Gordon EM, Wells JA

Replacement set mutagenesis of the four phosphate-binding arginine residues of thymidylate synthase.

Protein engineering

Kawase S, Cho SW, Rozelle J, Stroud RM, Finer-Moore J, Santi DV

Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding.

Proceedings of the National Academy of Sciences of the United States of America

Chen JC, Krucinski J, Miercke LJ, Finer-Moore JS, Tang AH, Leavitt AD, Stroud RM

Mesoscopic surfactant organization and membrane protein crystallization.

Protein science : a publication of the Protein Society

Wiener MC, Verkman AS, Stroud RM, van Hoek AN

The crystal structure of thymidylate synthase from Pneumocystis carinii reveals a fungal insert important for drug design.

Journal of molecular biology

Anderson AC, Perry KM, Freymann DM, Stroud RM

Effects of subunit occupancy on partitioning of an intermediate in thymidylate synthase mutants.

Biochemistry

Variath P, Liu Y, Lee TT, Stroud RM, Santi DV

Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance".

Biochemistry

Morse RJ, Kawase S, Santi DV, Finer-Moore J, Stroud RM

Active site water molecules revealed in the 2.1 A resolution structure of a site-directed mutant of isocitrate dehydrogenase.

Journal of molecular biology

Cherbavaz DB, Lee ME, Stroud RM, Koshland DE

The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I.

Nature structural biology

Foster PG, Huang L, Santi DV, Stroud RM

Signal sequence recognition and protein targeting.

Current opinion in structural biology

Stroud RM, Walter P

Expression, purification, and structural characterization of the bacteriorhodopsin-aspartyl transcarbamylase fusion protein.

Protein expression and purification

Turner GJ, Miercke LJ, Mitra AK, Stroud RM, Betlach MC, Winter-Vann A

The structural mechanism for half-the-sites reactivity in an enzyme, thymidylate synthase, involves a relay of changes between subunits.

Biochemistry

Anderson AC, O'Neil RH, DeLano WL, Stroud RM

Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP.

Nature structural biology

Freymann DM, Keenan RJ, Stroud RM, Walter P

Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition.

Journal of medicinal chemistry

Costi PM, Rinaldi M, Tondi D, Pecorari P, Barlocco D, Ghelli S, Stroud RM, Santi DV, Stout TJ, Musiu C, Marangiu EM, Pani A, Congiu D, Loi GA, La Colla P

Engineering a soluble extracellular erythropoietin receptor (EPObp) in Pichia pastoris to eliminate microheterogeneity, and its complex with erythropoietin.

Protein engineering

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, Stroud RM

Structure-based design of inhibitors specific for bacterial thymidylate synthase.

Biochemistry

Stout TJ, Tondi D, Rinaldi M, Barlocco D, Pecorari P, Santi DV, Kuntz ID, Stroud RM, Shoichet BK, Costi MP

Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer.

Journal of molecular biology

Reyes CL, Sage CR, Rutenber EE, Nissen RM, Finer-Moore JS, Stroud RM

Crystal structures of a unique thermal-stable thymidylate synthase from Bacillus subtilis.

Biochemistry

Stout TJ, Schellenberger U, Santi DV, Stroud RM

Efficiency of signalling through cytokine receptors depends critically on receptor orientation.

Nature

Syed RS, Reid SW, Li C, Cheetham JC, Aoki KH, Liu B, Zhan H, Osslund TD, Chirino AJ, Zhang J, Finer-Moore J, Elliott S, Sitney K, Katz BA, Matthews DJ, Wendoloski JJ, Egrie J, Stroud RM

D221 in thymidylate synthase controls conformation change, and thereby opening of the imidazolidine.

Biochemistry

Sage CR, Michelitsch MD, Stout TJ, Biermann D, Nissen R, Finer-Moore J, Stroud RM

Helical protein design.

Current opinion in biotechnology

Schafmeister CE, Stroud RM

Ion-channel-forming colicins.

Current opinion in structural biology

Stroud RM, Reiling K, Wiener M, Freymann D

Crystal structure of the signal sequence binding subunit of the signal recognition particle.

Cell

Keenan RJ, Freymann DM, Walter P, Stroud RM

The additivity of substrate fragments in enzyme-ligand binding.

Structure (London, England : 1993)

Stout TJ, Sage CR, Stroud RM

Structure of bovine pancreatic cholesterol esterase at 1.6 A: novel structural features involved in lipase activation.

Biochemistry

Chen JC, Miercke LJ, Krucinski J, Starr JR, Saenz G, Wang X, Spilburg CA, Lange LG, Ellsworth JL, Stroud RM

The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis.

Protein engineering

Birdsall DL, Huang W, Santi DV, Stroud RM, Finer-Moore J

Domain flexibility in retroviral proteases: structural implications for drug resistant mutations.

Biochemistry

Rose RB, Craik CS, Stroud RM

Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase.

Journal of molecular biology

Finer-Moore JS, Liu L, Birdsall DL, Brem R, Apfeld J, Santi DV, Stroud RM

Design of potent selective zinc-mediated serine protease inhibitors.

Nature

Katz BA, Clark JM, Finer-Moore JS, Jenkins TE, Johnson CR, Ross MJ, Luong C, Moore WR, Stroud RM

A novel dCMP methylase by engineering thymidylate synthase.

Biochemistry

Agarwalla S, LaPorte S, Liu L, Finer-Moore J, Stroud RM, Santi DV

A designed four helix bundle protein with native-like structure.

Nature structural biology

Schafmeister CE, LaPorte SL, Miercke LJ, Stroud RM

Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.

Biochemistry

Finer-Moore J, Tsutakawa SE, Cherbavaz DR, LaPorte DC, Koshland DE, Stroud RM

The discovery, characterization and crystallographically determined binding mode of an FMOC-containing inhibitor of HIV-1 protease.

Bioorganic & medicinal chemistry

Rutenber EE, De Voss JJ, Hoffman L, Stroud RM, Lee KH, Alvarez J, McPhee F, Craik C, Ortiz de Montellano PR

Crystal structure of colicin Ia.

Nature

Wiener M, Freymann D, Ghosh P, Stroud RM

Structure of the conserved GTPase domain of the signal recognition particle.

Nature

Freymann DM, Keenan RJ, Stroud RM, Walter P

An essential role for water in an enzyme reaction mechanism: the crystal structure of the thymidylate synthase mutant E58Q.

Biochemistry

Sage CR, Rutenber EE, Stout TJ, Stroud RM

Binding of the anticancer drug ZD1694 to E. coli thymidylate synthase: assessing specificity and affinity.

Structure (London, England : 1993)

Rutenber EE, Stroud RM

Three-dimensional structures of HIV-1 and SIV protease product complexes.

Biochemistry

Rose RB, Craik CS, Douglas NL, Stroud RM

A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.

Bioorganic & medicinal chemistry

Rutenber EE, McPhee F, Kaplan AP, Gallion SL, Hogan JC, Craik CS, Stroud RM

Balancing ATP in the cell.

Nature structural biology

Stroud RM

Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.

Biochemistry

Finer-Moore JS, Liu L, Schafmeister CE, Birdsall DL, Mau T, Santi DV, Stroud RM

Asparagine 229 mutants of thymidylate synthase catalyze the methylation of 3-methyl-2'-deoxyuridine 5'-monophosphate.

Biochemistry

Costi PM, Liu L, Finer-Moore JS, Stroud RM, Santi DV

Entropy in bi-substrate enzymes: proposed role of an alternate site in chaperoning substrate into, and products out of, thymidylate synthase.

Journal of molecular biology

Birdsall DL, Finer-Moore J, Stroud RM

The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition.

Structure (London, England : 1993)

Stout TJ, Stroud RM

Contribution of a salt bridge to binding affinity and dUMP orientation to catalytic rate: mutation of a substrate-binding arginine in thymidylate synthase.

Protein engineering

Finer-Moore JS, Fauman EB, Morse RJ, Santi DV, Stroud RM

Crystal structure of human thymidylate synthase: a structural mechanism for guiding substrates into the active site.

Biochemistry

Schiffer CA, Clifton IJ, Davisson VJ, Santi DV, Stroud RM

Significance of structural changes in proteins: expected errors in refined protein structures.

Protein science : a publication of the Protein Society

Stroud RM, Fauman EB

Topochemistry for preparing ligands that dimerize receptors.

Chemistry & biology

Katz BA, Stroud RM, Collins N, Liu B, Arze R

Ion channel forming colicins.

Current opinion in structural biology

Stroud R

Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface.

Biochemistry

Katz BA, Finer-Moore J, Mortezaei R, Rich DH, Stroud RM

Crystal structure of thymidylate synthase from T4 phage: component of a deoxynucleoside triphosphate-synthesizing complex.

Biochemistry

Finer-Moore JS, Maley GF, Maley F, Montfort WR, Stroud RM

The domain structure of the ion channel-forming protein colicin Ia.

Nature structural biology

Ghosh P, Mel SF, Stroud RM

An electrostatic highway.

Nature structural biology

Stroud RM

Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 A.

Biochemistry

Fauman EB, Rutenber EE, Maley GF, Maley F, Stroud RM

Structure of the protease from simian immunodeficiency virus: complex with an irreversible nonpeptide inhibitor.

Biochemistry

Rose RB, Rosé JR, Salto R, Craik CS, Stroud RM

Structure at 2.5 A of a designed peptide that maintains solubility of membrane proteins.

Science (New York, N.Y.)

Schafmeister CE, Miercke LJ, Stroud RM

Mapping a membrane-associated conformation of colicin Ia.

Biochemistry

Mel SF, Falick AM, Burlingame AL, Stroud RM

Two-dimensional crystallization of Escherichia coli-expressed bacteriorhodopsin and its D96N variant: high resolution structural studies in projection.

Biophysical journal

Mitra AK, Miercke LJ, Turner GJ, Shand RF, Betlach MC, Stroud RM

Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei.

Journal of molecular biology

Finer-Moore J, Fauman EB, Foster PG, Perry KM, Santi DV, Stroud RM

Structures of thymidylate synthase with a C-terminal deletion: role of the C-terminus in alignment of 2'-deoxyuridine 5'-monophosphate and 5,10-methylenetetrahydrofolate.

Biochemistry

Perry KM, Carreras CW, Chang LC, Santi DV, Stroud RM

Effects of Asp-96----Asn, Asp-85----Asn, and Arg-82----Gln single-site substitutions on the photocycle of bacteriorhodopsin.

Biochemistry

Thorgeirsson TE, Milder SJ, Miercke LJ, Betlach MC, Shand RF, Stroud RM, Kliger DS

Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.

Biochemistry

Hurley JH, Dean AM, Koshland DE, Stroud RM

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.

The Journal of biological chemistry

Lax I, Mitra AK, Ravera C, Hurwitz DR, Rubinstein M, Ullrich A, Stroud RM, Schlessinger J

Wild-type and mutant bacteriorhodopsins D85N, D96N, and R82Q: purification to homogeneity, pH dependence of pumping, and electron diffraction.

Biochemistry

Miercke LJ, Betlach MC, Mitra AK, Shand RF, Fong SK, Stroud RM

Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate.

Biochemistry

Montfort WR, Perry KM, Fauman EB, Finer-Moore JS, Maley GF, Hardy L, Maley F, Stroud RM

Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change in the free enzyme.

The Journal of biological chemistry

Hurley JH, Dean AM, Thorsness PE, Koshland DE, Stroud RM

Three-dimensional structure of the nicotinic acetylcholine receptor and location of the major associated 43-kD cytoskeletal protein, determined at 22 A by low dose electron microscopy and x-ray diffraction to 12.5 A.

The Journal of cell biology

Mitra AK, McCarthy MP, Stroud RM

Changes in conformation upon agonist binding, and nonequivalent labeling, of the membrane-spanning regions of the nicotinic acetylcholine receptor subunits.

The Journal of biological chemistry

McCarthy MP, Stroud RM

Purification of bacteriorhodopsin and characterization of mature and partially processed forms.

The Journal of biological chemistry

Miercke LJ, Ross PE, Stroud RM, Dratz EA

Conformational states of the nicotinic acetylcholine receptor from Torpedo californica induced by the binding of agonists, antagonists, and local anesthetics. Equilibrium measurements using tritium-hydrogen exchange.

Biochemistry

McCarthy MP, Stroud RM

Cesium ion liquid secondary ion mass spectrometry of membrane-bound glycoproteins: structural and topological considerations of acetylcholine receptor from Torpedo californica.

Biomedical & environmental mass spectrometry

Poulter L, Earnest JP, Stroud RM, Burlingame AL

Structural and functional conservation between yeast and human 3-hydroxy-3-methylglutaryl coenzyme A reductases, the rate-limiting enzyme of sterol biosynthesis.

Molecular and cellular biology

Basson ME, Thorsness M, Finer-Moore J, Stroud RM, Rine J

The crystal structure of alpha-bungarotoxin at 2.5 A resolution: relation to solution structure and binding to acetylcholine receptor.

Protein engineering

Love RA, Stroud RM

Topological mapping of acetylcholine receptor: evidence for a model with five transmembrane segments and a cytoplasmic COOH-terminal peptide.

Proceedings of the National Academy of Sciences of the United States of America

Young EF, Ralston E, Blake J, Ramachandran J, Hall ZW, Stroud RM

Purification and characterization of a macromolecular weight cofactor for C3b-inactivator, C4bC3bINA-cofactor, of human plasma.

Molecular immunology

Nagasawa S, Stroud RM

Protease effects on the structure of acetylcholine receptor membranes from Torpedo californica.

The Journal of cell biology

Klymkowsky MW, Heuser JE, Stroud RM

Immunospecific identification and three-dimensional structure of a membrane-bound acetylcholine receptor from Torpedo californica.

Journal of molecular biology

Klymkowsky MW, Stroud RM

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.

Biochemistry

Koeppe RE, Stroud RM

The structure of bovine trypsin: electron density maps of the inhibited enzyme at 5 Angstrom and at 2-7 Angstron resolution.

Journal of molecular biology

Stroud RM, Kay LM, Dickerson RE

The crystal and molecular structure of DIP-inhibited bovine trypsin at2.7Angstrom resolution.

Cold Spring Harbor symposia on quantitative biology

Stroud RM, Kay LM, Dickerson RE

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