-
1
-
-
37349070773
-
A theory of protein dynamics to predict NMR relaxation
-
Caballero-Manrique, E., J. K. Bray, ..., M. G. Guenza. 2007. A theory of protein dynamics to predict NMR relaxation. Biophys. J. 93:4128-4140.
-
(2007)
Biophys. J
, vol.93
, pp. 4128-4140
-
-
Caballero-Manrique, E.1
Bray, J.K.2
Guenza, M.G.3
-
2
-
-
33749007969
-
Backbone dynamics of TEM-1 determined by NMR: Evidence for a highly ordered protein
-
Savard, P.-Y., and S. M. Gagné. 2006. Backbone dynamics of TEM-1 determined by NMR: evidence for a highly ordered protein. Biochemistry. 45:11414-11424.
-
(2006)
Biochemistry
, vol.45
, pp. 11414-11424
-
-
Savard, P.-Y.1
Gagné, S.M.2
-
3
-
-
0032586776
-
pKa calculations for class A b-lactamases: Influence of substrate binding
-
Lamotte-Brasseur, J., V. Lounnas, ..., R. C. Wade. 1999. pKa calculations for class A b-lactamases: influence of substrate binding. Protein Sci. 8:404-409.
-
(1999)
Protein Sci
, vol.8
, pp. 404-409
-
-
Lamotte-Brasseur, J.1
Lounnas, V.2
Wade, R.C.3
-
4
-
-
0042125389
-
Identification of Glu166 as the general base in the acylation reaction of class A β-lactamases through QM/MM modeling
-
Hermann, J. C., L. Ridder, ..., H. D. Höltje. 2003. Identification of Glu166 as the general base in the acylation reaction of class A β-lactamases through QM/MM modeling. J. Am. Chem. Soc. 125:9590-9591.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 9590-9591
-
-
Hermann, J.C.1
Ridder, L.2
Höltje, H.D.3
-
5
-
-
27644522933
-
Ab initio QM/ MM study of class A β-lactamase acylation: Dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70
-
Meroueh, S. O., J. F. Fisher, ..., S. Mobashery. 2005. Ab initio QM/ MM study of class A β-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70. J. Am. Chem. Soc. 127:15397-15407.
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 15397-15407
-
-
Meroueh, S.O.1
Fisher, J.F.2
Mobashery, S.3
-
7
-
-
0037094114
-
An ultrahigh resolution structure of TEM-1 β-lactamase suggests a role for Glu166 as the general base in acylation
-
Minasov, G., X. Wang, and B. K. Shoichet. 2002. An ultrahigh resolution structure of TEM-1 β-lactamase suggests a role for Glu166 as the general base in acylation. J. Am. Chem. Soc. 124:5333-5340.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 5333-5340
-
-
Minasov, G.1
Wang, X.2
Shoichet, B.K.3
-
8
-
-
0026534561
-
β-lactamase TEM1 of E. coli. Crystal structure determination at 2.5 Å resolution
-
Jelsch, C., F. Lenfant, ..., J. P. Samama. 1992. β-lactamase TEM1 of E. coli. Crystal structure determination at 2.5 Å resolution. FEBS Lett. 299:135-142.
-
(1992)
FEBS Lett
, vol.299
, pp. 135-142
-
-
Jelsch, C.1
Lenfant, F.2
Samama, J.P.3
-
9
-
-
0028870390
-
TEM1 β-lactamase structure solved by molecular replacement and refined structure of the S235A mutant
-
Fonzé, E., P. Charlier, ..., J. M. Frère. 1995. TEM1 β-lactamase structure solved by molecular replacement and refined structure of the S235A mutant. Acta Crystallogr. D Biol. Crystallogr. 51:682-694.
-
(1995)
Acta Crystallogr. D Biol. Crystallogr
, vol.51
, pp. 682-694
-
-
Fonzé, E.1
Charlier, P.2
Frère, J.M.3
-
10
-
-
34547097310
-
NMR investigation of Tyr105 mutants in TEM-1 β-lactamase: Dynamics are correlated with function
-
Doucet, N., P.-Y. Savard,., S. M. Gagné. 2007. NMR investigation of Tyr105 mutants in TEM-1 β-lactamase: dynamics are correlated with function. J. Biol. Chem. 282:21448-21459.
-
(2007)
J. Biol. Chem
, vol.282
, pp. 21448-21459
-
-
Doucet, N.1
Savard, P.-Y.2
Gagné, S.M.3
-
11
-
-
0025768209
-
Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G
-
Lamotte-Brasseur, J., G. Dive,., J. M. Ghuysen. 1991. Mechanism of acyl transfer by the class A serine β-lactamase of Streptomyces albus G. Biochem. J. 279:213-221.
-
(1991)
Biochem. J
, vol.279
, pp. 213-221
-
-
Lamotte-Brasseur, J.1
Dive, G.2
Ghuysen, J.M.3
-
12
-
-
4544384195
-
The importance of a critical protonation state and the fate of the catalytic steps in class A β-lactamases and penicillin-binding proteins
-
Golemi-Kotra, D., S. O. Meroueh,., S. Mobashery. 2004. The importance of a critical protonation state and the fate of the catalytic steps in class A β-lactamases and penicillin-binding proteins. J. Biol. Chem. 279:34665-34673.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 34665-34673
-
-
Golemi-Kotra, D.1
Meroueh, S.O.2
Mobashery, S.3
-
13
-
-
26644435522
-
Dynamical aspects of TEM-1 b-lactamase probed by molecular dynamics
-
Roccatano, D., G. Sbardella, ..., F. Mazza. 2005. Dynamical aspects of TEM-1 b-lactamase probed by molecular dynamics. J. Comput. Aided Mol. Des. 19:329-340.
-
(2005)
J. Comput. Aided Mol. Des
, vol.19
, pp. 329-340
-
-
Roccatano, D.1
Sbardella, G.2
Mazza, F.3
-
14
-
-
14844362964
-
Bacterial resistance to b-lactam antibiotics: Compelling opportunism, compelling opportunity
-
Fisher, J. F., S. O. Meroueh, and S. Mobashery. 2005. Bacterial resistance to b-lactam antibiotics: compelling opportunism, compelling opportunity. Chem. Rev. 105:395-424.
-
(2005)
Chem. Rev
, vol.105
, pp. 395-424
-
-
Fisher, J.F.1
Meroueh, S.O.2
Mobashery, S.3
-
15
-
-
2942562249
-
Evolution of the serine β-lactamases: Past, present and future
-
Hall, B. G., and M. Barlow. 2004. Evolution of the serine β-lactamases: past, present and future. Drug Resist. Updat. 7:111-123.
-
(2004)
Drug Resist. Updat
, vol.7
, pp. 111-123
-
-
Hall, B.G.1
Barlow, M.2
-
16
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
-
Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:4546-4559.
-
(1982)
J. Am. Chem. Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
17
-
-
0025046144
-
Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
-
Clore, G. M., A. Szabo, ..., A. M. Gronenborn. 1990. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112:4989-4991.
-
(1990)
J. Am. Chem. Soc
, vol.112
, pp. 4989-4991
-
-
Clore, G.M.1
Szabo, A.2
Gronenborn, A.M.3
-
18
-
-
33645786604
-
Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme
-
Buck, M., S. Bouguet-Bonnet, ..., A. D. MacKerell, Jr. 2006. Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme. Biophys. J. 90:L36-L38.
-
(2006)
Biophys. J
, vol.90
-
-
Buck, M.1
Bouguet-Bonnet, S.2
MacKerell Jr., A.D.3
-
19
-
-
44949111351
-
Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins
-
Maragakis, P., K. Lindorff-Larsen, ..., D. E. Shaw. 2008. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J. Phys. Chem. B. 112:6155-6158.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6155-6158
-
-
Maragakis, P.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
20
-
-
34047136004
-
Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein
-
MacRaild, C. A., A. H. Daranas, ..., S.W. Homans. 2007. Global changes in local protein dynamics reduce the entropic cost of carbohydrate binding in the arabinose-binding protein. J. Mol. Biol. 368:822-832.
-
(2007)
J. Mol. Biol
, vol.368
, pp. 822-832
-
-
MacRaild, C.A.1
Daranas, A.H.2
Homans, S.W.3
-
21
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, ..., M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Karplus, M.3
-
22
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
Mackerell, A. D., D. Bashford, ..., M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Karplus, M.3
-
23
-
-
0037266991
-
The use of model selection in the model-free analysis of protein dynamics
-
d'Auvergne, E. J., and P. R. Gooley. 2003. The use of model selection in the model-free analysis of protein dynamics. J. Biomol. NMR. 25: 25-39.
-
(2003)
J. Biomol. NMR
, vol.25
, pp. 25-39
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
24
-
-
33745623124
-
Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data
-
d'Auvergne, E. J., and P. R. Gooley. 2006. Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR. 35:117-135.
-
(2006)
J. Biomol. NMR
, vol.35
, pp. 117-135
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
25
-
-
38349077155
-
Optimization of NMR dynamic models. I. Minimization algorithms and their performance within the model-free and Brownian rotational diffusion spaces
-
d'Auvergne, E. J., and P. R. Gooley. 2008. Optimization of NMR dynamic models. I. Minimization algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR. 40:107-119.
-
(2008)
J. Biomol. NMR
, vol.40
, pp. 107-119
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
26
-
-
38349050193
-
Optimization of NMR dynamic models. II. A new methodology for the dual optimization of the model-free parameters and the Brownian rotational diffusion tensor
-
d'Auvergne, E. J., and P. R. Gooley. 2008. Optimization of NMR dynamic models. II. A new methodology for the dual optimization of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR. 40:121-133.
-
(2008)
J. Biomol. NMR
, vol.40
, pp. 121-133
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
27
-
-
0028941877
-
Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme
-
Mandel, A. M., M. Akke, and A. G. Palmer, 3rd. 1995. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 246:144-163.
-
(1995)
J. Mol. Biol
, vol.246
, pp. 144-163
-
-
Mandel, A.M.1
Akke, M.2
Palmer 3rd, A.G.3
-
28
-
-
34250781656
-
Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm
-
d'Auvergne, E. J., and P. R. Gooley. 2007. Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. Biosyst. 3:483-494.
-
(2007)
Mol. Biosyst
, vol.3
, pp. 483-494
-
-
d'Auvergne, E.J.1
Gooley, P.R.2
-
29
-
-
68949086333
-
NMR dynamics of PSE-4 b-lactamase: An interplay of ps-ns order and ms-ms motions in the active site
-
Morin, S., and S. M. Gagné. 2009. NMR dynamics of PSE-4 b-lactamase: an interplay of ps-ns order and ms-ms motions in the active site. Biophys. J. 96:4681-4691.
-
(2009)
Biophys. J
, vol.96
, pp. 4681-4691
-
-
Morin, S.1
Gagné, S.M.2
-
30
-
-
46749096337
-
Starting structure dependence of NMR order parameters derived from MD simulations: Implications for judging force-field quality
-
Koller, A. N., H. Schwalbe, and H. Gohlke. 2008. Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality. Biophys. J. 95:L04-L06.
-
(2008)
Biophys. J
, vol.95
-
-
Koller, A.N.1
Schwalbe, H.2
Gohlke, H.3
-
31
-
-
3042846786
-
Model-free analysis of protein dynamics: Assessment of accuracy and model selection protocols based on molecular dynamics simulation
-
Chen, J., C. L. Brooks, 3rd, and P. E. Wright. 2004. Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J. Biomol. NMR. 29:243-257.
-
(2004)
J. Biomol. NMR
, vol.29
, pp. 243-257
-
-
Chen, J.1
Brooks 3rd, C.L.2
Wright, P.E.3
-
32
-
-
0034919305
-
Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules
-
Palmer, 3rd, A. G., C. D. Kroenke, and J. P. Loria. 2001. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 339:204-238.
-
(2001)
Methods Enzymol
, vol.339
, pp. 204-238
-
-
Palmer 3rd, A.G.1
Kroenke, C.D.2
Loria, J.P.3
-
33
-
-
41149138253
-
Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation
-
Trbovic, N., B. Kim,., A. G. Palmer, 3rd. 2008. Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation. Proteins. 71:684-694.
-
(2008)
Proteins
, vol.71
, pp. 684-694
-
-
Trbovic, N.1
Kim, B.2
Palmer 3rd, A.G.3
-
35
-
-
0027275788
-
Crystal structure of Escherichia coli TEM1 β-lactamase at 1.8 Å resolution
-
Jelsch, C., L. Mourey, ..., J. P. Samama. 1993. Crystal structure of Escherichia coli TEM1 β-lactamase at 1.8 Å resolution. Proteins. 16:364-383.
-
(1993)
Proteins
, vol.16
, pp. 364-383
-
-
Jelsch, C.1
Mourey, L.2
Samama, J.P.3
-
36
-
-
0031041590
-
Site-directed mutagenesis of glutamate 166 in two β-lactamases. Kinetic and molecular modeling studies
-
Guillaume, G., M. Vanhove, ..., J. M. Frère. 1997. Site-directed mutagenesis of glutamate 166 in two β-lactamases. Kinetic and molecular modeling studies. J. Biol. Chem. 272:5438-5444.
-
(1997)
J. Biol. Chem
, vol.272
, pp. 5438-5444
-
-
Guillaume, G.1
Vanhove, M.2
Frère, J.M.3
-
37
-
-
0014653970
-
The nature of general base-general acid catalysis in serine proteases
-
Polgár, L., and M. L. Bender. 1969. The nature of general base-general acid catalysis in serine proteases. Proc. Natl. Acad. Sci. USA. 64:1335-1342.
-
(1969)
Proc. Natl. Acad. Sci. USA
, vol.64
, pp. 1335-1342
-
-
Polgár, L.1
Bender, M.L.2
-
38
-
-
33644864228
-
Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: Probing T7 DNA polymerase with variably sized base pairs
-
Kim, T. W., L. G. Brieba,., E. T. Kool. 2006. Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: probing T7 DNA polymerase with variably sized base pairs. J. Biol. Chem. 281:2289-2295.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 2289-2295
-
-
Kim, T.W.1
Brieba, L.G.2
Kool, E.T.3
-
39
-
-
0021403736
-
Diffusion-limited component of reactions catalyzed by Bacillus cereus β-lactamase I
-
Hardy, L. W., and J. F. Kirsch. 1984. Diffusion-limited component of reactions catalyzed by Bacillus cereus β-lactamase I. Biochemistry. 23:1275-1282.
-
(1984)
Biochemistry
, vol.23
, pp. 1275-1282
-
-
Hardy, L.W.1
Kirsch, J.F.2
|