-
1
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern, D., and E. R. P. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13:748-757.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.P.2
-
2
-
-
33746911627
-
Dynamic coupling and allosteric behavior in a nonallosteric protein
-
Clarkson, M. W., S. A. Gilmore, M. H. Edgell, and A. L. Lee. 2006. Dynamic coupling and allosteric behavior in a nonallosteric protein. Biochemistry. 45:7693-7699.
-
(2006)
Biochemistry
, vol.45
, pp. 7693-7699
-
-
Clarkson, M.W.1
Gilmore, S.A.2
Edgell, M.H.3
Lee, A.L.4
-
3
-
-
0034821747
-
Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase
-
table of contents
-
Helmstaedt, K., S. Krappmann, and G. H. Braus. 2001. Allosteric regulation of catalytic activity: Escherichia coli aspartate transcarbamoylase versus yeast chorismate mutase. Microbiol. Mol. Biol. Rev. 65:404-421 (table of contents.).
-
(2001)
Microbiol. Mol. Biol. Rev
, vol.65
, pp. 404-421
-
-
Helmstaedt, K.1
Krappmann, S.2
Braus, G.H.3
-
4
-
-
0025126519
-
Conformational substates and motions in myoglobin. External influences on structure and dynamics
-
Hong, M. K., D. Braunstein, B. R. Cowen, H. Frauenfelder, I. E. Iben, J. R. Mourant, P. Ormos, R. Scholl, A. Schulte, and P. J. Steinbach. 1990. Conformational substates and motions in myoglobin. External influences on structure and dynamics. Biophys. J. 58:429-436.
-
(1990)
Biophys. J
, vol.58
, pp. 429-436
-
-
Hong, M.K.1
Braunstein, D.2
Cowen, B.R.3
Frauenfelder, H.4
Iben, I.E.5
Mourant, J.R.6
Ormos, P.7
Scholl, R.8
Schulte, A.9
Steinbach, P.J.10
-
5
-
-
34547460183
-
Molecular evolution of affinity and flexibility in the immune system
-
Thorpe, I. F., I. Brooks, and L. Charles. 2007. Molecular evolution of affinity and flexibility in the immune system. Proc. Natl. Acad. Sci. USA. 104:8821-8826.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 8821-8826
-
-
Thorpe, I.F.1
Brooks, I.2
Charles, L.3
-
6
-
-
34547471963
-
Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates
-
Dioumaev, A. K., and J. K. Lanyi. 2007. Bacteriorhodopsin photocycle at cryogenic temperatures reveals distributed barriers of conformational substates. Proc. Natl. Acad. Sci. USA. 104:9621-9626.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 9621-9626
-
-
Dioumaev, A.K.1
Lanyi, J.K.2
-
7
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder, H., S. G. Sligar, and P. G. Wolynes. 1991. The energy landscapes and motions of proteins. Science. 254:1598-1603.
-
(1991)
Science
, vol.254
, pp. 1598-1603
-
-
Frauenfelder, H.1
Sligar, S.G.2
Wolynes, P.G.3
-
8
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
9
-
-
0000580978
-
Proteins and pressure
-
Frauenfelder, H., N. A. Alberding, A. Ansari, D. Braunstein, B. R. Cowen, M. K. Hong, I. E. T. Iben, J. B. Johnson, S. Luck, M. C. Marsden, J. R. Mourant, P. Ormos, L. Reinisch, R. Scholl, A. Schulte, E. Shyamsunder, L. B. Sorensen, P. J. Steinbach, A. Xie, R. D. Young, and K. T. Yue. 1990. Proteins and pressure. J. Phys. Chem. 94:1024-1037.
-
(1990)
J. Phys. Chem
, vol.94
, pp. 1024-1037
-
-
Frauenfelder, H.1
Alberding, N.A.2
Ansari, A.3
Braunstein, D.4
Cowen, B.R.5
Hong, M.K.6
Iben, I.E.T.7
Johnson, J.B.8
Luck, S.9
Marsden, M.C.10
Mourant, J.R.11
Ormos, P.12
Reinisch, L.13
Scholl, R.14
Schulte, A.15
Shyamsunder, E.16
Sorensen, L.B.17
Steinbach, P.J.18
Xie, A.19
Young, R.D.20
Yue, K.T.21
more..
-
10
-
-
0035958744
-
Statistical thermodynamics: Taking a walk on a landscape
-
Brooks, C. L., J. N. Onuchic, and D. J. Wales. 2001. Statistical thermodynamics: taking a walk on a landscape. Science. 293:612-613.
-
(2001)
Science
, vol.293
, pp. 612-613
-
-
Brooks, C.L.1
Onuchic, J.N.2
Wales, D.J.3
-
11
-
-
0002237761
-
Biomolecules: Where the physics of complexity and simplicity meet
-
Frauenfelder, H., and P. G. Wolynes. 1994. Biomolecules: where the physics of complexity and simplicity meet. Phys. Today. 47:58-64.
-
(1994)
Phys. Today
, vol.47
, pp. 58-64
-
-
Frauenfelder, H.1
Wolynes, P.G.2
-
13
-
-
0036535895
-
Protein folding: The free energy surface
-
Gruebele, M. 2002. Protein folding: the free energy surface. Curr. Opin. Struct. Biol. 12:161-168.
-
(2002)
Curr. Opin. Struct. Biol
, vol.12
, pp. 161-168
-
-
Gruebele, M.1
-
14
-
-
5144223810
-
Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions
-
Fenimore, P. W., H. Frauenfelder, B. H. McMahon, and R. D. Young. 2004. Bulk-solvent and hydration-shell fluctuations, similar to α- and β-fluctuations in glasses, control protein motions and functions. Proc. Natl. Acad. Sci. USA. 101:14408-14413.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14408-14413
-
-
Fenimore, P.W.1
Frauenfelder, H.2
McMahon, B.H.3
Young, R.D.4
-
15
-
-
0032574827
-
Dynamics and function of proteins: The search for general concepts
-
Frauenfelder, H., and B. McMahon. 1998. Dynamics and function of proteins: the search for general concepts. Proc. Natl. Acad. Sci. USA. 95:4795-4797.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 4795-4797
-
-
Frauenfelder, H.1
McMahon, B.2
-
16
-
-
0032552138
-
Archetypal energy landscapes
-
Wales, D. J., M. A. Miller, and T. R. Walsh. 1998. Archetypal energy landscapes. Nature. 394:758-760.
-
(1998)
Nature
, vol.394
, pp. 758-760
-
-
Wales, D.J.1
Miller, M.A.2
Walsh, T.R.3
-
17
-
-
0000370391
-
The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
-
Becker, O. M., and M. Karplus. 1997. The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics. J. Chem. Phys. 106:1495-1517.
-
(1997)
J. Chem. Phys
, vol.106
, pp. 1495-1517
-
-
Becker, O.M.1
Karplus, M.2
-
18
-
-
0035128033
-
Energy landscapes of conformationally constrained peptides
-
Levy, Y., and O. M. Becker. 2001. Energy landscapes of conformationally constrained peptides. J. Chem. Phys. 114:993-1009.
-
(2001)
J. Chem. Phys
, vol.114
, pp. 993-1009
-
-
Levy, Y.1
Becker, O.M.2
-
19
-
-
6944235051
-
Hidden complexity of free energy surfaces for peptide (protein) folding
-
Krivov, S. V., and M. Karplus. 2004. Hidden complexity of free energy surfaces for peptide (protein) folding. Proc. Natl. Acad. Sci. USA. 101:14766-14770.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14766-14770
-
-
Krivov, S.V.1
Karplus, M.2
-
20
-
-
0033613185
-
Hierarchies and logarithmic oscillations in the temporal relaxation patterns of proteins and other complex systems
-
Metzler, R., J. Klafter, and J. Jortner. 1999. Hierarchies and logarithmic oscillations in the temporal relaxation patterns of proteins and other complex systems. Proc. Natl. Acad. Sci. USA. 96:11085-11089.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11085-11089
-
-
Metzler, R.1
Klafter, J.2
Jortner, J.3
-
21
-
-
0242268469
-
Nonlinear elasticity, protein quakes, and the energy landscapes of functional transitions in proteins
-
Miyashita, O., J. N. Onuchic, and P. G. Wolynes. 2003. Nonlinear elasticity, protein quakes, and the energy landscapes of functional transitions in proteins. Proc. Natl. Acad. Sci. USA. 100:12570-12575.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
22
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling, C., B. Strockbine, and A. E. Roitberg. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-11259.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
23
-
-
0037065310
-
The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
-
Snow, C., B. Zagrovic, and V. Pande. 2002. The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J. Am. Chem. Soc. 124:14548-14549.
-
(2002)
J. Am. Chem. Soc
, vol.124
, pp. 14548-14549
-
-
Snow, C.1
Zagrovic, B.2
Pande, V.3
-
25
-
-
0030165480
-
Correlated energy landscape model for finite, random heteropolymers
-
Plotkin, S. S., J. Wang, and P. G. Wolynes. 1996. Correlated energy landscape model for finite, random heteropolymers. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics. 53:6271-6296.
-
(1996)
Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics
, vol.53
, pp. 6271-6296
-
-
Plotkin, S.S.1
Wang, J.2
Wolynes, P.G.3
-
26
-
-
0007463680
-
Statistical mechanics of a correlated energy landscape model for protein folding funnels
-
Plotkin, S. S., J. Wang, and P. G. Wolynes. 1997. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J. Chem. Phys. 106:2932-2948.
-
(1997)
J. Chem. Phys
, vol.106
, pp. 2932-2948
-
-
Plotkin, S.S.1
Wang, J.2
Wolynes, P.G.3
-
27
-
-
0034687712
-
Associative memory Hamiltonians for structure prediction without homology: α-helical proteins
-
Hardin, C., M. P. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes. 2000. Associative memory Hamiltonians for structure prediction without homology: α-helical proteins. Proc. Natl. Acad. Sci. USA. 97:14235-14240.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 14235-14240
-
-
Hardin, C.1
Eastwood, M.P.2
Luthey-Schulten, Z.3
Wolynes, P.G.4
-
28
-
-
0028963362
-
Toward an outline of the topography of a realistic protein-folding funnel
-
Onuchic, J. N., P. G. Wolynes, Z. Luthey-Schulten, and N. D. Socci. 1995. Toward an outline of the topography of a realistic protein-folding funnel. Proc. Natl. Acad. Sci. USA. 92:3626-3630.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 3626-3630
-
-
Onuchic, J.N.1
Wolynes, P.G.2
Luthey-Schulten, Z.3
Socci, N.D.4
-
29
-
-
0000710672
-
Diffusive dynamics of the reaction coordinate for protein folding funnels
-
Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1996. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104:5860-5868.
-
(1996)
J. Chem. Phys
, vol.104
, pp. 5860-5868
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
30
-
-
0033520751
-
Folding free energy surface of a three-stranded β-sheet protein
-
Bursulaya, B., and C. Brooks. 1999. Folding free energy surface of a three-stranded β-sheet protein. J. Am. Chem. Soc. 121:9947-9951.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 9947-9951
-
-
Bursulaya, B.1
Brooks, C.2
-
31
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
Zhou, R. 2003. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins. 53:148-161.
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.1
-
32
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
MacKerell, A. D., N. Banavali, and N. Foloppe. 2000. Development and current status of the CHARMM force field for nucleic acids. Biopolymers. 56:257-265.
-
(2000)
Biopolymers
, vol.56
, pp. 257-265
-
-
MacKerell, A.D.1
Banavali, N.2
Foloppe, N.3
-
33
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules
-
Kumar, S., J. M. Rosenberg, D. Bouzida, R. H. Swendsen, and P. A. Kollman. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. J. Comput. Chem. 13:1011-1021.
-
(1992)
J. Comput. Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
34
-
-
0033665510
-
BALL - rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library
-
Kohlbacher, O., and H. P. Lenhof. 2000. BALL - rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library. Bioinformatics. 16:815-824.
-
(2000)
Bioinformatics
, vol.16
, pp. 815-824
-
-
Kohlbacher, O.1
Lenhof, H.P.2
-
35
-
-
0002467378
-
Fast parallel algorithms for short-range molecular dynamics
-
Plimpton, S. 1995. Fast parallel algorithms for short-range molecular dynamics. J. Comput. Phys. 117:1-19.
-
(1995)
J. Comput. Phys
, vol.117
, pp. 1-19
-
-
Plimpton, S.1
-
36
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C., R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kal, and K. Schulten. 2005. Scalable molecular dynamics with NAMD. J. Comput. Chem. 26:1781-1802.
-
(2005)
J. Comput. Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kal, L.9
Schulten, K.10
-
38
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward, J. H. 1963. Hierarchical grouping to optimize an objective function. J. Am. Stat. Assoc. 58:236-244.
-
(1963)
J. Am. Stat. Assoc
, vol.58
, pp. 236-244
-
-
Ward, J.H.1
-
39
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou, R. 2003. Trp-cage: folding free energy landscape in explicit water. Proc. Natl. Acad. Sci. USA. 100:13280-13285.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13280-13285
-
-
Zhou, R.1
-
41
-
-
33847776838
-
On the characterization of protein native state ensembles
-
Shehu, A., L. E. Kavraki, and C. Clementi. 2007. On the characterization of protein native state ensembles. Biophys. J. 92:1503-1511.
-
(2007)
Biophys. J
, vol.92
, pp. 1503-1511
-
-
Shehu, A.1
Kavraki, L.E.2
Clementi, C.3
-
42
-
-
34547472077
-
Sampling conformation space to model equilibrium fluctuations in proteins
-
Shenu, A., C. Clementi, and L. E. Kavraki. 2007. Sampling conformation space to model equilibrium fluctuations in proteins. Algorithmica. 48:303-327.
-
(2007)
Algorithmica
, vol.48
, pp. 303-327
-
-
Shenu, A.1
Clementi, C.2
Kavraki, L.E.3
-
43
-
-
35348942279
-
Allosteric communication in dihydrofolate reductase: Signaling network and pathways for closed to occluded transition and back
-
Chen, J., R. I. Dima, and D. Thirumalai. 2007. Allosteric communication in dihydrofolate reductase: signaling network and pathways for closed to occluded transition and back. J. Mol. Biol. 374:250-266.
-
(2007)
J. Mol. Biol
, vol.374
, pp. 250-266
-
-
Chen, J.1
Dima, R.I.2
Thirumalai, D.3
-
44
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar, I., and A. J. Rader. 2005. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15:586-592.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
45
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward, S., and N. Go. 1995. Collective variable description of native protein dynamics. Annu. Rev. Phys. Chem. 46:223-250.
-
(1995)
Annu. Rev. Phys. Chem
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
46
-
-
14844286108
-
Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes
-
Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380.
-
(2005)
Structure
, vol.13
, pp. 373-380
-
-
Ma, J.1
-
47
-
-
32344450229
-
Network and graph analyses of folding free energy surfaces
-
Caflisch, A. 2006. Network and graph analyses of folding free energy surfaces. Curr. Opin. Struct. Biol. 16:71-78.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 71-78
-
-
Caflisch, A.1
-
48
-
-
0034602653
-
Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins
-
Schwille, P., S. Kummer, A. A. Heikal, W. E. Moerner, and W. W. Webb. 2000. Fluorescence correlation spectroscopy reveals fast optical excitation-driven intramolecular dynamics of yellow fluorescent proteins. Proc. Natl. Acad. Sci. USA. 97:151-156.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 151-156
-
-
Schwille, P.1
Kummer, S.2
Heikal, A.A.3
Moerner, W.E.4
Webb, W.W.5
-
49
-
-
0038329308
-
Folding at the speed limit
-
Yang, W. Y., and M. Gruebele. 2003. Folding at the speed limit. Nature. 423:193-197.
-
(2003)
Nature
, vol.423
, pp. 193-197
-
-
Yang, W.Y.1
Gruebele, M.2
-
50
-
-
33744481566
-
Folding of ubiquitin: A simple model describes the strange kinetics
-
Chekmarev, S. F., S. V. Krivov, and M. Karplus. 2006. Folding of ubiquitin: a simple model describes the strange kinetics. J. Phys. Chem. B. 110:8865-8869.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 8865-8869
-
-
Chekmarev, S.F.1
Krivov, S.V.2
Karplus, M.3
-
51
-
-
40649128566
-
An experimental survey of the transition between two-state and downhill protein folding scenarios
-
Liu, F., D. Du, A. A. Fuller, J. E. Davoren, P. Wipf, J. W. Kelly, and M. Gruebele. 2008. An experimental survey of the transition between two-state and downhill protein folding scenarios. Proc. Natl. Acad. Sci. USA. 105:2369-2374.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 2369-2374
-
-
Liu, F.1
Du, D.2
Fuller, A.A.3
Davoren, J.E.4
Wipf, P.5
Kelly, J.W.6
Gruebele, M.7
-
52
-
-
85031351333
-
-
Reference deleted in proof
-
Reference deleted in proof.
-
-
-
-
53
-
-
33750468665
-
Sampling the multiple folding mechanisms of Trp-cage in explicit solvent
-
Juraszek, J., and P. G. Bolhuis. 2006. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent. Proc. Natl. Acad. Sci. USA. 103:15859-15864.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 15859-15864
-
-
Juraszek, J.1
Bolhuis, P.G.2
|