-
1
-
-
0026556882
-
β-Trefoil fold. patterns of structure and sequence in the kunitz inhibitors interleukin-1β and 1α and fibroblast growth factors
-
A.G. Murzin, A.M. Lesk, and C. Chothia β-Trefoil fold. patterns of structure and sequence in the kunitz inhibitors interleukin-1β and 1α and fibroblast growth factors J. Mol. Biol. 223 1992 531 543
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 531-543
-
-
Murzin, A.G.1
Lesk, A.M.2
Chothia, C.3
-
2
-
-
0028348081
-
Principles determining the structure of β-sheet barrels in proteins i. a theoretical analysis
-
A.G. Murzin, A.M. Lesk, and C. Chothia Principles determining the structure of β-sheet barrels in proteins i. A theoretical analysis J. Mol. Biol. 236 1994 1369 1381
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1369-1381
-
-
Murzin, A.G.1
Lesk, A.M.2
Chothia, C.3
-
3
-
-
0028330220
-
Principles determining the structure of β-sheet barrels in proteins ii. the observed structures
-
A.G. Murzin, A.M. Lesk, and C. Chothia Principles determining the structure of β-sheet barrels in proteins ii. The observed structures J. Mol. Biol. 236 1994 1382 1400
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 1382-1400
-
-
Murzin, A.G.1
Lesk, A.M.2
Chothia, C.3
-
4
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
K.W. Plaxco, K.T. Simmons, and D. Baker Contact order, transition state placement and the refolding rates of single domain proteins J. Mol. Biol. 277 1998 985 994
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simmons, K.T.2
Baker, D.3
-
5
-
-
0027190613
-
Kinetics of folding of the all-β sheet protein interleukin-1β
-
P. Varley, H. Christensen, P.T. Wingfield, R.H. Pain, and G.M. Clore Kinetics of folding of the all-β sheet protein interleukin-1β Science 260 1993 1110 1113
-
(1993)
Science
, vol.260
, pp. 1110-1113
-
-
Varley, P.1
Christensen, H.2
Wingfield, P.T.3
Pain, R.H.4
Clore, G.M.5
-
8
-
-
0037126728
-
Interleukin-1β folding between pH 5 and 7: Experimental evidence for three-state folding behavior and robust transition state positions late in folding
-
J.M. Finke, and P.A. Jennings Interleukin-1β folding between pH 5 and 7: experimental evidence for three-state folding behavior and robust transition state positions late in folding Biochemistry 41 2002 15056 15067
-
(2002)
Biochemistry
, vol.41
, pp. 15056-15067
-
-
Finke, J.M.1
Jennings, P.A.2
-
9
-
-
0035799360
-
Thermodynamics and denaturation of hisactophilin, a β-trefoil protein
-
C. Liu, D. Chu, R.D. Wideman, R.S. Houliston, H.J. Wong, and E.M. Meiering Thermodynamics and denaturation of hisactophilin, a β-trefoil protein Biochemistry 40 2001 3817 3827
-
(2001)
Biochemistry
, vol.40
, pp. 3817-3827
-
-
Liu, C.1
Chu, D.2
Wideman, R.D.3
Houliston, R.S.4
Wong, H.J.5
Meiering, E.M.6
-
10
-
-
0036183061
-
Conserved and nonconserved features of the folding pathway of hisactophilin, a β-trefoil protein
-
C. Liu, J.A. Gaspar, H.J. Wong, and E.M. Meiering Conserved and nonconserved features of the folding pathway of hisactophilin, a β-trefoil protein Protein Sci. 11 2002 669 679
-
(2002)
Protein Sci.
, vol.11
, pp. 669-679
-
-
Liu, C.1
Gaspar, J.A.2
Wong, H.J.3
Meiering, E.M.4
-
11
-
-
0023449962
-
Spin-glasses and the statistical-mechanics of protein folding
-
J.D. Bryngelson, and P.G. Wolynes Spin-glasses and the statistical-mechanics of protein folding Proc. Natl Acad. Sci. USA 84 1987 7524 7528
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 7524-7528
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
13
-
-
0034581317
-
The energy landscape of protein folding: Insights into folding mechanisms and scenarios
-
J.N. Onuchic, H. Nymeyer, A.E. Garcia, J. Chahine, and N.D. Socci The energy landscape of protein folding: insights into folding mechanisms and scenarios Advan. Protein Chem. 53 2000 87 152
-
(2000)
Advan. Protein Chem.
, vol.53
, pp. 87-152
-
-
Onuchic, J.N.1
Nymeyer, H.2
Garcia, A.E.3
Chahine, J.4
Socci, N.D.5
-
14
-
-
0343632363
-
Submillisecond kinetics of protein folding
-
W.A. Eaton, V. Munoz, P. Thompson, C.K. Chan, and J. Hofrichter Submillisecond kinetics of protein folding Curr. Opin. Struct. Biol. 7 1997 10 14
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 10-14
-
-
Eaton, W.A.1
Munoz, V.2
Thompson, P.3
Chan, C.K.4
Hofrichter, J.5
-
15
-
-
0031043161
-
Nucleation mechanisms in protein folding
-
A.R. Fersht Nucleation mechanisms in protein folding Curr. Opin. Struct. Biol. 7 1997 3 9
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 3-9
-
-
Fersht, A.R.1
-
16
-
-
0026723063
-
Protein folding funnels: Kinetic pathways through a compact conformation space
-
P.E. Leopold, M. Montal, and J.N. Onuchic Protein folding funnels: kinetic pathways through a compact conformation space Proc. Natl Acad. Sci. USA 89 1992 8721 8725
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 8721-8725
-
-
Leopold, P.E.1
Montal, M.2
Onuchic, J.N.3
-
17
-
-
0037079583
-
Folding funnels: The key to robust protein structure prediction
-
C. Hardin, M.P. Eastwood, M. Prentiss, Z. Luthey-Schulten, and P.G. Wolynes Folding funnels: the key to robust protein structure prediction J. Comput. Chem. 23 2002 138 146
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 138-146
-
-
Hardin, C.1
Eastwood, M.P.2
Prentiss, M.3
Luthey-Schulten, Z.4
Wolynes, P.G.5
-
18
-
-
0034872511
-
Transition states and the meaning of φ-values in protein folding kinetics
-
S.B. Ozkan, I. Bahar, and K.A. Dill Transition states and the meaning of φ-values in protein folding kinetics Nature Struct. Biol. 8 2001 765 769
-
(2001)
Nature Struct. Biol.
, vol.8
, pp. 765-769
-
-
Ozkan, S.B.1
Bahar, I.2
Dill, K.A.3
-
20
-
-
0020972782
-
Theoretical studies of protein folding
-
N. Go Theoretical studies of protein folding Annu. Rev. Biophys. Bioeng. 12 1983 183 210
-
(1983)
Annu. Rev. Biophys. Bioeng.
, vol.12
, pp. 183-210
-
-
Go, N.1
-
21
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and enroute intermediates for protein folding? An investigation for small globular proteins
-
C. Clementi, H. Nymeyer, and J.N. Onuchic Topological and energetic factors: what determines the structural details of the transition state ensemble and enroute intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 2000 937 953
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
22
-
-
0032568599
-
Folding funnels and frustration in off-lattice minimalist protein landscapes
-
H. Nymeyer, A.E. Garcia, and J.N. Onuchic Folding funnels and frustration in off-lattice minimalist protein landscapes Proc. Natl Acad. Sci. USA 95 1998 5921 5928
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 5921-5928
-
-
Nymeyer, H.1
Garcia, A.E.2
Onuchic, J.N.3
-
23
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
-
M.S. Cheung, A.E. García, and J.N. Onuchic Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse Proc. Natl Acad. Sci. USA 99 2002 685 690
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
García, A.E.2
Onuchic, J.N.3
-
24
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a go-like model
-
N. Koga, and S. Takada Roles of native topology and chain-length scaling in protein folding: a simulation study with a go-like model J. Mol. Biol. 313 2001 171 180
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
25
-
-
0037346726
-
The physics and bioinformatics of binding and folding - An energy landscape perspective
-
G.A. Papaoian, and P.G. Wolynes The physics and bioinformatics of binding and folding - an energy landscape perspective Biopolymers 68 2003 333 349
-
(2003)
Biopolymers
, vol.68
, pp. 333-349
-
-
Papaoian, G.A.1
Wolynes, P.G.2
-
27
-
-
0034705115
-
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1β
-
C. Clementi, P.A. Jennings, and J.N. Onuchic How native-state topology affects the folding of dihydrofolate reductase and interleukin-1β Proc. Natl Acad. Sci. USA 97 2000 5871 5876
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5871-5876
-
-
Clementi, C.1
Jennings, P.A.2
Onuchic, J.N.3
-
28
-
-
4243819810
-
New Monte Carlo technique for studying phase transitions
-
A.M. Ferrenberg, and R.H. Swendsen New Monte Carlo technique for studying phase transitions Phys. Rev. Letters 61 1988 2635 2638
-
(1988)
Phys. Rev. Letters
, vol.61
, pp. 2635-2638
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
29
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. i. the method
-
S. Kumar, D. Bouzida, R.H. Swendsen, P.A. Kollman, and J.M. Rosenberg The weighted histogram analysis method for free-energy calculations on biomolecules. i. The method J. Comput. Chem. 13 1992 1011 1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
30
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment b of protein a
-
J.E. Shea, J.N. Onuchic, and C.L. Brooks Exploring the origins of topological frustration: design of a minimally frustrated model of fragment b of protein a Proc. Natl Acad. Sci. USA 96 1999 12512 12517
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks, C.L.3
-
31
-
-
0000007199
-
On the role of conformational geometry in protein folding
-
R. Du, V.S. Pande, A.Y. Grosberg, T. Tanaka, and E. Shakhnovich On the role of conformational geometry in protein folding J. Chem. Phys. 111 1999 10375 10380
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 10375-10380
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.5
-
32
-
-
0033117927
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
D. Thirumalai, and D.K. Klimov Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models Curr. Opin. Struct. Biol. 9 1999 197 207
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 197-207
-
-
Thirumalai, D.1
Klimov, D.K.2
-
33
-
-
0036785556
-
The origins of asymmetry in the folding transition states of protein l and protein g
-
J. Karanicolas, and C.L. Brooks 3rd The origins of asymmetry in the folding transition states of protein l and protein g Protein Sci. 11 2002 2351 2361
-
(2002)
Protein Sci.
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
34
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein l
-
C. Clementi, A.E. García, and J.N. Onuchic Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein l J. Mol. Biol. 326 2003 933 954
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 933-954
-
-
Clementi, C.1
García, A.E.2
Onuchic, J.N.3
-
36
-
-
0034691247
-
Inhibiting protein-protein interactions: A model for antagonist design
-
B.A. Chrunyk, M.H. Rosner, Y. Cong, A.S. McColl, I.G. Otterness, and G.O. Daumy Inhibiting protein-protein interactions: a model for antagonist design Biochemistry 39 2000 7092 7099
-
(2000)
Biochemistry
, vol.39
, pp. 7092-7099
-
-
Chrunyk, B.A.1
Rosner, M.H.2
Cong, Y.3
McColl, A.S.4
Otterness, I.G.5
Daumy, G.O.6
-
37
-
-
0344196965
-
The interleukin-1 receptor: Ligand interactions and signal transduction
-
B.A. Chrunyk, M.H. Rosner, Y. Cong, A.S. McColl, I.G. Otterness, and G.O. Daumy The interleukin-1 receptor: ligand interactions and signal transduction Cytokine Growth Factor Rev. 9 1998 221 237
-
(1998)
Cytokine Growth Factor Rev.
, vol.9
, pp. 221-237
-
-
Chrunyk, B.A.1
Rosner, M.H.2
Cong, Y.3
McColl, A.S.4
Otterness, I.G.5
Daumy, G.O.6
-
38
-
-
0034612228
-
Investigation of routes and funnels in protein folding by free energy functional methods
-
S.S. Plotkin, and J.N. Onuchic Investigation of routes and funnels in protein folding by free energy functional methods Proc. Natl Acad. Sci. USA 97 2000 6509 6514
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 6509-6514
-
-
Plotkin, S.S.1
Onuchic, J.N.2
-
39
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
L.L. Chavez, J.N. Onuchic, and C. Clementi Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates J. Am. Chem. Soc. 126 2004 8426 8432
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
40
-
-
0033607790
-
Folding kinetics of the all-beta-sheet protein human basic fibroblast growth factor, a structural homolog of interleukin-1β
-
D. Estape, and U. Rinas Folding kinetics of the all-beta-sheet protein human basic fibroblast growth factor, a structural homolog of interleukin-1β J. Biol. Chem. 274 1999 34083 34088
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 34083-34088
-
-
Estape, D.1
Rinas, U.2
-
41
-
-
0037033066
-
Characterization of the structure and dynamics of a near-native equilibrium intermediate in the unfolding pathway of an all β-barrel protein
-
T. Srimathi, T.K.S. Kumar, Y.H. Chi, I.M. Chiu, and C. Yu Characterization of the structure and dynamics of a near-native equilibrium intermediate in the unfolding pathway of an all β-barrel protein J. Biol. Chem. 277 2002 47507 47516
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 47507-47516
-
-
Srimathi, T.1
Kumar, T.K.S.2
Chi, Y.H.3
Chiu, I.M.4
Yu, C.5
-
42
-
-
0033012341
-
Reversible thermal denaturation of human fgf-1 induced by low concentrations of guanidine hydrochloride
-
S.I. Blaber, J.F. Culajay, A. Khurana, and M. Blaber Reversible thermal denaturation of human fgf-1 induced by low concentrations of guanidine hydrochloride Biophys. J. 77 1999 470 477
-
(1999)
Biophys. J.
, vol.77
, pp. 470-477
-
-
Blaber, S.I.1
Culajay, J.F.2
Khurana, A.3
Blaber, M.4
-
43
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
A. Mitsutake, Y. Sugita, and Y. Okamoto Generalized-ensemble algorithms for molecular simulations of biopolymers Biopolymers 60 2001 96 123
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
44
-
-
16244417212
-
The native energy landscape for interleukin-1β. Modulation of the population ensemble through native-state topology
-
M. Roy, L.L. Chavez, J.M. Finke, D.K. Heidary, J.N. Onuchic, and P.A. Jennings The native energy landscape for interleukin-1β. Modulation of the population ensemble through native-state topology J. Mol. Biol. 348 2005 335 347
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 335-347
-
-
Roy, M.1
Chavez, L.L.2
Finke, J.M.3
Heidary, D.K.4
Onuchic, J.N.5
Jennings, P.A.6
-
46
-
-
0038329308
-
Folding at the speed limit
-
W.Y. Yang, and M. Gruebele Folding at the speed limit Nature 423 2003 193 197
-
(2003)
Nature
, vol.423
, pp. 193-197
-
-
Yang, W.Y.1
Gruebele, M.2
-
47
-
-
0028774340
-
Stability and function: Two constraints in the evolution of barstar and other proteins
-
G. Schreiber, A.M. Buckle, and A.R. Fersht Stability and function: two constraints in the evolution of barstar and other proteins Structure 2 1994 945 951
-
(1994)
Structure
, vol.2
, pp. 945-951
-
-
Schreiber, G.1
Buckle, A.M.2
Fersht, A.R.3
-
49
-
-
0029760018
-
Binding of hisactophilin i and ii to lipid membranes is controlled by a ph-dependent myristoyl-histidine switch
-
F. Hanakam, G. Gerisch, S. Lotz, T. Alt, and A. Seelig Binding of hisactophilin i and ii to lipid membranes is controlled by a ph-dependent myristoyl-histidine switch Biochemistry 35 1996 11036 11044
-
(1996)
Biochemistry
, vol.35
, pp. 11036-11044
-
-
Hanakam, F.1
Gerisch, G.2
Lotz, S.3
Alt, T.4
Seelig, A.5
-
50
-
-
0026478716
-
Structure of hisactophilin is similar to interleukin-1β and fibroblast growth factor
-
J. Habazettl, D. Gondol, R. Wiltscheck, J. Otlewski, M. Schleicher, and T.A. Holak Structure of hisactophilin is similar to interleukin-1β and fibroblast growth factor Nature 359 1992 855 858
-
(1992)
Nature
, vol.359
, pp. 855-858
-
-
Habazettl, J.1
Gondol, D.2
Wiltscheck, R.3
Otlewski, J.4
Schleicher, M.5
Holak, T.A.6
-
51
-
-
0028936379
-
The pH-sensitive actin-binding protein hisactophilin of dictyostelium exists in 2 isoforms which both are myristoylated and distributed between plasma-membrane and cytoplasm
-
F. Hanakam, C. Eckerskorn, F. Lottspeich, A. Muller-Taubenberger, and G. Gerisch The pH-sensitive actin-binding protein hisactophilin of dictyostelium exists in 2 isoforms which both are myristoylated and distributed between plasma-membrane and cytoplasm J. Biol. Chem. 270 1995 596 602
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 596-602
-
-
Hanakam, F.1
Eckerskorn, C.2
Lottspeich, F.3
Muller-Taubenberger, A.4
Gerisch, G.5
-
53
-
-
0031733974
-
Diversity does make a difference: Fibroblast growth factor-heparin interactions
-
S. Faham, R.J. Linhardt, and D.C. Rees Diversity does make a difference: fibroblast growth factor-heparin interactions Curr. Opin. Struct. Biol. 8 1998 578 586
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 578-586
-
-
Faham, S.1
Linhardt, R.J.2
Rees, D.C.3
-
54
-
-
13044272912
-
Automated analysis of interatomic contacts in proteins
-
V. Sobolev, A. Sorokine, J. Prilusky, E.E. Abola, and M. Edelman Automated analysis of interatomic contacts in proteins Bioinformatics 15 1999 327 332
-
(1999)
Bioinformatics
, vol.15
, pp. 327-332
-
-
Sobolev, V.1
Sorokine, A.2
Prilusky, J.3
Abola, E.E.4
Edelman, M.5
-
55
-
-
0029633186
-
DeBolt, Amber, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules
-
D.A. Pearlman, D.A. Case, J.W. Caldwell, W.R. Ross, I. Cheatham, and T.E. S DeBolt, Amber, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules Comput. Phys. Commun. 91 1995 1 41
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.R.4
Cheatham, I.5
-
56
-
-
0038487248
-
Multicanonical simulations step by step
-
B.A. Berg Multicanonical simulations step by step Comput. Phys. Commun. 153 2003 397 406
-
(2003)
Comput. Phys. Commun.
, vol.153
, pp. 397-406
-
-
Berg, B.A.1
|