1990–1995

1995

Significance of structural changes in proteins: Expected errors in refined protein structures.
Stroud, RM; and Fauman, EB. (1995).
Protein Science 4, 2392-2404.
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Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface.
Katz, BA; Finer-Moore, J; Mortezaei, R; Rich, DH; Stroud, RM. (1995)
Biochemistry 34, 8264-8280.
PDB Accession Numbers:1BTX, 1BTW, 1BTY and 1BTZ.
View PDB structure  1BTX, 1BTW, 1BTY, 1BTZ
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Crystal structure of human thymidylate synthase: A structural mechanism for guiding substrates into the active site.
Schiffer, CA; Clifton, IJ; Davisson, VJ; Santi, DV; Stroud, RM (1995).
Biochemistry 34, 16279-16287.
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Topochemistry for preparing ligands that dimerize receptors.
Katz, BA; Stroud, RM; Collins, N; Liu, B; and Arze, R. (1995).
Chemistry & Biology 2, 591-600.
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Ion channel forming colicins.
Stroud, RM. (1995).
Current Opinion in Structural Biology 5, 514-520.
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An inducement to collaboration. Review of Crystal structure analysis
for chemists and biologists by J. Glusker with M. Lewis and M. Rossi
Stroud, RM. (1995) (UCH Publishers, New York, 1994).
Nature Structural Biology 2, 619-620.
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1994

An electrostatic highway.
Stroud, RM. (1994)
Nature Structural Biology 1, 131-134. 
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Crystal structure of thymidylate synthase from T4 phage: component of a deoxynucleoside triphosphate-synthesizing complex.
Finer-Moore, JS; Maley, GF; Maley, F; Montfort, WR; Stroud, RM. (1994)
Biochemistry 33, 15459-15468. 
PDB Accession No. 1TIS
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The domain structure of the ion channel-forming protein colicin Ia.
Ghosh, P; Mel, SF; and Stroud, RM. (1994) 
Nature Structural Biology 1, 597-604. 
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Water-mediated substrate/product discimination: The product complex of thymidylate synthase at 1.83 Å.
Fauman EB; Rutenber, EE; Maley, G; Maley, F; and Stroud, RM. (1994) 
Biochemistry 33, 1502-1511. 
PDB Accession No. 1TYS
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1993

Structure at 2.5 Å of a designed peptide that maintains solubility of membrane proteins.
Schafmeister, CE; Mierkce, LJW; and Stroud, RM. (1993)
Science 262, 734-738. 
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Structure of the protease from simian immunodeficiency virus: Complex with an irreversible non-peptide inhibitor.
Rose, RB; Rose, JR; Salto, R; Craik, CS; and Stroud, RM. (1993) 
Biochemistry 32, 12498-12507. 
PDB Accession No. 2SAM
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Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei.
Finer-Moore, JS; Fauman, EB; Foster, PG; Perry, KM; 
Santi, DV; and Stroud, RM. (1993). 
Journal of Molecular Biology 232, 1101-1116. 
PDB Accession Nos: 1LCA, 1LCB, 1LCE, 2TDM (replaces 1TDM) , 1THY 
View PDB structure 1LCA, 1LCB, 1LCE, 2TDM, 1THY
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A carboxy-terminal fragment of colicin Ia forms ion channels.
Ghosh, P; Mel, SF; and Stroud, RM. (1993) 
Journal of Membrane Biology 134, 85-92.
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Colicin Ia inserts into negatively charged membranes at low pH with a tertiary but little secondary structural change.
Mel, S; and Stroud, RM. (1993) 
Biochemistry 32, 2082-2089. 
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Mapping a membrane-associated conformation of colicin Ia.
Mel, SF; Falick, AM; Burlingame, AL; and Stroud, RM. (1993) 
Biochemistry 32, 9473-9479. 
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Two-dimensional crystallization of Escherichia coli-expressed bacteriorhodopsin and its D96N variant: High resolution structural studies in projection. 
Mitra, AK; Miercke, LJW; Shand, RF; Betlach, MC; Stroud, RM. (1993) 
Biophysical Journal 65, 1295-1306. 
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Structure of a non-peptide inhibitor complexed with HIV-1 protease: Developing a cycle of structure-based drug design.
Rutenber, E; Fauman, EB; Keenan, RJ; Fong, S; Furth, PS; Ortiz de Montellano, PR; Meng, E; Kuntz, ID; DeCamp, DL; Salto, R; Rose, JR; Craik, CS; and Stroud, RM. (1993) 
Journal of Biological Chemistry268, 15343-15346. 
PDB Accession Nos. 1AID , 2AID 
View PDB structure 1AID, 2AID
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Protein structure prediction with a combined solvation free energy-molecular mechanics force field.
Schiffer, CA; Caldwell, JW; Kollman, PA; and Stroud, RM. (1993) 
Molecular Simulation 10, 121-149. 
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Structure-based discovery of inhibitors of thymidylate synthase. 
Shoichet, BK; Stroud, RM; Santi, DV; Kuntz, ID; and Perry, KM. (1993) 
Science 259, 1445-1450. 
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Practical Proteins. Review of Protein Structure - New Approaches to Disease and Therapy by Max Perutz (Freeman, New York, 1992). 
Stroud, RM. (1993) 
Science 262, 443-444. 
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Stereochemistry of a multistep/ bipartite methyl transfer reaction: thymidylate synthase.
Stroud, RM; and Finer-Moore, JS. (1993) 
FASEB Journal 7, 671-677. 
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Bacteriorhodopsin D85N: Three spectroscopic species in equilibrium.
Turner, GJ; Miercke, LJW; Thorgeirsson, TE; Kliger, DS; Betlach, MC; and Stroud, RM. (1993) 
Biochemistry 32, 1332-1337. 
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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.
Perry, KM; Carreras, CW; Chang, LC; Santi, DV; and Stroud, RM. (1993) 
Biochemistry 32, 7116-7125. 
PDB Accession Nos: 1TDA (V316Am inbound), 1TDB (V316Am·FdUMP), 1TDC (V316Am·dUMP), , 2TDD (V316Am·FdUMP·5-HOCH2H4folate) 
View PDB structure 1TDA, 1TDB, 1TDC, 2TDD
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1992

Inclusion of solvation free energy with molecular mechanics energy: alanyl dipeptide as a test case.
Schiffer, CA; Caldwell, JW; Stroud, RM; and Kollman, PA. (1992)
Protein Science 1, 396-400. 
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Solvent structure in crystals of trypsin determined by x-ray and neutron diffraction.
Finer-Moore, JS; Kossiakoff, AA; Hurley, JH; Earnest, T; and Stroud, RM. (1992) 
Proteins 12, 203-222. 
PDB Accession No. 5PTP
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Reversible dissociation and unfolding of the dimeric protein thymidylate synthase.
Perry, KM; Pookanjanatavip, M; Zhao, J; Santi, DV; Stroud, RM. (1992)
Protein Science 1, 796-800. 
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Structural basis for recognition of polyglutamyl folates by thymidylate synthase.
Kamb A; Finer-Moore J; Calvert AH; and Stroud RM. (1992) 
Biochemistry 31, 9883-9890. 
PDB Accession No. 2BBQ (replaces1BBQ referenced in  Biochemistry 31, pp 9883)
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Cofactor triggers the conformational change in thymidylate synthase: implications for an ordered binding mechanism.
Kamb A; Finer-Moore JS; and Stroud RM. (1992) 
Biochemistry 31, 12876-12884.

1991

Ion channels formed by a highly charged peptide.
Ghosh, P; and Stroud, RM. (1991)
Biochemistry 30, 3551-3557. 
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Wild-type and mutant bacteriorhodopsins D85N, D96N, and R82Q: purification to homogeneity, pH dependence of pumping, and electron diffraction.
Miercke, LJ; Betlach, MC; Mitra, AK; Shand, RF; Fong, SK; and Stroud, RM. (1991) 
Biochemistry 30, 3088-3098. 

Wild-type and mutant bacterioopsins D85N, D96N, and R82Q: high-level expression in Escherichia coli.
Shand, RF; Miercke, LJ; Mitra, AK; Fong, SK; Stroud, RM; and Betlach, MC. (1991) 
Biochemistry 30, 3082-3088. 
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Crystallization of human thymidylate synthase.
Schiffer, CA; Davisson, VJ; Santi, DV; and Stroud, RM. (1991) 
Journal of Molecular Biology 219, 161-163. 
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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.
Lax, I; Mitra, AK; Ravera, C; Hurwitz, DR; Rubinstein, M;Ullrich, A; Stroud, RM; and Schlessinger, J. (1991) 
Journal of Biological Chemistry 266, 13828-13833. 
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Mechanisms of biological control by phosphorylation.
Stroud, RM. (1991) 
Current Opinion in Structural Biology 1, 826-835. 

Catalytic mechanism of NADP(+)-dependent isocitrate dehydrogenase: implications from the structures of magnesium-isocitrate and NADP+ complexes.
Hurley, JH; Dean, AM; Koshland, DE Jr; and Stroud, RM. (1991)
Biochemistry 30, 8671-8678. 
PDB Accession No. 9ICD
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Effects of Asp-96—Asn, Asp-85—Asn, and Arg-82—Gln single-site substitutions on the photocycle of bacteriorhodopsin.
Thorgeirsson, TE; Milder, SJ; Miercke, LJ; Betlach, MC; Shand, RF; Stroud, RM; and Kliger, DS. (1991)
Biochemistry 30, 9133-9142. 
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Resonance raman spectra of bacteriorhodopsin mutants with substitutions at Asp-85, Asp-96, and Arg-82.
Lin, SW; Fodor, SP; Miercke, LJ; Shand, RF; Betlach, MC; Stroud, RM; and Mathies, RA. (1991). 
Photochemistry and Photobiology 53, 341-346. 
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Effects of detergent environments on the photocycle of purified monomeric bacteriorhodopsin.
Milder, SJ; Thorgeirsson, TE; Miercke, LJ; Stroud, RM; Kliger DS. (1991) 
Biochemistry 30, 1751-1761. 
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1.59 Å structure of trypsin at 120K: comparison of low temperature and room temperature structures.
Earnest, T; Fauman, E; Craik, CS; and Stroud, R. (1991) 
Proteins 10, 171-187. 
PDB Accession No. 1DPO
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1990

Nicotinic acetylcholine receptor superfamily of ligand-gated ion channels.
Stroud, RM; McCarthy, MP; and Shuster, M. (1990)
Biochemistry 29, 11009-11023.
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Structure of an acyl-enzyme intermediate during catalysis: (guanidinobenzoyl) trypsin.
Mangel, WF; Singer, PT; Cyr, DM; Umland, TC; Toledo, DL; Stroud, RM; Pflugrath, JW; and Sweet, RM. (1990) 
Biochemistry 29, 8351-8357. 
PDB Accession No. 1GBT
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Regulation of an enzyme by phosphorylation at the active site.
Hurley, JH; Dean, AM; Sohl, JL; Koshland, DE Jr; Stroud, RM. (1990) 
Science 249, 1012-1016. 
PDB Accession Nos. 5ICD, 6ICD, 7ICD , 8ICD
View PDB structure 5ICD, 6ICD, 7ICD, 8ICD
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Saturation site-directed mutagenesis of thymidylate synthase.
Climie, S; Ruiz-Perez, L; Gonzalez-Pacanowska, D; Prapunwattana, P; Cho, SW; Stroud, R; and Santi, DV. (1990). Journal of Biological Chemistry 265, 18776-18779. 
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Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases.
Perry, KM; Fauman, EB; Finer-Moore, JS; Montfort, WR; Maley, GF; Maley, F; and Stroud, RM. (1990) 
Proteins 8, 315-333.
PDB Accession Nos. 3TMS , 4TMS 
View PDB structure 3TMS, 4TMS
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Pairwise specificity and sequential binding in enzyme catalysis: thymidylate synthase.
Finer-Moore, JS; Montfort, WR; and Stroud, RM. (1990) 
Biochemistry 29, 6977-6986. 
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Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate.
Montfort, WR; Perry, KM; Fauman, EB; Finer-Moore, JS;Maley, GF; Hardy, L; Maley, F; and Stroud, RM. (1990)
Biochemistry 29, 6964-6977. 
PDB Accession No. 2TSC (replaces 1TSC, 1TMS referenced in  Biochemistry 29, pp 6964)
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Segmental accommodation: A novel conformational change induced upon ligand binding by thymidylate synthase. Montfort, WR; Fauman, EB; Perry, KM; and Stroud, RM.  (1990)
Current Research in Protein Chemistry, Chapter 34, pp 367-382, Academic Press Inc.

Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change in the free enzyme.
Hurley, JH; Dean, AM; Thorsness, PE; Koshland, DE Jr; Stroud, RM. (1990)
Journal of Biological Chemistry 265, 3599-3602. 
PDB Accession No. 4ICD
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High sensitivity electron diffraction analysis. A study of divalent cation binding to purple membrane.
Mitra, AK; and Stroud, RM. (1990) 
Biophysical Journal 57, 301-311.
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Prediction of homologous protein structures based on conformational searches and energetics.
Schiffer, CA; Caldwell, JW; Kollman, PA; and Stroud, RM. (1990) 
Proteins 8, 30-43. 
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The Acetylcholine Receptor.
Shuster, MJ; Mitra, AK; Stroud, RM. (1990)
Protein and Pharmaceutical Engineering 55-70.
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