-
1
-
-
36749023459
-
Mutations as trapdoors to two competing native conformations of the Rop-dimer
-
Schug A, Whitford PC, Levy Y, Onuchic JN (2007) Mutations as trapdoors to two competing native conformations of the Rop-dimer. Proc Natl Acad Sci USA 104:17674-17679.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 17674-17679
-
-
Schug, A.1
Whitford, P.C.2
Levy, Y.3
Onuchic, J.N.4
-
2
-
-
32344447726
-
Promiscuous vs. native protein function. Insights from studying collective motions in proteins with elastic network models
-
and references therein
-
Kloczkowski A, Sen TZ, Jernigan RL (2005) Promiscuous vs. native protein function. Insights from studying collective motions in proteins with elastic network models. J Biomol Struct Dyn 22:621-624 and references therein.
-
(2005)
J Biomol Struct Dyn
, vol.22
, pp. 621-624
-
-
Kloczkowski, A.1
Sen, T.Z.2
Jernigan, R.L.3
-
3
-
-
33746607765
-
Single-molecule dynamics reveals cooperative binding-folding in protein recognition
-
Wang J, Lu Q, Lu HP (2006) Single-molecule dynamics reveals cooperative binding-folding in protein recognition. PLoS Comp Biol 2:e78-842.
-
(2006)
PLoS Comp Biol
, vol.2
-
-
Wang, J.1
Lu, Q.2
Lu, H.P.3
-
4
-
-
0033056708
-
Folding funnels, binding funnels, and protein function
-
Tsai CJ, Kumar S, Ma B, Nussinov R (1999) Folding funnels, binding funnels, and protein function. Protein Sci 8:1181-1190.
-
(1999)
Protein Sci
, vol.8
, pp. 1181-1190
-
-
Tsai, C.J.1
Kumar, S.2
Ma, B.3
Nussinov, R.4
-
5
-
-
0026320866
-
The energy landscapes and motions of proteins
-
Frauenfelder H, Sligar SG, Wolynes PG (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
-
6
-
-
8644263303
-
Coupling of functioning and folding: Photoactive yellow protein as an example system
-
Itoh K, Sasai M (2004) Coupling of functioning and folding: Photoactive yellow protein as an example system. Chem Phys 307:121-127.
-
(2004)
Chem Phys
, vol.307
, pp. 121-127
-
-
Itoh, K.1
Sasai, M.2
-
7
-
-
0038786579
-
Cooperative omega loops in cytochrome c: Role in folding and function
-
Krishna MMG, Lin Y, Rumbley JN, Englander SW (2003) Cooperative omega loops in cytochrome c: Role in folding and function. J Mol Biol 331:29-36.
-
(2003)
J Mol Biol
, vol.331
, pp. 29-36
-
-
Krishna, M.M.G.1
Lin, Y.2
Rumbley, J.N.3
Englander, S.W.4
-
8
-
-
0034697986
-
What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis
-
Abkevich VI, Shakhnovich EI (2000) What can disulfide bonds tell us about protein energetics, function and folding: Simulations and bioinformatics analysis. J Mol Biol 300:975-985.
-
(2000)
J Mol Biol
, vol.300
, pp. 975-985
-
-
Abkevich, V.I.1
Shakhnovich, E.I.2
-
9
-
-
34447092609
-
Spackling the crack: Stabilizing human fibroblast growth factor-1 by targeting the N and C terminus β-strand interactions
-
Dubey VK, Jihun Lee J, Somasundaram T, Blaber S, Blaber M (2007) Spackling the crack: Stabilizing human fibroblast growth factor-1 by targeting the N and C terminus β-strand interactions. J Mol Biol 371:256-268.
-
(2007)
J Mol Biol
, vol.371
, pp. 256-268
-
-
Dubey, V.K.1
Jihun Lee, J.2
Somasundaram, T.3
Blaber, S.4
Blaber, M.5
-
10
-
-
0032901422
-
Solution structure and dynamics of a serpin reactive site loop using interleukin-1β as a presentation scaffold
-
Arico-Muendel CC, Patera A, Pochapsky TC, Kuti M, Wolfson AJ (1999) Solution structure and dynamics of a serpin reactive site loop using interleukin-1β as a presentation scaffold. Prot Eng 12:189-202.
-
(1999)
Prot Eng
, vol.12
, pp. 189-202
-
-
Arico-Muendel, C.C.1
Patera, A.2
Pochapsky, T.C.3
Kuti, M.4
Wolfson, A.J.5
-
12
-
-
0028774340
-
Stability and function: Two constraints in the evolution of barstar and other proteins
-
Schreiber G, Buckle AM, Fersht AR (1994) Stability and function: Two constraints in the evolution of barstar and other proteins. Structure (London) 2:945-951.
-
(1994)
Structure (London)
, vol.2
, pp. 945-951
-
-
Schreiber, G.1
Buckle, A.M.2
Fersht, A.R.3
-
13
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT, Baker D (1998) Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 277:985-994.
-
(1998)
J Mol Biol
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
14
-
-
25644452032
-
Evolutionary information for specifying a protein fold
-
Socolich M, et al. (2005) Evolutionary information for specifying a protein fold. Nature 437:512-518.
-
(2005)
Nature
, vol.437
, pp. 512-518
-
-
Socolich, M.1
-
15
-
-
25644442464
-
Natural-like function in artificial WW domains
-
Russ W, Lowery DM, Mishra P, Yaffe MB, Ranganathan R (2005) Natural-like function in artificial WW domains. Nature 437:579-583.
-
(2005)
Nature
, vol.437
, pp. 579-583
-
-
Russ, W.1
Lowery, D.M.2
Mishra, P.3
Yaffe, M.B.4
Ranganathan, R.5
-
16
-
-
1542723482
-
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
-
Karanicolas J, Brooks III CL (2004) Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain. Proc Natl Acad Sci USA 101:3432-3437.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 3432-3437
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
17
-
-
23944522022
-
Fast protein folding: Evolution meets physics
-
Gruebele M (2005) Fast protein folding: Evolution meets physics. C R Biol 328:701-712.
-
(2005)
C R Biol
, vol.328
, pp. 701-712
-
-
Gruebele, M.1
-
18
-
-
33746042979
-
Structure-function-folding relationship in a WW domain
-
Jäger M, et al. (2006) Structure-function-folding relationship in a WW domain. Proc Natl Acad Sci USA 103:10648-10653.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 10648-10653
-
-
Jäger, M.1
-
20
-
-
18644374105
-
Blocking IL-1 in systemic inflammation
-
Dinarello CA (2005) Blocking IL-1 in systemic inflammation. J Exp Med 201:1355-1359.
-
(2005)
J Exp Med
, vol.201
, pp. 1355-1359
-
-
Dinarello, C.A.1
-
21
-
-
0030998098
-
Crystal structure of type-I interleukin-1 receptor complexed with interleukin-1β
-
Vigers GPA, Anderson LJ, Caffes P, Brandhuber BJ (1997) Crystal structure of type-I interleukin-1 receptor complexed with interleukin-1β. Nature 386:190-194.
-
(1997)
Nature
, vol.386
, pp. 190-194
-
-
Vigers, G.P.A.1
Anderson, L.J.2
Caffes, P.3
Brandhuber, B.J.4
-
22
-
-
0031000052
-
A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist
-
Schreuder H, et al. (1997) A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist. Nature 386:194-200.
-
(1997)
Nature
, vol.386
, pp. 194-200
-
-
Schreuder, H.1
-
23
-
-
34147140748
-
Biophysical characterization of structural properties and folding of interleukin-1 receptor antagonist
-
Latypov RF, et al. (2007) Biophysical characterization of structural properties and folding of interleukin-1 receptor antagonist. J Mol Biol 368:1187-1201.
-
(2007)
J Mol Biol
, vol.368
, pp. 1187-1201
-
-
Latypov, R.F.1
-
25
-
-
0026556882
-
β-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukin-1β and 1α and fibroblast growth factors
-
Murzin AG, Lesk AM, Chothia C (1992) β-Trefoil fold. Patterns of structure and sequence in the Kunitz inhibitors interleukin-1β and 1α and fibroblast growth factors. J Mol Biol 223:531-543.
-
(1992)
J Mol Biol
, vol.223
, pp. 531-543
-
-
Murzin, A.G.1
Lesk, A.M.2
Chothia, C.3
-
26
-
-
33745931359
-
In the energy landscape of the β-trefoil family, multiple routes lead to the folded state
-
Chavez LL, Gosavi S, Jennings PA, Onuchic JN (2006) In the energy landscape of the β-trefoil family, multiple routes lead to the folded state. Proc Natl Acad Sci USA 103:10254-10258.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 10254-10258
-
-
Chavez, L.L.1
Gosavi, S.2
Jennings, P.A.3
Onuchic, J.N.4
-
28
-
-
0030772992
-
Evidence for an obligatory intermediate in the folding of interleukin-1β
-
Heidary DK, Gross LA, Roy M, Jennings PA (1997) Evidence for an obligatory intermediate in the folding of interleukin-1β. Nat Struct Biol 4:1-583.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 1-583
-
-
Heidary, D.K.1
Gross, L.A.2
Roy, M.3
Jennings, P.A.4
-
30
-
-
0344196965
-
The interleukin-1 receptor: Ligand interactions and signal transduction
-
Auron PE (1998) The interleukin-1 receptor: Ligand interactions and signal transduction. Cytokine Growth Factor Rev 9:221-237.
-
(1998)
Cytokine Growth Factor Rev
, vol.9
, pp. 221-237
-
-
Auron, P.E.1
-
31
-
-
9944262882
-
Analysis of fish IL-1β and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: Implications for pharmacological design
-
Koussounadis AI, Ritchie DW, Kemp GJL, Secombes CJ (2004) Analysis of fish IL-1β and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: Implications for pharmacological design. Curr Pharm Des 10:3857-3871.
-
(2004)
Curr Pharm Des
, vol.10
, pp. 3857-3871
-
-
Koussounadis, A.I.1
Ritchie, D.W.2
Kemp, G.J.L.3
Secombes, C.J.4
-
32
-
-
0026743174
-
Multiple protein sequence alignment from tertiary structure comparison
-
Russell RB, Barton GJ (1992) Multiple protein sequence alignment from tertiary structure comparison. Proteins Struct Funct Genet 14:309-323.
-
(1992)
Proteins Struct Funct Genet
, vol.14
, pp. 309-323
-
-
Russell, R.B.1
Barton, G.J.2
-
35
-
-
13044272912
-
Automated analysis of interatomic contacts in proteins
-
Sobolev V, Sorokine A, Prilusky J, Abola EE, Edelman M (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics 15:327-332.
-
(1999)
Bioinformatics
, vol.15
, pp. 327-332
-
-
Sobolev, V.1
Sorokine, A.2
Prilusky, J.3
Abola, E.E.4
Edelman, M.5
-
36
-
-
17744402452
-
Insertion of a structural domain of interleukin (IL)-1β confers agonist activity to the IL-1 receptor antagonist
-
Greenfeder SA, et al. (1995) Insertion of a structural domain of interleukin (IL)-1β confers agonist activity to the IL-1 receptor antagonist. J Biol Chem 270:22460-22466.
-
(1995)
J Biol Chem
, vol.270
, pp. 22460-22466
-
-
Greenfeder, S.A.1
-
37
-
-
0025890012
-
TConversion of the interleukin-1 receptor antagonist into an agonist by site-specific mutagenesis
-
Ju G, et al. (1991) TConversion of the interleukin-1 receptor antagonist into an agonist by site-specific mutagenesis. Proc Natl Acad Sci USA 88:2658-2662.
-
(1991)
Proc Natl Acad Sci USA
, vol.88
, pp. 2658-2662
-
-
Ju, G.1
-
38
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
Clementi C, Nymeyer H, Onuchic JN (2000) Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 298:937-953.
-
(2000)
J Mol Biol
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
39
-
-
0141431057
-
High-resolution structure of murine interleukin 1 homologue IL-1F5 reveals unique loop conformations for receptor binding specificity
-
Dunn EF, et al. (2003) High-resolution structure of murine interleukin 1 homologue IL-1F5 reveals unique loop conformations for receptor binding specificity. Biochemistry 42:10938-10944.
-
(2003)
Biochemistry
, vol.42
, pp. 10938-10944
-
-
Dunn, E.F.1
-
40
-
-
0242407130
-
The structure and binding mode of interleukin-18
-
Kato Z, et al. (2003) The structure and binding mode of interleukin-18. Nat Struct Biol 10:966-971.
-
(2003)
Nat Struct Biol
, vol.10
, pp. 966-971
-
-
Kato, Z.1
-
41
-
-
0033117927
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
Thirumalai D, Klimov DK (1999) Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Op Struct Biol 9:197-207.
-
(1999)
Curr Op Struct Biol
, vol.9
, pp. 197-207
-
-
Thirumalai, D.1
Klimov, D.K.2
-
42
-
-
0034581317
-
The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
-
Onuchic JN, Nymeyer H, Garcia AE, Chahine J, Socci ND (2000) The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios. Adv Prot Chem 53:87-152.
-
(2000)
Adv Prot Chem
, vol.53
, pp. 87-152
-
-
Onuchic, J.N.1
Nymeyer, H.2
Garcia, A.E.3
Chahine, J.4
Socci, N.D.5
-
43
-
-
0032993447
-
Polymer principles and protein folding
-
Dill KA (1999) Polymer principles and protein folding. Prot Sci 8:1166-1180.
-
(1999)
Prot Sci
, vol.8
, pp. 1166-1180
-
-
Dill, K.A.1
-
46
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
-
Shea JE, Onuchic JN, Brooks CL (1999) Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci USA 96:12512-12517.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks, C.L.3
-
47
-
-
33846916730
-
Malleability of protein folding pathways: A simple reason for complex behaviour
-
Lindberg MO, Oliveberg M (2007) Malleability of protein folding pathways: a simple reason for complex behaviour. Curr Op Struct Biol 17:21-29.
-
(2007)
Curr Op Struct Biol
, vol.17
, pp. 21-29
-
-
Lindberg, M.O.1
Oliveberg, M.2
-
48
-
-
0035782687
-
What can structural classifications reveal about protein evolution?
-
Orengo CA, Sillitoe I, Reeves G, Pearl FMG (2001) What can structural classifications reveal about protein evolution? J Struct Biol 134:145-165.
-
(2001)
J Struct Biol
, vol.134
, pp. 145-165
-
-
Orengo, C.A.1
Sillitoe, I.2
Reeves, G.3
Pearl, F.M.G.4
-
49
-
-
34548057017
-
Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins
-
Watson E, Matousek WM, Irimies EL, Alexandrescu AT (2007) Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 46:9484-9494.
-
(2007)
Biochemistry
, vol.46
, pp. 9484-9494
-
-
Watson, E.1
Matousek, W.M.2
Irimies, E.L.3
Alexandrescu, A.T.4
-
50
-
-
0029633186
-
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
-
Pearlman DA, et al. (1995) 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 Comm 91:1-41.
-
(1995)
Comput Phys Comm
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
-
51
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar S, Bouzida D, Swendsen RH, Kollman PA, Rosenberg JM (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J Comp Chem 13:1011-1021.
-
(1992)
J Comp Chem
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
|