-
1
-
-
77957117205
-
Rate theories for biologists
-
Zhou H.X. Rate theories for biologists. Q Rev Biophys 2010, 43:219-293.
-
(2010)
Q Rev Biophys
, vol.43
, pp. 219-293
-
-
Zhou, H.X.1
-
2
-
-
84862658718
-
Kinetic control of translation initiation in bacteria
-
Milon P., Rodnina M.V. Kinetic control of translation initiation in bacteria. Crit Rev Biochem Mol Biol 2012, 47:334-348.
-
(2012)
Crit Rev Biochem Mol Biol
, vol.47
, pp. 334-348
-
-
Milon, P.1
Rodnina, M.V.2
-
3
-
-
44649131886
-
Kinetic partitioning between alternative protein-protein interactions controls a transcriptional switch
-
Zhao H., Beckett D. Kinetic partitioning between alternative protein-protein interactions controls a transcriptional switch. J Mol Biol 2008, 380:223-236.
-
(2008)
J Mol Biol
, vol.380
, pp. 223-236
-
-
Zhao, H.1
Beckett, D.2
-
4
-
-
33745943856
-
How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis
-
Antoun A., Pavlov M.Y., Lovmar M., Ehrenberg M. How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis. Mol Cell 2006, 23:183-193.
-
(2006)
Mol Cell
, vol.23
, pp. 183-193
-
-
Antoun, A.1
Pavlov, M.Y.2
Lovmar, M.3
Ehrenberg, M.4
-
5
-
-
79960380134
-
Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav
-
Chen C.H., Martin V.A., Gorenstein N.M., Geahlen R.L., Post C.B. Two closely spaced tyrosines regulate NFAT signaling in B cells via Syk association with Vav. Mol Cell Biol 2011, 31:2984-2996.
-
(2011)
Mol Cell Biol
, vol.31
, pp. 2984-2996
-
-
Chen, C.H.1
Martin, V.A.2
Gorenstein, N.M.3
Geahlen, R.L.4
Post, C.B.5
-
6
-
-
84856708599
-
Intrinsic disorder: signaling via highly specific but short-lived association
-
Zhou H.X. Intrinsic disorder: signaling via highly specific but short-lived association. Trends Biochem Sci 2012, 37:43-48.
-
(2012)
Trends Biochem Sci
, vol.37
, pp. 43-48
-
-
Zhou, H.X.1
-
7
-
-
70350452750
-
Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling
-
Kiel C., Serrano L. Cell type-specific importance of ras-c-raf complex association rate constants for MAPK signaling. Sci Signal 2009, 2:ra38.
-
(2009)
Sci Signal
, vol.2
-
-
Kiel, C.1
Serrano, L.2
-
8
-
-
36549102274
-
Brownian dynamics simulation of diffusion-influenced bimolecular reactions
-
Northrup S.H., Allison S.A., Mccammon J.A. Brownian dynamics simulation of diffusion-influenced bimolecular reactions. J Chem Phys 1984, 80:1517-1526.
-
(1984)
J Chem Phys
, vol.80
, pp. 1517-1526
-
-
Northrup, S.H.1
Allison, S.A.2
Mccammon, J.A.3
-
9
-
-
0001518899
-
Kinetics of diffusion-influenced reactions studied by Brownian dynamics
-
Zhou H.X. Kinetics of diffusion-influenced reactions studied by Brownian dynamics. J Phys Chem 1990, 94:8794-8800.
-
(1990)
J Phys Chem
, vol.94
, pp. 8794-8800
-
-
Zhou, H.X.1
-
10
-
-
0026607545
-
Kinetics of protein-protein association explained by Brownian dynamics computer simulation
-
Northrup S.H., Erickson H.P. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc Natl Acad Sci U S A 1992, 89:3338-3342.
-
(1992)
Proc Natl Acad Sci U S A
, vol.89
, pp. 3338-3342
-
-
Northrup, S.H.1
Erickson, H.P.2
-
12
-
-
78349288528
-
Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association
-
Frembgen-Kesner T., Elcock A.H. Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association. Biophys J 2010, 99:L75-L77.
-
(2010)
Biophys J
, vol.99
-
-
Frembgen-Kesner, T.1
Elcock, A.H.2
-
13
-
-
40549134985
-
Electrostatic rate enhancement and transient complex of protein-protein association
-
Alsallaq R., Zhou H.X. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 2008, 71:320-335.
-
(2008)
Proteins
, vol.71
, pp. 320-335
-
-
Alsallaq, R.1
Zhou, H.X.2
-
14
-
-
65249099497
-
Fundamental aspects of protein-protein association kinetics
-
Schreiber G., Haran G., Zhou H.X. Fundamental aspects of protein-protein association kinetics. Chem Rev 2009, 109:839-860.
-
(2009)
Chem Rev
, vol.109
, pp. 839-860
-
-
Schreiber, G.1
Haran, G.2
Zhou, H.X.3
-
15
-
-
82955239904
-
Automated prediction of protein association rate constants
-
Qin S., Pang X., Zhou H.X. Automated prediction of protein association rate constants. Structure 2011, 19:1744-1751.
-
(2011)
Structure
, vol.19
, pp. 1744-1751
-
-
Qin, S.1
Pang, X.2
Zhou, H.X.3
-
16
-
-
0025216077
-
An early immunoreactive folding intermediate of the tryptophan synthease beta 2 subunit is a 'molten globule'
-
Goldberg M.E., Semisotnov G.V., Friguet B., Kuwajima K., Ptitsyn O.B., Sugai S. An early immunoreactive folding intermediate of the tryptophan synthease beta 2 subunit is a 'molten globule'. FEBS Lett 1990, 263:51-56.
-
(1990)
FEBS Lett
, vol.263
, pp. 51-56
-
-
Goldberg, M.E.1
Semisotnov, G.V.2
Friguet, B.3
Kuwajima, K.4
Ptitsyn, O.B.5
Sugai, S.6
-
17
-
-
0037126728
-
Interleukin-1 beta folding between pH 5 and 7: experimental evidence for three-state folding behavior and robust transition state positions late in folding
-
Finke J.M., Jennings P.A. Interleukin-1 beta folding between pH 5 and 7: experimental evidence for three-state folding behavior and robust transition state positions late in folding. Biochemistry 2002, 41:15056-15067.
-
(2002)
Biochemistry
, vol.41
, pp. 15056-15067
-
-
Finke, J.M.1
Jennings, P.A.2
-
18
-
-
33846789583
-
Energy landscape and transition state of protein-protein association
-
Alsallaq R., Zhou H.X. Energy landscape and transition state of protein-protein association. Biophys J 2007, 92:1486-1502.
-
(2007)
Biophys J
, vol.92
, pp. 1486-1502
-
-
Alsallaq, R.1
Zhou, H.X.2
-
19
-
-
80052476429
-
Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines
-
Pang X., Qin S., Zhou H.X. Rationalizing 5000-fold differences in receptor-binding rate constants of four cytokines. Biophys J 2011, 101:1175-1183.
-
(2011)
Biophys J
, vol.101
, pp. 1175-1183
-
-
Pang, X.1
Qin, S.2
Zhou, H.X.3
-
20
-
-
84868120066
-
Prediction and dissection of widely-varying association rate constants of actin-binding proteins
-
Pang X., Zhou K.H., Qin S., Zhou H.X. Prediction and dissection of widely-varying association rate constants of actin-binding proteins. PLoS Comput Biol 2012, 8:e1002696.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Pang, X.1
Zhou, K.H.2
Qin, S.3
Zhou, H.X.4
-
21
-
-
84869022006
-
Rigid body energy minimization on manifolds for molecular docking
-
Mirzaei H., Beglov D., Paschalidis I.C., Vajda S., Vakili P., Kozakov D. Rigid body energy minimization on manifolds for molecular docking. J Chem Theory Comput 2012, 8:4374-4380.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 4374-4380
-
-
Mirzaei, H.1
Beglov, D.2
Paschalidis, I.C.3
Vajda, S.4
Vakili, P.5
Kozakov, D.6
-
22
-
-
66049101759
-
Dissection of the high rate constant for the binding of a ribotoxin to the ribosome
-
Qin S.B., Zhou H.X. Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Proc Natl Acad Sci U S A 2009, 106:6974-6979.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 6974-6979
-
-
Qin, S.B.1
Zhou, H.X.2
-
23
-
-
82455219434
-
Electrostatically biased binding of kinesin to microtubules
-
Grant B.J., Gheorghe D.M., Zheng W., Alonso M., Huber G., Dlugosz M., McCammon J.A., Cross R.A. Electrostatically biased binding of kinesin to microtubules. PLoS Biol 2011, 9:e1001207.
-
(2011)
PLoS Biol
, vol.9
-
-
Grant, B.J.1
Gheorghe, D.M.2
Zheng, W.3
Alonso, M.4
Huber, G.5
Dlugosz, M.6
McCammon, J.A.7
Cross, R.A.8
-
24
-
-
79551482915
-
Predicting kinetic constants of protein-protein interactions based on structural properties
-
Bai H., Yang K., Yu D., Zhang C., Chen F., Lai L. Predicting kinetic constants of protein-protein interactions based on structural properties. Proteins 2011, 79:720-734.
-
(2011)
Proteins
, vol.79
, pp. 720-734
-
-
Bai, H.1
Yang, K.2
Yu, D.3
Zhang, C.4
Chen, F.5
Lai, L.6
-
25
-
-
84857490154
-
Kinetic rate constant prediction supports the conformational selection mechanism of protein binding
-
Moal I.H., Bates P.A. Kinetic rate constant prediction supports the conformational selection mechanism of protein binding. PLoS Comput Biol 2012, 8:e1002351.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Moal, I.H.1
Bates, P.A.2
-
27
-
-
0028367073
-
Simulation of enzyme-substrate encounter with gated active sites
-
Wade R.C., Luty B.A., Demchuk E., Madura J.D., Davis M.E., Briggs J.M., McCammon J.A. Simulation of enzyme-substrate encounter with gated active sites. Nat Struct Biol 1994, 1:65-69.
-
(1994)
Nat Struct Biol
, vol.1
, pp. 65-69
-
-
Wade, R.C.1
Luty, B.A.2
Demchuk, E.3
Madura, J.D.4
Davis, M.E.5
Briggs, J.M.6
McCammon, J.A.7
-
28
-
-
80053937582
-
Gating and intermolecular interactions in ligand-protein association: coarse-grained modeling of HIV-1 protease
-
Kang M., Roberts C., Cheng Y.H., Chang C.E.A. Gating and intermolecular interactions in ligand-protein association: coarse-grained modeling of HIV-1 protease. J Chem Theory Comput 2011, 7:3438-3446.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 3438-3446
-
-
Kang, M.1
Roberts, C.2
Cheng, Y.H.3
Chang, C.E.A.4
-
29
-
-
84870177629
-
BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations
-
Greives N., Zhou H.X. BDflex: a method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations. J Chem Phys 2012, 137:135105.
-
(2012)
J Chem Phys
, vol.137
, pp. 135105
-
-
Greives, N.1
Zhou, H.X.2
-
30
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch I., Giorgino T., De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A 2011, 108:10184-10189.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
31
-
-
0037188377
-
Intrinsic disorder and protein function
-
Dunker A.K., Brown C.J., Lawson J.D., Iakoucheva L.M., Obradovic Z. Intrinsic disorder and protein function. Biochemistry 2002, 41:6573-6582.
-
(2002)
Biochemistry
, vol.41
, pp. 6573-6582
-
-
Dunker, A.K.1
Brown, C.J.2
Lawson, J.D.3
Iakoucheva, L.M.4
Obradovic, Z.5
-
32
-
-
84873194008
-
Protein flexibility, not disorder, is intrinsic to molecular recognition
-
Janin J., Sternberg M.J. Protein flexibility, not disorder, is intrinsic to molecular recognition. F1000 Biol Rep 2013, 5:2.
-
(2013)
F1000 Biol Rep
, vol.5
, pp. 2
-
-
Janin, J.1
Sternberg, M.J.2
-
34
-
-
84863979552
-
Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets
-
Zhou H.X., Pang X.D., Lu C. Rate constants and mechanisms of intrinsically disordered proteins binding to structured targets. Phys Chem Chem Phys 2012, 14:10466-10476.
-
(2012)
Phys Chem Chem Phys
, vol.14
, pp. 10466-10476
-
-
Zhou, H.X.1
Pang, X.D.2
Lu, C.3
-
35
-
-
0037309985
-
Extended disordered proteins: targeting function with less scaffold
-
Gunasekaran K., Tsai C.J., Kumar S., Zanuy D., Nussinov R. Extended disordered proteins: targeting function with less scaffold. Trends Biochem Sci 2003, 28:81-85.
-
(2003)
Trends Biochem Sci
, vol.28
, pp. 81-85
-
-
Gunasekaran, K.1
Tsai, C.J.2
Kumar, S.3
Zanuy, D.4
Nussinov, R.5
-
36
-
-
54749087040
-
Mechanism of fast peptide recognition by SH3 domains
-
Ahmad M., Gu W., Helms V. Mechanism of fast peptide recognition by SH3 domains. Angew Chem Int Ed Engl 2008, 47:7626-7630.
-
(2008)
Angew Chem Int Ed Engl
, vol.47
, pp. 7626-7630
-
-
Ahmad, M.1
Gu, W.2
Helms, V.3
-
38
-
-
67949106402
-
Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting"
-
Chen J. Intrinsically disordered p53 extreme C-terminus binds to S100B(betabeta) through "fly-casting". J Am Chem Soc 2009, 131:2088-2089.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 2088-2089
-
-
Chen, J.1
-
39
-
-
82655179907
-
Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP
-
De Sancho D., Best R.B. Modulation of an IDP binding mechanism and rates by helix propensity and non-native interactions: association of HIF1alpha with CBP. Mol Biosyst 2012, 8:256-267.
-
(2012)
Mol Biosyst
, vol.8
, pp. 256-267
-
-
De Sancho, D.1
Best, R.B.2
-
40
-
-
0024466381
-
Quantitative evaluation of the contribution of ionic interactions to the formation of the thrombin-hirudin complex
-
Stone S.R., Dennis S., Hofsteenge J. Quantitative evaluation of the contribution of ionic interactions to the formation of the thrombin-hirudin complex. Biochemistry 1989, 28:6857-6863.
-
(1989)
Biochemistry
, vol.28
, pp. 6857-6863
-
-
Stone, S.R.1
Dennis, S.2
Hofsteenge, J.3
-
41
-
-
0026633347
-
Interaction of the N-terminal region of hirudin with the active-site cleft of thrombin
-
Betz A., Hofsteenge J., Stone S.R. Interaction of the N-terminal region of hirudin with the active-site cleft of thrombin. Biochemistry 1992, 31:4557-4562.
-
(1992)
Biochemistry
, vol.31
, pp. 4557-4562
-
-
Betz, A.1
Hofsteenge, J.2
Stone, S.R.3
-
42
-
-
0035942306
-
Electrostatic steering and ionic tethering in the formation of thrombin-hirudin complexes: the role of the thrombin anion-binding exosite-I
-
Myles T., Le Bonniec B.F., Betz A., Stone S.R. Electrostatic steering and ionic tethering in the formation of thrombin-hirudin complexes: the role of the thrombin anion-binding exosite-I. Biochemistry 2001, 40:4972-4979.
-
(2001)
Biochemistry
, vol.40
, pp. 4972-4979
-
-
Myles, T.1
Le Bonniec, B.F.2
Betz, A.3
Stone, S.R.4
-
43
-
-
1842473094
-
P27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding
-
Lacy E.R., Filippov I., Lewis W.S., Otieno S., Xiao L., Weiss S., Hengst L., Kriwacki R.W. p27 binds cyclin-CDK complexes through a sequential mechanism involving binding-induced protein folding. Nat Struct Mol Biol 2004, 11:358-364.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 358-364
-
-
Lacy, E.R.1
Filippov, I.2
Lewis, W.S.3
Otieno, S.4
Xiao, L.5
Weiss, S.6
Hengst, L.7
Kriwacki, R.W.8
-
44
-
-
70350012289
-
Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism
-
Huang Y., Liu Z. Kinetic advantage of intrinsically disordered proteins in coupled folding-binding process: a critical assessment of the "fly-casting" mechanism. J Mol Biol 2009, 393:1143-1159.
-
(2009)
J Mol Biol
, vol.393
, pp. 1143-1159
-
-
Huang, Y.1
Liu, Z.2
-
45
-
-
41049090929
-
Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences
-
Zhou H.X., Rivas G., Minton A.P. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 2008, 37:375-397.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 375-397
-
-
Zhou, H.X.1
Rivas, G.2
Minton, A.P.3
-
46
-
-
84877043455
-
Simulation and modeling of crowding effects on the thermodynamic and kinetic properties of proteins with atomic details
-
Zhou H.X., Qin S. Simulation and modeling of crowding effects on the thermodynamic and kinetic properties of proteins with atomic details. Biophys Rev 2013, 5:207-215.
-
(2013)
Biophys Rev
, vol.5
, pp. 207-215
-
-
Zhou, H.X.1
Qin, S.2
-
47
-
-
0001023302
-
Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid
-
Zhou H.X., Szabo A. Comparison between molecular dynamics simulations and the Smoluchowski theory of reactions in a hard sphere liquid. J Chem Phys 1991, 95:5948-5952.
-
(1991)
J Chem Phys
, vol.95
, pp. 5948-5952
-
-
Zhou, H.X.1
Szabo, A.2
-
48
-
-
68949110044
-
Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability
-
Qin S., Zhou H.X. Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability. Biophys J 2009, 97:12-19.
-
(2009)
Biophys J
, vol.97
, pp. 12-19
-
-
Qin, S.1
Zhou, H.X.2
-
49
-
-
84871205477
-
A method for computing association rate constants of atomistically represented proteins under macromolecular crowding
-
Qin S., Cai L., Zhou H.X. A method for computing association rate constants of atomistically represented proteins under macromolecular crowding. Phys Biol 2012, 9:066008.
-
(2012)
Phys Biol
, vol.9
, pp. 066008
-
-
Qin, S.1
Cai, L.2
Zhou, H.X.3
-
50
-
-
84865735110
-
Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents
-
Phillip Y., Harel M., Khait R., Qin S., Zhou H.X., Schreiber G. Contrasting factors on the kinetic path to protein complex formation diminish the effects of crowding agents. Biophys J 2012, 103:1011-1019.
-
(2012)
Biophys J
, vol.103
, pp. 1011-1019
-
-
Phillip, Y.1
Harel, M.2
Khait, R.3
Qin, S.4
Zhou, H.X.5
Schreiber, G.6
-
52
-
-
84879411842
-
Allosteric inhibition through suppression of transient conformational states
-
Tzeng H.-S., Kalodimos C.G. Allosteric inhibition through suppression of transient conformational states. Nat Chem Biol 2013, 9:462-465.
-
(2013)
Nat Chem Biol
, vol.9
, pp. 462-465
-
-
Tzeng, H.-S.1
Kalodimos, C.G.2
-
53
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
-
Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 2003, 15:221-231.
-
(2003)
Curr Opin Cell Biol
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
54
-
-
44349125602
-
Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system
-
Schmierer B., Tournier A.L., Bates P.A., Hill C.S. Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proc Natl Acad Sci U S A 2008, 105:6608-6613.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 6608-6613
-
-
Schmierer, B.1
Tournier, A.L.2
Bates, P.A.3
Hill, C.S.4
-
55
-
-
84868094052
-
A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins
-
Cheng T.M., Goehring L., Jeffery L., Lu Y.E., Hayles J., Novak B., Bates P.A. A structural systems biology approach for quantifying the systemic consequences of missense mutations in proteins. PLoS Comput Biol 2012, 8:e1002738.
-
(2012)
PLoS Comput Biol
, vol.8
-
-
Cheng, T.M.1
Goehring, L.2
Jeffery, L.3
Lu, Y.E.4
Hayles, J.5
Novak, B.6
Bates, P.A.7
|