-
1
-
-
0347357617
-
Protein folding and misfolding
-
Dobson CM (2003) Protein folding and misfolding. Nature 426: 884-890.
-
(2003)
Nature
, vol.426
, pp. 884-890
-
-
Dobson, C.M.1
-
2
-
-
0034604105
-
A surprising simplicity to protein folding
-
Baker D (2000) A surprising simplicity to protein folding. Nature 405: 39-42.
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
3
-
-
0035997388
-
Mechanisms of fast protein folding
-
Myers JK, Oas TG (2002) Mechanisms of fast protein folding. Annu Rev Biochem 71: 783-815.
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 783-815
-
-
Myers, J.K.1
Oas, T.G.2
-
4
-
-
0037686252
-
The present view of the mechanism of protein folding
-
Daggett V, Fersht AR (2003) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4: 497-502.
-
(2003)
Nat Rev Mol Cell Biol
, vol.4
, pp. 497-502
-
-
Daggett, V.1
Fersht, A.R.2
-
6
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein-folding: A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG (1995) Funnels, pathways, and the energy landscape of protein-folding: A synthesis. Proteins Struct Funct Genet 21: 167-195.
-
(1995)
Proteins Struct Funct Genet
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
7
-
-
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
-
8
-
-
0242299187
-
Predictions without templates: New folds, secondary structure and contacts in CASP5
-
Aloy P, Stark A, Hadley C, Russell RB (2003) Predictions without templates: New folds, secondary structure and contacts in CASP5. Proteins Struct Funct Genet 53: 436-456.
-
(2003)
Proteins Struct Funct Genet
, vol.53
, pp. 436-456
-
-
Aloy, P.1
Stark, A.2
Hadley, C.3
Russell, R.B.4
-
9
-
-
0034924812
-
Folding of newly translated proteins in vivo: The role of molecular chaperones
-
Frydman J (2001) Folding of newly translated proteins in vivo: The role of molecular chaperones. Annu Rev Biochem 70: 603-647.
-
(2001)
Annu Rev Biochem
, vol.70
, pp. 603-647
-
-
Frydman, J.1
-
11
-
-
11444271010
-
Chaperone-assisted folding of newly synthesized proteins in the cytosol
-
Deuerling E, Bukau B (2005) Chaperone-assisted folding of newly synthesized proteins in the cytosol. Crit Rev Biochem Mol Biol 39: 261-277.
-
(2005)
Crit Rev Biochem Mol Biol
, vol.39
, pp. 261-277
-
-
Deuerling, E.1
Bukau, B.2
-
12
-
-
0030844281
-
Recombination of protein domains facilitated by co-translational folding in eukaryotes
-
Netzer WJ, Hartl F-U (1997) Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 388: 343-349.
-
(1997)
Nature
, vol.388
, pp. 343-349
-
-
Netzer, W.J.1
Hartl, F.-U.2
-
13
-
-
0035404969
-
Cotranslational protein folding
-
Kolb VA (2001) Cotranslational protein folding. Mol Biol 35: 584-590.
-
(2001)
Mol Biol
, vol.35
, pp. 584-590
-
-
Kolb, V.A.1
-
15
-
-
4644285228
-
Protein folding in the cell: Reshaping the folding funnel
-
Clark PL (2004) Protein folding in the cell: Reshaping the folding funnel. Trends Biochem Sci 29: 527-534.
-
(2004)
Trends Biochem Sci
, vol.29
, pp. 527-534
-
-
Clark, P.L.1
-
16
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276: 10577-10580.
-
(2001)
J Biol Chem
, vol.276
, pp. 10577-10580
-
-
Minton, A.P.1
-
17
-
-
0035478585
-
Macromolecular crowding: Obvious but underappreciated
-
Ellis RJ (2001) Macromolecular crowding: Obvious but underappreciated. Trends Biochem Sci 26: 597-604.
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 597-604
-
-
Ellis, R.J.1
-
18
-
-
0041931122
-
Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges
-
Hall D, Minton AP (2003) Macromolecular crowding: Qualitative and semiquantitative successes, quantitative challenges. Biochim Biophys Acta (Prot Proteom) 1649: 127-139.
-
(2003)
Biochim Biophys Acta (Prot Proteom)
, vol.1649
, pp. 127-139
-
-
Hall, D.1
Minton, A.P.2
-
19
-
-
0141482088
-
How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations
-
USA
-
Takagi F, Koga N, Takada S (2003) How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations. Proc Natl Acad Sci USA 100: 11367-11372.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 11367-11372
-
-
Takagi, F.1
Koga, N.2
Takada, S.3
-
20
-
-
4444330162
-
Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: Creation of an alternate fast folding pathway
-
USA
-
Jewett AI, Baumketner A, Shea JE (2004) Accelerated folding in the weak hydrophobic environment of a chaperonin cavity: Creation of an alternate fast folding pathway. Proc Natl Acad Sci USA 101: 13192-13197.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 13192-13197
-
-
Jewett, A.I.1
Baumketner, A.2
Shea, J.E.3
-
21
-
-
0035949430
-
Stabilization of proteins in confined spaces
-
Zhou HX, Dill KA (2001) Stabilization of proteins in confined spaces. Biochemistry 40: 11289-11293.
-
(2001)
Biochemistry
, vol.40
, pp. 11289-11293
-
-
Zhou, H.X.1
Dill, K.A.2
-
22
-
-
30044447928
-
Ribosome exit tunnel can entropically stabilize α-helices
-
USA
-
Ziv G, Haran G, Thirumalai D (2005) Ribosome exit tunnel can entropically stabilize α-helices. Proc Natl Acad Sci USA 102: 18956-18961.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 18956-18961
-
-
Ziv, G.1
Haran, G.2
Thirumalai, D.3
-
23
-
-
0037418340
-
Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage
-
USA
-
Elcock AH (2003) Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage. Proc Natl Acad Sci USA 100: 2340-2344.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 2340-2344
-
-
Elcock, A.H.1
-
24
-
-
16344364032
-
Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited
-
Minton AP (2005) Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: Macromolecular crowding and protein stability revisited. Biophys J 88: 971-985.
-
(2005)
Biophys J
, vol.88
, pp. 971-985
-
-
Minton, A.P.1
-
25
-
-
16344389134
-
Molecular crowding enhances native state stability and refolding rates of globular proteins
-
USA
-
Cheung MS, Klimov D, Thirumalai D (2005) Molecular crowding enhances native state stability and refolding rates of globular proteins. Proc Natl Acad Sci USA 102: 4753-4758.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 4753-4758
-
-
Cheung, M.S.1
Klimov, D.2
Thirumalai, D.3
-
26
-
-
84961341319
-
Simple folding model for HP lattice proteins
-
Hofestaedt R, Lengauer T, Loeffler T, Schomburg D, editors. Berlin: Springer
-
Bornberg-Bauer E (1997) Simple folding model for HP lattice proteins. In: Hofestaedt R, Lengauer T, Loeffler T, Schomburg D, editors. German conference on bioinformatics: Selected papers. Volume 1278, Lecture notes in computer science. Berlin: Springer. pp 125-136.
-
(1997)
German Conference on Bioinformatics: Selected Papers. Volume 1278, Lecture Notes in Computer Science
, vol.1278
, pp. 125-136
-
-
Bornberg-Bauer, E.1
-
27
-
-
0345862088
-
The role of cotranslation in protein folding: A lattice model study
-
Morrissey MP, Ahmed Z, Shakhnovich EI (2004) The role of cotranslation in protein folding: A lattice model study. Polymer 45: 557-571.
-
(2004)
Polymer
, vol.45
, pp. 557-571
-
-
Morrissey, M.P.1
Ahmed, Z.2
Shakhnovich, E.I.3
-
28
-
-
0020972782
-
Theoretical studies of protein folding
-
Gō N (1983) Theoretical studies of protein folding. Annu Rev Biophys Bioeng 12: 183-210.
-
(1983)
Annu Rev Biophys Bioeng
, vol.12
, pp. 183-210
-
-
Go, N.1
-
29
-
-
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
-
30
-
-
0035850732
-
Role of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model
-
Koga N, Takada S (2001) Role of native topology and chain-length scaling in protein folding: A simulation study with a Go-like model. J Mol Biol 313: 171-180.
-
(2001)
J Mol Biol
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
31
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
Chavez LL, Onuchic JN, Clementi C (2004) Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates. J Am Chem Soc 126: 8426-8432.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
32
-
-
26844543506
-
Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment
-
USA
-
Das P, Wilson CJ, Fossati G, Wittung-Stafshede P, Matthews KS, et al. (2005) Characterization of the folding landscape of monomeric lactose repressor: Quantitative comparison of theory and experiment. Proc Natl Acad Sci USA 102: 14569-14574.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 14569-14574
-
-
Das, P.1
Wilson, C.J.2
Fossati, G.3
Wittung-Stafshede, P.4
Matthews, K.S.5
-
33
-
-
0029053552
-
Folding of a nascent polypeptide chain in vitro: Cooperative formation of structure in a protein module
-
USA
-
de Prat Gay G, Ruiz-Sanz J, Neira JL, Itzhaki LS, Fersht AR (1995) Folding of a nascent polypeptide chain in vitro: Cooperative formation of structure in a protein module. Proc Natl Acad Sci USA 92: 3683-3686.
-
(1995)
Proc Natl Acad Sci
, vol.92
, pp. 3683-3686
-
-
De Prat Gay, G.1
Ruiz-Sanz, J.2
Neira, J.L.3
Itzhaki, L.S.4
Fersht, A.R.5
-
34
-
-
0029558960
-
Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its N-terminus in vitro. Parallels with the protein folding pathway
-
de Prat Gay G, Ruiz-Sanz J, Neira JL, Corrales FJ, Otzen DE, et al. (1995) Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its N-terminus in vitro. Parallels with the protein folding pathway. J Mol Biol 254: 968-979.
-
(1995)
J Mol Biol
, vol.254
, pp. 968-979
-
-
De Prat Gay, G.1
Ruiz-Sanz, J.2
Neira, J.L.3
Corrales, F.J.4
Otzen, D.E.5
-
35
-
-
0031585993
-
Following co-operative formation of secondary and tertiary structure in a single protein module
-
Neira JL, Itzhaki LS, Ladurner AG, Davis B, de Prat Gay G, et al. (1997) Following co-operative formation of secondary and tertiary structure in a single protein module. J Mol Biol 268: 185-197.
-
(1997)
J Mol Biol
, vol.268
, pp. 185-197
-
-
Neira, J.L.1
Itzhaki, L.S.2
Ladurner, A.G.3
Davis, B.4
De Prat Gay, G.5
-
36
-
-
0033593272
-
Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments
-
Neira JL, Fersht AR (1999) Exploring the folding funnel of a polypeptide chain by biophysical studies on protein fragments. J Mol Biol 285: 1309-1333.
-
(1999)
J Mol Biol
, vol.285
, pp. 1309-1333
-
-
Neira, J.L.1
Fersht, A.R.2
-
37
-
-
0033605823
-
Acquisition of native-like interactions in C-terminal fragments of barnase
-
Neira JL, Fersht AR (1999) Acquisition of native-like interactions in C-terminal fragments of barnase. J Mol Biol 287: 421-432.
-
(1999)
J Mol Biol
, vol.287
, pp. 421-432
-
-
Neira, J.L.1
Fersht, A.R.2
-
38
-
-
33746623274
-
Folding and misfolding as a function of polypeptide chain elongation: Conformational trends and implications for intracellular events
-
Tsai AM, Murphy RM, editors. New York: Springer
-
Cavagnero S, Kurt N (2006) Folding and misfolding as a function of polypeptide chain elongation: Conformational trends and implications for intracellular events. In: Tsai AM, Murphy RM, editors. Misbehaving proteins: Protein (mis)folding, aggregation, and stability. New York: Springer. pp. 217-246.
-
(2006)
Misbehaving Proteins: Protein (Mis)folding, Aggregation, and Stability
, pp. 217-246
-
-
Cavagnero, S.1
Kurt, N.2
-
39
-
-
0026345750
-
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
-
Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30: 10428-10435.
-
(1991)
Biochemistry
, vol.30
, pp. 10428-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
40
-
-
0026553768
-
The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability
-
Serrano L, Kellis JT Jr, Cann P, Matouschek A, Fersht AR (1992) The folding of an enzyme. II. Substructure of barnase and the contribution of different interactions to protein stability. J Mol Biol 224: 783-804.
-
(1992)
J Mol Biol
, vol.224
, pp. 783-804
-
-
Serrano, L.1
Kellis Jr., J.T.2
Cann, P.3
Matouschek, A.4
Fersht, A.R.5
-
41
-
-
0032519376
-
The path of the growing peptide chain through the 23S rRNA in the 50S ribosomal subunit; a comparative cross-linking study with three different peptide families
-
Choi KM, Brimacombe R (1998) The path of the growing peptide chain through the 23S rRNA in the 50S ribosomal subunit; a comparative cross-linking study with three different peptide families. Nucleic Acids Res 26: 887-895.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 887-895
-
-
Choi, K.M.1
Brimacombe, R.2
-
42
-
-
0026550397
-
The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure
-
Matouschek A, Serrano L, Fersht AR (1992) The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure. J Mol Biol 224: 819-835.
-
(1992)
J Mol Biol
, vol.224
, pp. 819-835
-
-
Matouschek, A.1
Serrano, L.2
Fersht, A.R.3
-
43
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki LS, Otzen DE, Fersht AR (1995) The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J Mol Biol 254: 260-288.
-
(1995)
J Mol Biol
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
44
-
-
0028143603
-
Characterization of the transition-state of protein unfolding by use of molecular-dynamics: Chymotrypsin inhibitor 2
-
USA
-
Li A, Daggett V (1994) Characterization of the transition-state of protein unfolding by use of molecular-dynamics: Chymotrypsin inhibitor 2. Proc Natl Acad Sci USA 91: 10430-10434.
-
(1994)
Proc Natl Acad Sci
, vol.91
, pp. 10430-10434
-
-
Li, A.1
Daggett, V.2
-
45
-
-
0031465967
-
"New view" of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M (1997) "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278: 1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
46
-
-
0035818481
-
Constructing, verifying and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
USA
-
Li L, Shakhnovich EI (2001) Constructing, verifying and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc Natl Acad Sci USA 98: 13014-13018.
-
(2001)
Proc Natl Acad Sci
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
47
-
-
0032579189
-
Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
-
Li AJ, Daggett V (1998) Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate. J Mol Biol 275: 677-694.
-
(1998)
J Mol Biol
, vol.275
, pp. 677-694
-
-
Li, A.J.1
Daggett, V.2
-
48
-
-
0032539209
-
Combined molecular dynamics and phivalue analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects
-
Daggett V, Li A, Fersht AR (1998) Combined molecular dynamics and phivalue analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects. J Am Chem Soc 120: 12740-12754.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 12740-12754
-
-
Daggett, V.1
Li, A.2
Fersht, A.R.3
-
49
-
-
0036304480
-
Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
-
Kaya H, Chan HS (2002) Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding? J Mol Biol 315: 899-909.
-
(2002)
J Mol Biol
, vol.315
, pp. 899-909
-
-
Kaya, H.1
Chan, H.S.2
-
50
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek A, Kellis Jr JT, Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340: 122-126.
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
51
-
-
0026511656
-
The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding
-
Fersht AR, Matouschek A, Serrano L (1992) The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J Mol Biol 224: 771-782.
-
(1992)
J Mol Biol
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
52
-
-
31444452031
-
P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes
-
USA
-
Cho SS, Levy Y, Wolynes PG (2006) P versus Q: Structural reaction coordinates capture protein folding on smooth landscapes. Proc Natl Acad Sci USA 103: 586-591.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 586-591
-
-
Cho, S.S.1
Levy, Y.2
Wolynes, P.G.3
-
53
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution
-
Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 angstrom resolution. Science 289: 905-920.
-
(2000)
Science
, vol.289
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
54
-
-
0033203533
-
Co-translational folding of an alphavirus capsid protein in the cytosol of living cells
-
Nicola AV, Chen W, Helenius A (1999) Co-translational folding of an alphavirus capsid protein in the cytosol of living cells. Nat Cell Biol 1: 341-345.
-
(1999)
Nat Cell Biol
, vol.1
, pp. 341-345
-
-
Nicola, A.V.1
Chen, W.2
Helenius, A.3
-
55
-
-
17344384932
-
Fast folding of the two-domain Semliki forest virus capsid protein explains cotranslational proteolytic activity
-
Sánchez IE, Morillas M, Zobeley E, Kiefhaber T, Glockshuber R (2004) Fast folding of the two-domain Semliki forest virus capsid protein explains cotranslational proteolytic activity. J Mol Biol 338: 159-167.
-
(2004)
J Mol Biol
, vol.338
, pp. 159-167
-
-
Sánchez, I.E.1
Morillas, M.2
Zobeley, E.3
Kiefhaber, T.4
Glockshuber, R.5
-
56
-
-
0027527209
-
Circular dichroism studies of barnase and its mutants: Characterization of the contribution of aromatic side chains
-
Vuilleumier S, Sancho J, Loewenthal R, Fersht AR (1993) Circular dichroism studies of barnase and its mutants: Characterization of the contribution of aromatic side chains. Biochemistry 32: 10303-10313.
-
(1993)
Biochemistry
, vol.32
, pp. 10303-10313
-
-
Vuilleumier, S.1
Sancho, J.2
Loewenthal, R.3
Fersht, A.R.4
-
57
-
-
27844563112
-
The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation
-
Kurt N, Cavagnero S (2005) The burial of solvent-accessible surface area is a predictor of polypeptide folding and misfolding as a function of chain elongation. J Am Chem Soc 127: 15690-15691.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 15690-15691
-
-
Kurt, N.1
Cavagnero, S.2
-
58
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich EI (1998) On the transition coordinate for protein folding. J Chem Phys 108: 334-350.
-
(1998)
J Chem Phys
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.I.5
-
59
-
-
18844459862
-
Nucleation and the transition state of the SH3 domain
-
Hubner IA, Edmonds KA, Shakhnovich EI (2005) Nucleation and the transition state of the SH3 domain. J Mol Biol 349: 424-434.
-
(2005)
J Mol Biol
, vol.349
, pp. 424-434
-
-
Hubner, I.A.1
Edmonds, K.A.2
Shakhnovich, E.I.3
-
60
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow CD, Nguyen N, Pande VS, Gruebele M (2002) Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420: 102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, N.2
Pande, V.S.3
Gruebele, M.4
-
61
-
-
0037235952
-
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
-
Pande VS, Baker I, Chapman J, Elmer SP, Khaliq S, et al. (2003) Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers 68: 91-109.
-
(2003)
Biopolymers
, vol.68
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.P.4
Khaliq, S.5
-
62
-
-
11144226928
-
Phylogeny of protein-folding trajectories reveals a unique pathway to native structure
-
USA
-
Ota M, Ikeguchi M, Kidera A (2004) Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. Proc Natl Acad Sci USA 101: 17658-17663.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 17658-17663
-
-
Ota, M.1
Ikeguchi, M.2
Kidera, A.3
-
63
-
-
0019824131
-
Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translation system
-
Ikemura T (1981) Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translation system. J Mol Biol 151: 389-409.
-
(1981)
J Mol Biol
, vol.151
, pp. 389-409
-
-
Ikemura, T.1
-
64
-
-
0026409389
-
Absolute in vivo translation rates of individual codons in Escherichia-coli: The two glutamic-acid codons GAA and GAG are translated with a threefold difference in rate
-
Sorensen MA, Pedersen S (1991) Absolute in vivo translation rates of individual codons in Escherichia-coli: The two glutamic-acid codons GAA and GAG are translated with a threefold difference in rate. J Mol Biol 222: 265-280.
-
(1991)
J Mol Biol
, vol.222
, pp. 265-280
-
-
Sorensen, M.A.1
Pedersen, S.2
-
65
-
-
0024962419
-
Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
-
Curran JF, Yarus M (1989) Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol 209: 65-77.
-
(1989)
J Mol Biol
, vol.209
, pp. 65-77
-
-
Curran, J.F.1
Yarus, M.2
-
66
-
-
0018791280
-
Nonuniform size distribution of nascent peptides: Effect of messenger RNA structure upon the rate of translation
-
Chaney WG, Morris AJ (1979) Nonuniform size distribution of nascent peptides: Effect of messenger RNA structure upon the rate of translation. Arch Biochem Biophys 194: 283-291.
-
(1979)
Arch Biochem Biophys
, vol.194
, pp. 283-291
-
-
Chaney, W.G.1
Morris, A.J.2
-
67
-
-
0030018101
-
Ribosome-mediated translational pause and protein domain organization
-
Thanaraj TA, Argos P (1994) Ribosome-mediated translational pause and protein domain organization. Protein Sci 5: 1594-1612.
-
(1994)
Protein Sci
, vol.5
, pp. 1594-1612
-
-
Thanaraj, T.A.1
Argos, P.2
-
68
-
-
0036908375
-
Distribution of rare triplets along mRNA and their relation to protein folding
-
Makhoul CH, Trifonov EN (2002) Distribution of rare triplets along mRNA and their relation to protein folding. J Biomol Struct Dyn 20: 413-420.
-
(2002)
J Biomol Struct Dyn
, vol.20
, pp. 413-420
-
-
Makhoul, C.H.1
Trifonov, E.N.2
-
69
-
-
0037070194
-
Single synonymous codon substitution eliminates pausing during chloramphenicol acetyl transferase synthesis on Escherichia coli ribosomes in vitro
-
Ramachanidran V, Kramer G, Horowitz PM, Hardesty B (2002) Single synonymous codon substitution eliminates pausing during chloramphenicol acetyl transferase synthesis on Escherichia coli ribosomes in vitro. FEBS Lett 512: 209-212.
-
(2002)
FEBS Lett
, vol.512
, pp. 209-212
-
-
Ramachanidran, V.1
Kramer, G.2
Horowitz, P.M.3
Hardesty, B.4
-
71
-
-
27644502679
-
Simulating movement of tRNA into the ribosome during docoding
-
U S A
-
Sanbonmatsu KY, Joseph S, Tung CS (2005) Simulating movement of tRNA into the ribosome during docoding. Proc Natl Acad Sci U S A 102: 15854-15859.
-
(2005)
Proc Natl Acad Sci
, vol.102
, pp. 15854-15859
-
-
Sanbonmatsu, K.Y.1
Joseph, S.2
Tung, C.S.3
-
72
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
Trylska J, Tozzini V, McCammon JA (2005) Exploring global motions and correlations in the ribosome. Biophys J 89: 1455-1463.
-
(2005)
Biophys J
, vol.89
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
73
-
-
1542358892
-
Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins
-
Woolhead CA, McCormick PJ, Johnson AE (2004) Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins. Cell 116: 725-736.
-
(2004)
Cell
, vol.116
, pp. 725-736
-
-
Woolhead, C.A.1
McCormick, P.J.2
Johnson, A.E.3
-
74
-
-
14544282996
-
The co-translational folding and interactions of nascent protein chains: A new approach using fluorescence resonance energy transfer
-
Johnson AE (2005) The co-translational folding and interactions of nascent protein chains: A new approach using fluorescence resonance energy transfer. FEBS Lett 579: 916-920.
-
(2005)
FEBS Lett
, vol.579
, pp. 916-920
-
-
Johnson, A.E.1
-
75
-
-
5144234840
-
Structure acquisition of the T1 domain of Kv1.3 during biogenesis
-
Kosolapov A, Tu LW, Wang J, Deutsch C (2004) Structure acquisition of the T1 domain of Kv1.3 during biogenesis. Neuron 44: 295-307.
-
(2004)
Neuron
, vol.44
, pp. 295-307
-
-
Kosolapov, A.1
Tu, L.W.2
Wang, J.3
Deutsch, C.4
-
76
-
-
28544449949
-
Folding zones inside the ribosomal exit tunnel
-
Lu JL, Deutsch C (2005) Folding zones inside the ribosomal exit tunnel. Nat Struct Mol Biol 12: 1123-1129.
-
(2005)
Nat Struct Mol Biol
, vol.12
, pp. 1123-1129
-
-
Lu, J.L.1
Deutsch, C.2
-
77
-
-
1842635571
-
Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection
-
Scalley-Kim M, Baker D (2004) Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J Mol Biol 338: 573-583.
-
(2004)
J Mol Biol
, vol.338
, pp. 573-583
-
-
Scalley-Kim, M.1
Baker, D.2
-
79
-
-
1842766175
-
Three-dimensional structures of translating ribosomes by Cryo-EM
-
Gilbert RJC, Fucini P, Connell S, Fuller SD, Nierhaus KH, et al. (2004) Three-dimensional structures of translating ribosomes by Cryo-EM. Mol Cell 14: 57-66.
-
(2004)
Mol Cell
, vol.14
, pp. 57-66
-
-
Gilbert, R.J.C.1
Fucini, P.2
Connell, S.3
Fuller, S.D.4
Nierhaus, K.H.5
-
80
-
-
0037040406
-
Regulatory nascent peptides in the ribosomal tunnel
-
Tenson T, Ehrenberg M (2002) Regulatory nascent peptides in the ribosomal tunnel. Cell 108: 591-594.
-
(2002)
Cell
, vol.108
, pp. 591-594
-
-
Tenson, T.1
Ehrenberg, M.2
-
81
-
-
0031471055
-
Both lumenal and cytosolic gating of the aqueous ER translocon pore are regulated from inside the ribosome during membrane protein integration
-
Liao S, Lin J, Do H, Johnson AE (1997) Both lumenal and cytosolic gating of the aqueous ER translocon pore are regulated from inside the ribosome during membrane protein integration. Cell 90: 31-41.
-
(1997)
Cell
, vol.90
, pp. 31-41
-
-
Liao, S.1
Lin, J.2
Do, H.3
Johnson, A.E.4
-
82
-
-
0032742688
-
Going for the prediction of protein folding mechanisms
-
U S A
-
Takada S (1999) Going for the prediction of protein folding mechanisms. Proc Natl Acad Sci U S A 96: 11698-11700.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 11698-11700
-
-
Takada, S.1
-
83
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend G (1990) WHAT IF: A molecular modeling and drug design program. J Mol Graph 8: 52-56.
-
(1990)
J Mol Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
84
-
-
0023652256
-
Crystal and molecular structure of the serine protease-inhibitor CI-2 from barley seeds
-
McPhalen CA, James MNG (1987) Crystal and molecular structure of the serine protease-inhibitor CI-2 from barley seeds. Biochemistry 26: 261-269.
-
(1987)
Biochemistry
, vol.26
, pp. 261-269
-
-
McPhalen, C.A.1
James, M.N.G.2
-
85
-
-
0026279527
-
Crystal-structure of a barnase-d(GpC) complex at 1.9 Å resolution
-
Baudet S, Janin J (1991) Crystal-structure of a barnase-d(GpC) complex at 1.9 Å resolution. J Mol Biol 219: 123-132.
-
(1991)
J Mol Biol
, vol.219
, pp. 123-132
-
-
Baudet, S.1
Janin, J.2
-
86
-
-
0030890291
-
Structure of Semliki Forest virus core protein
-
Choi HK, Lu GG, Lee S, Wengler G, Rossmann MG (1997) Structure of Semliki Forest virus core protein. Proteins Struct Funct Genet 27: 345-349.
-
(1997)
Proteins Struct Funct Genet
, vol.27
, pp. 345-349
-
-
Choi, H.K.1
Lu, G.G.2
Lee, S.3
Wengler, G.4
Rossmann, M.G.5
-
87
-
-
0347753598
-
Energetics of protein thermodynamic cooperativity: Contributions of local and nonlocal interactions
-
Knott M, Kaya H, Chan HS (2004) Energetics of protein thermodynamic cooperativity: Contributions of local and nonlocal interactions. Polymer 45: 623-632.
-
(2004)
Polymer
, vol.45
, pp. 623-632
-
-
Knott, M.1
Kaya, H.2
Chan, H.S.3
-
88
-
-
33750652614
-
Brownian dynamics with hydrodynamic interactions
-
Ermak DL, McCammon JA (1978) Brownian dynamics with hydrodynamic interactions. J Chem Phys 69: 1352-1360.
-
(1978)
J Chem Phys
, vol.69
, pp. 1352-1360
-
-
Ermak, D.L.1
McCammon, J.A.2
-
90
-
-
4243819810
-
New Monte Carlo technique for studying phase transitions
-
Ferrenberg AM, Swendsen RH (1988) New Monte Carlo technique for studying phase transitions. Phys Rev Lett 61: 2635-2638.
-
(1988)
Phys Rev Lett
, vol.61
, pp. 2635-2638
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
91
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
Ferrenberg AM, Swendsen RH (1989) Optimized Monte Carlo data analysis. Phys Rev Lett 63: 1195-1198.
-
(1989)
Phys Rev Lett
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
92
-
-
0030998184
-
P-SEA: A new efficient assignment of secondary structure from C alpha trace of proteins
-
Labesse G, Colloc'h N, Pothier J, Mornon JP (1997) P-SEA: A new efficient assignment of secondary structure from C alpha trace of proteins. Comput App Biosci 13: 291-295.
-
(1997)
Comput App Biosci
, vol.13
, pp. 291-295
-
-
Labesse, G.1
Colloc'h, N.2
Pothier, J.3
Mornon, J.P.4
-
93
-
-
0034572230
-
Cotranslational folding of proteins
-
Mosc
-
Basharov MA (2000) Cotranslational folding of proteins. Biochemistry (Mosc) 65: 1380-1384.
-
(2000)
Biochemistry
, vol.65
, pp. 1380-1384
-
-
Basharov, M.A.1
|