-
1
-
-
78651189765
-
On the nature of allosteric transitions: A plausible model
-
Monod J, Wyman J, Changeux JP. On the nature of allosteric transitions: a plausible model. J Mol Biol 1965;12:88-118.
-
(1965)
J Mol Biol
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
2
-
-
0033970020
-
Folding and binding cascades: Dynamic landscapes and population shifts
-
Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000;9:10-19.
-
(2000)
Protein Sci
, vol.9
, pp. 10-19
-
-
Kumar, S.1
Ma, B.2
Tsai, C.J.3
Sinha, N.4
Nussinov, R.5
-
3
-
-
0030665488
-
Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting
-
Moore FJ, Tsutakawa SE, Cherbavaz DR, LaPorte DC, Koshland DE, Jr, Stroud RM. Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting. Biochemistry 1997;36:13890-13896.
-
(1997)
Biochemistry
, vol.36
, pp. 13890-13896
-
-
Moore, F.J.1
Tsutakawa, S.E.2
Cherbavaz, D.R.3
LaPorte, D.C.4
Koshland Jr, D.E.5
Stroud, R.M.6
-
4
-
-
0031015737
-
Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: Crystallographic evidence
-
Sawaya MR, Kraut J. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 1997;36:586-603.
-
(1997)
Biochemistry
, vol.36
, pp. 586-603
-
-
Sawaya, M.R.1
Kraut, J.2
-
5
-
-
0032562224
-
Domain flexibility in retroviral proteases: Structural implications for drug resistant mutations
-
Rose RB, Craik CS, Stroud RM. Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. Biochemistry 1998;37:2607-2621.
-
(1998)
Biochemistry
, vol.37
, pp. 2607-2621
-
-
Rose, R.B.1
Craik, C.S.2
Stroud, R.M.3
-
6
-
-
4143085329
-
Modulating functional loop movements: The role of highly conserved residues in the correlated loop motions
-
Gunasekaran K, Nussinov R. Modulating functional loop movements: the role of highly conserved residues in the correlated loop motions. Chembiochem 2004;5:224-230.
-
(2004)
Chembiochem
, vol.5
, pp. 224-230
-
-
Gunasekaran, K.1
Nussinov, R.2
-
7
-
-
33144487234
-
Roles of static and dynamic domains in stability and catalysis of adenylate kinase
-
Bae E, Phillips GN, Jr. Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc Natl Acad Sci USA 2006;103:2132-2137.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 2132-2137
-
-
Bae, E.1
Phillips Jr, G.N.2
-
8
-
-
0037646540
-
Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
-
Hayashi H, Mizuguchi H, Miyahara I, Nakajima Y, Hirotsu K, Kagamiyama H. Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis. J Biol Chem 2003;278:9481-9488.
-
(2003)
J Biol Chem
, vol.278
, pp. 9481-9488
-
-
Hayashi, H.1
Mizuguchi, H.2
Miyahara, I.3
Nakajima, Y.4
Hirotsu, K.5
Kagamiyama, H.6
-
9
-
-
0034797062
-
Structural determinants for ligand binding and catalysis of triosephosphate isomerase
-
Kursula I, Partanen S, Lambeir AM, Antonov DM, Augustyns K, Wierenga RK. Structural determinants for ligand binding and catalysis of triosephosphate isomerase. Eur J Biochem 2001;268:5189-5196.
-
(2001)
Eur J Biochem
, vol.268
, pp. 5189-5196
-
-
Kursula, I.1
Partanen, S.2
Lambeir, A.M.3
Antonov, D.M.4
Augustyns, K.5
Wierenga, R.K.6
-
10
-
-
0034681465
-
Convergent solutions to binding at a protein-protein interface
-
DeLano WL, Ultsch MH, de Vos AM, Wells JA. Convergent solutions to binding at a protein-protein interface. Science 2000; 287:1279-1283.
-
(2000)
Science
, vol.287
, pp. 1279-1283
-
-
DeLano, W.L.1
Ultsch, M.H.2
de Vos, A.M.3
Wells, J.A.4
-
11
-
-
0033534526
-
RNA recognition by human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface
-
Kranz JK, Hall KB. RNA recognition by human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface. J Mol Biol 1999;285:215-231.
-
(1999)
J Mol Biol
, vol.285
, pp. 215-231
-
-
Kranz, J.K.1
Hall, K.B.2
-
12
-
-
0033215221
-
Strain in protein structures as viewed through nonrotameric side chains. II. effects upon ligand binding
-
Heringa J, Argos P. Strain in protein structures as viewed through nonrotameric side chains. II. effects upon ligand binding. Proteins 1999;37:44-55.
-
(1999)
Proteins
, vol.37
, pp. 44-55
-
-
Heringa, J.1
Argos, P.2
-
13
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
-
Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 2002;11:184-197.
-
(2002)
Protein Sci
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
14
-
-
0035793701
-
How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding
-
Serre L, Verdon G, Choinowski T, Hervouet N, Risler JL, Zelwer C. How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. J Mol Biol 2001;306:863-876.
-
(2001)
J Mol Biol
, vol.306
, pp. 863-876
-
-
Serre, L.1
Verdon, G.2
Choinowski, T.3
Hervouet, N.4
Risler, J.L.5
Zelwer, C.6
-
15
-
-
0035119935
-
Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase
-
Sekine S, Nureki O, Shimada A, Vassylyev DG, Yokoyama S. Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat Struct Biol 2001;8:203-206.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 203-206
-
-
Sekine, S.1
Nureki, O.2
Shimada, A.3
Vassylyev, D.G.4
Yokoyama, S.5
-
16
-
-
0034705342
-
The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain
-
Sauter C, Lorber B, Cavarelli J, Moras D, Giege R. The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain. J Mol Biol 2000; 299:1313-1324.
-
(2000)
J Mol Biol
, vol.299
, pp. 1313-1324
-
-
Sauter, C.1
Lorber, B.2
Cavarelli, J.3
Moras, D.4
Giege, R.5
-
17
-
-
0030593503
-
A concerted tryptophanyl-adenylate-dependent conformational change in Bacillus subtilis tryptophanyl-tRNA synthetase revealed by the fluorescence of Trp92
-
Hogue CW, Doublie S, Xue H, Wong JT, Carter CW, Jr, Szabo AG. A concerted tryptophanyl-adenylate-dependent conformational change in Bacillus subtilis tryptophanyl-tRNA synthetase revealed by the fluorescence of Trp92. J Mol Biol 1996;260:446-466.
-
(1996)
J Mol Biol
, vol.260
, pp. 446-466
-
-
Hogue, C.W.1
Doublie, S.2
Xue, H.3
Wong, J.T.4
Carter Jr, C.W.5
Szabo, A.G.6
-
18
-
-
0018369994
-
Aminoacyl-tRNA synthetases: General features and recognition of Transfer RNAs
-
Schimmel PR, Soll D. Aminoacyl-tRNA synthetases: general features and recognition of Transfer RNAs. Ann Rev Biochem 1979; 48:601-648.
-
(1979)
Ann Rev Biochem
, vol.48
, pp. 601-648
-
-
Schimmel, P.R.1
Soll, D.2
-
19
-
-
0037255536
-
Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: Structures of ATP bound to open and closed, pre-transition-state conformations
-
Retailleau P, Huang X, Yin Y, Hu M, Vachette VWP, Vonrhein C, Bricogne G, Roversi P, Ilyin V, Carter CW, Jr. Interconversion of ATP binding and conformational free energies by tryptophanyl-tRNA synthetase: structures of ATP bound to open and closed, pre-transition-state conformations. J Mol Biol 2003;325: 39-63.
-
(2003)
J Mol Biol
, vol.325
, pp. 39-63
-
-
Retailleau, P.1
Huang, X.2
Yin, Y.3
Hu, M.4
Vachette, V.W.P.5
Vonrhein, C.6
Bricogne, G.7
Roversi, P.8
Ilyin, V.9
Carter Jr., C.W.10
-
20
-
-
28444453011
-
A network representation of protein structures: Implications for protein stability
-
Brinda KV, Vishveshwara S. A network representation of protein structures: implications for protein stability. Biophys J 2005;89:4159-4170.
-
(2005)
Biophys J
, vol.89
, pp. 4159-4170
-
-
Brinda, K.V.1
Vishveshwara, S.2
-
21
-
-
0033578690
-
Identification of Side chain-clusters from protein structures using Graph spectral method
-
Kannan N, Vishveshwara S. Identification of Side chain-clusters from protein structures using Graph spectral method. J Mol Biol 1999;292:441-464.
-
(1999)
J Mol Biol
, vol.292
, pp. 441-464
-
-
Kannan, N.1
Vishveshwara, S.2
-
24
-
-
2542445427
-
Identification of functional region of proteins by surface-mapping of phylogenetic information
-
Glaser F, Pupko T, Paz I, Bell RE, Shental BD, Martz E, BenTal N. CONSURF. Identification of functional region of proteins by surface-mapping of phylogenetic information. Bioinformatics 2003;19:163-164.
-
(2003)
Bioinformatics
, vol.19
, pp. 163-164
-
-
Glaser, F.1
Pupko, T.2
Paz, I.3
Bell, R.E.4
Shental, B.D.5
Martz, E.6
BenTal, N.7
CONSURF8
-
25
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressivemultiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Higgins, D.1
Thompson, J.2
Gibson, T.3
Thompson, J.D.4
Higgins, D.G.5
Gibson, T.J.6
-
27
-
-
0026244229
-
a program to produce both detailed and schematic plots of protein structures
-
Kraulis PJ. MOLSCRIPT. a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991; 24:946-950.
-
(1991)
J Appl Cryst
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
MOLSCRIPT2
-
28
-
-
0030815133
-
Raster 3D: Photorealistic molecular graphics
-
Merritt EA, David BJ. Raster 3D: photorealistic molecular graphics. Methods Enzymol 1997;277:505-524.
-
(1997)
Methods Enzymol
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
David, B.J.2
-
30
-
-
0038662765
-
tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase
-
Sherlin LD, Perona JJ. tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase. Structure 2003;11:591-603.
-
(2003)
Structure
, vol.11
, pp. 591-603
-
-
Sherlin, L.D.1
Perona, J.J.2
-
31
-
-
0027165755
-
Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase
-
Perona JJ, Rould MA, Steitz TA. Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry 1993;32:8758-8771.
-
(1993)
Biochemistry
, vol.32
, pp. 8758-8771
-
-
Perona, J.J.1
Rould, M.A.2
Steitz, T.A.3
-
32
-
-
0032522422
-
How glutaminyl-tRNA synthetase selects glutamine
-
Rath VL, Silvian LF, Beijer B, Sproat BS, Steitz TA. How glutaminyl-tRNA synthetase selects glutamine. Structure 1998; 6:439-449.
-
(1998)
Structure
, vol.6
, pp. 439-449
-
-
Rath, V.L.1
Silvian, L.F.2
Beijer, B.3
Sproat, B.S.4
Steitz, T.A.5
-
33
-
-
0037466332
-
Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants
-
Bullock TL, Uter N, Nissan AT, Perona JJ. Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. J Mol Biol 2003;328:395-408.
-
(2003)
J Mol Biol
, vol.328
, pp. 395-408
-
-
Bullock, T.L.1
Uter, N.2
Nissan, A.T.3
Perona, J.J.4
-
34
-
-
21244444325
-
Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase
-
Uter NT, Gruic-Sovulj I, Perona JJ. Amino acid-dependent transfer RNA affinity in a class I aminoacyl-tRNA synthetase. J Biol Chem 2005;280:23966-23977.
-
(2005)
J Biol Chem
, vol.280
, pp. 23966-23977
-
-
Uter, N.T.1
Gruic-Sovulj, I.2
Perona, J.J.3
-
35
-
-
5144223811
-
Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics
-
Uter NT, Perona JJ. Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics. Proc Natl Acad Sci USA 2004;101:14396-14401.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 14396-14401
-
-
Uter, N.T.1
Perona, J.J.2
-
36
-
-
0029913295
-
Functional connectivity between tRNA binding domains in glutaminyl-tRNA synthetase
-
Sherman JM, Thomann HU, Soll D. Functional connectivity between tRNA binding domains in glutaminyl-tRNA synthetase. J Mol Biol 1996;256:818-828.
-
(1996)
J Mol Biol
, vol.256
, pp. 818-828
-
-
Sherman, J.M.1
Thomann, H.U.2
Soll, D.3
-
37
-
-
0027468553
-
Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA
-
Durasevic IW, Schwob E, Soll D. Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA. Proc Natl Acad Sci USA 1993;90:2010-2014.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 2010-2014
-
-
Durasevic, I.W.1
Schwob, E.2
Soll, D.3
-
38
-
-
0028058089
-
Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase
-
Rogers M, Adachi T, Inokuci H, Soll D. Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proc Natl Acad Sci 1994;91:291-295.
-
(1994)
Proc Natl Acad Sci
, vol.91
, pp. 291-295
-
-
Rogers, M.1
Adachi, T.2
Inokuci, H.3
Soll, D.4
-
39
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
40
-
-
0025744439
-
A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism
-
Bhattacharyya T, Bhattacharya A, Roy S. A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism. Eur J Biochem 1991;200:739-745.
-
(1991)
Eur J Biochem
, vol.200
, pp. 739-745
-
-
Bhattacharyya, T.1
Bhattacharya, A.2
Roy, S.3
-
41
-
-
21744438306
-
Slow solvation dynamics at the active site of an enzyme: Implications for catalysis
-
Guha S, Sahu K, Roy D, Mondal SK, Roy S, Bhattacharyya K. Slow solvation dynamics at the active site of an enzyme: implications for catalysis. Biochemistry 2005;44:8940-8947.
-
(2005)
Biochemistry
, vol.44
, pp. 8940-8947
-
-
Guha, S.1
Sahu, K.2
Roy, D.3
Mondal, S.K.4
Roy, S.5
Bhattacharyya, K.6
-
42
-
-
34250794175
-
-
Barabasi AL. Linked. How everything is connected to everything else and what it means for businnes, science, and everyday life. USA: Plume; 2003.
-
Barabasi AL. Linked. How everything is connected to everything else and what it means for businnes, science, and everyday life. USA: Plume; 2003.
-
-
-
-
43
-
-
0029915506
-
Genetic analysis of functional connectivity between substrate recognition domains of Escherichia coli glutaminyl-tRNA synthetase
-
Kitabatake M, Ibba M, Hong KW, Soll D, Inokuchi H. Genetic analysis of functional connectivity between substrate recognition domains of Escherichia coli glutaminyl-tRNA synthetase. Mol Gen Genet 1996;252:717-722.
-
(1996)
Mol Gen Genet
, vol.252
, pp. 717-722
-
-
Kitabatake, M.1
Ibba, M.2
Hong, K.W.3
Soll, D.4
Inokuchi, H.5
-
44
-
-
0032508381
-
Switching the amino acid specificity of an aminoacyl-tRNA synthetase
-
Agou F, Quevillon S, Kerjan P, Mirande M. Switching the amino acid specificity of an aminoacyl-tRNA synthetase. Biochemistry 1998;37:11309-11314.
-
(1998)
Biochemistry
, vol.37
, pp. 11309-11314
-
-
Agou, F.1
Quevillon, S.2
Kerjan, P.3
Mirande, M.4
-
45
-
-
0035874146
-
Analysis of a data set of paired uncomplexed protein structures: New metrics for side-chain flexibility and model evaluation
-
Zhao S, Goodsell DS, Olson AL. Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation. Proteins: Struct Funct Genet 2001;43:271-279.
-
(2001)
Proteins: Struct Funct Genet
, vol.43
, pp. 271-279
-
-
Zhao, S.1
Goodsell, D.S.2
Olson, A.L.3
-
46
-
-
15244353539
-
Side-chain flexibility in protein-ligand binding: The minimal rotation hypothesis
-
Zavodszky MI, Kuhn LA. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci 2005; 14:1104-1114.
-
(2005)
Protein Sci
, vol.14
, pp. 1104-1114
-
-
Zavodszky, M.I.1
Kuhn, L.A.2
-
47
-
-
33244482490
-
Correlation of the side-chain hubs with the functional residues in DNA binding protein structures
-
Sathyapriya R, Brinda KV, Vishveshwara S. Correlation of the side-chain hubs with the functional residues in DNA binding protein structures. J Chem Inf Model 2006;46:123-129.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 123-129
-
-
Sathyapriya, R.1
Brinda, K.V.2
Vishveshwara, S.3
-
48
-
-
0031692909
-
Retracing the evolution of amino acid specificity in glutaminyl-tRNA synthetase
-
Hong KW, Ibba M, Soll D. Retracing the evolution of amino acid specificity in glutaminyl-tRNA synthetase. FEBS Lett 1998;434: 149-154.
-
(1998)
FEBS Lett
, vol.434
, pp. 149-154
-
-
Hong, K.W.1
Ibba, M.2
Soll, D.3
|