-
2
-
-
66849106554
-
An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms
-
Bartlett A.I., Radford S.E. An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. Nat Struct Mol Biol 2009, 16:582-588.
-
(2009)
Nat Struct Mol Biol
, vol.16
, pp. 582-588
-
-
Bartlett, A.I.1
Radford, S.E.2
-
3
-
-
70350348011
-
NMR spectroscopy brings invisible protein states into focus
-
Baldwin A.J., Kay L.E. NMR spectroscopy brings invisible protein states into focus. Nat Chem Biol 2009, 5:808-814.
-
(2009)
Nat Chem Biol
, vol.5
, pp. 808-814
-
-
Baldwin, A.J.1
Kay, L.E.2
-
4
-
-
70349856159
-
From biomolecular structure to functional understanding: new NMR developments narrow the gap
-
Grzesiek S., Sass H.J. From biomolecular structure to functional understanding: new NMR developments narrow the gap. Curr Opin Struct Biol 2009, 19:585-595.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 585-595
-
-
Grzesiek, S.1
Sass, H.J.2
-
5
-
-
39149087014
-
Protein folding studied by single-molecule FRET
-
Schuler B., Eaton W.A. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol 2008, 18:16-26.
-
(2008)
Curr Opin Struct Biol
, vol.18
, pp. 16-26
-
-
Schuler, B.1
Eaton, W.A.2
-
6
-
-
45449109207
-
Small angle neutron and X-ray scattering in structural biology: recent examples from the literature
-
Neylon C. Small angle neutron and X-ray scattering in structural biology: recent examples from the literature. Eur Biophys J 2008, 37:531-541.
-
(2008)
Eur Biophys J
, vol.37
, pp. 531-541
-
-
Neylon, C.1
-
7
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis J.L., Lindorff-Larsen K., Dror R.O., Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 2009, 19:120-127.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
9
-
-
77952337788
-
Entropic mechanism of large fluctuation in allosteric transition
-
Itoh K., Sasai M. Entropic mechanism of large fluctuation in allosteric transition. Proc Natl Acad Sci USA 2010, 107:7775-7780.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 7775-7780
-
-
Itoh, K.1
Sasai, M.2
-
10
-
-
70450245183
-
Conformational ensemble modulates cooperativity in the rate-determining catalytic step in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex
-
Kale S., Jordan F. Conformational ensemble modulates cooperativity in the rate-determining catalytic step in the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex. J Biol Chem 2009, 284:33122-33129.
-
(2009)
J Biol Chem
, vol.284
, pp. 33122-33129
-
-
Kale, S.1
Jordan, F.2
-
11
-
-
70350523594
-
Relationship between protein stabilization and protein rigidification induced by mannosylglycerate
-
Pais T.M., Lamosa P., Garcia-Moreno B., Turner D.L., Santos H. Relationship between protein stabilization and protein rigidification induced by mannosylglycerate. J Mol Biol 2009, 394:237-250.
-
(2009)
J Mol Biol
, vol.394
, pp. 237-250
-
-
Pais, T.M.1
Lamosa, P.2
Garcia-Moreno, B.3
Turner, D.L.4
Santos, H.5
-
12
-
-
27544475025
-
Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: spatial propagation of differential flexibility in rubredoxin hybrids
-
LeMaster D.M., Tang J., Paredes D.I., Hernandez G. Enhanced thermal stability achieved without increased conformational rigidity at physiological temperatures: spatial propagation of differential flexibility in rubredoxin hybrids. Proteins 2005, 61:608-616.
-
(2005)
Proteins
, vol.61
, pp. 608-616
-
-
LeMaster, D.M.1
Tang, J.2
Paredes, D.I.3
Hernandez, G.4
-
13
-
-
47649098600
-
Cooperativity and biological complexity
-
Whitty A. Cooperativity and biological complexity. Nat Chem Biol 2008, 4:435-439.
-
(2008)
Nat Chem Biol
, vol.4
, pp. 435-439
-
-
Whitty, A.1
-
14
-
-
53549116738
-
The complex inter-relationships between protein flexibility and stability
-
Kamerzell T.J., Middaugh C.R. The complex inter-relationships between protein flexibility and stability. J Pharm Sci 2008, 97:3494-3517.
-
(2008)
J Pharm Sci
, vol.97
, pp. 3494-3517
-
-
Kamerzell, T.J.1
Middaugh, C.R.2
-
15
-
-
34347218159
-
Conformational dynamics and ensembles in protein folding
-
Muñoz V. Conformational dynamics and ensembles in protein folding. Annu Rev Biophys Biomol Struct 2007, 36:395-412.
-
(2007)
Annu Rev Biophys Biomol Struct
, vol.36
, pp. 395-412
-
-
Muñoz, V.1
-
16
-
-
78149498758
-
-
Humana Press, 14
-
Cho J.H., Raleigh D.P. Experimental characterization of the denatured state ensemble of proteins. Protein Structure, Stability, and Interactions, Springer Protocols 2009, Vol. 490. Humana Press, 14.
-
(2009)
Experimental characterization of the denatured state ensemble of proteins. Protein Structure, Stability, and Interactions, Springer Protocols
, vol.490
-
-
Cho, J.H.1
Raleigh, D.P.2
-
17
-
-
33745759471
-
Ensemble-based convergence analysis of biomolecular trajectories
-
Lyman E., Zuckerman D.M. Ensemble-based convergence analysis of biomolecular trajectories. Biophys J 2006, 91:164-172.
-
(2006)
Biophys J
, vol.91
, pp. 164-172
-
-
Lyman, E.1
Zuckerman, D.M.2
-
18
-
-
47249116944
-
Understanding ensemble protein folding at atomic detail
-
283101
-
Wallin S., Shakhnovich E.I. Understanding ensemble protein folding at atomic detail. J Phys Condens Matter 2008, 20. 283101.
-
(2008)
J Phys Condens Matter
, vol.20
-
-
Wallin, S.1
Shakhnovich, E.I.2
-
19
-
-
33847776838
-
On the characterization of protein native state ensembles
-
Shehu A., Kavraki L.E., Clementi C. On the characterization of protein native state ensembles. Biophys J 2007, 92:1503-1511.
-
(2007)
Biophys J
, vol.92
, pp. 1503-1511
-
-
Shehu, A.1
Kavraki, L.E.2
Clementi, C.3
-
20
-
-
68149125150
-
Multiscale characterization of protein conformational ensembles
-
Shehu A., Kavraki L.E., Clementi C. Multiscale characterization of protein conformational ensembles. Proteins 2009, 76:837-851.
-
(2009)
Proteins
, vol.76
, pp. 837-851
-
-
Shehu, A.1
Kavraki, L.E.2
Clementi, C.3
-
21
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm E., Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci USA 1999, 96:11305-11310.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
22
-
-
0035312345
-
What can we learn about protein folding from Ising-like models?
-
Muñoz V. What can we learn about protein folding from Ising-like models?. Curr Opin Struct Biol 2001, 11:212-216.
-
(2001)
Curr Opin Struct Biol
, vol.11
, pp. 212-216
-
-
Muñoz, V.1
-
23
-
-
0030580089
-
Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors
-
Hilser V.J., Freire E. Structure-based calculation of the equilibrium folding pathway of proteins. Correlation with hydrogen exchange protection factors. J Mol Biol 1996, 262:756-772.
-
(1996)
J Mol Biol
, vol.262
, pp. 756-772
-
-
Hilser, V.J.1
Freire, E.2
-
24
-
-
0000627329
-
Thermodynamics of protein folding and molecular recognition
-
Freire E. Thermodynamics of protein folding and molecular recognition. Pure Appl Chem 1997, 69:2253-2261.
-
(1997)
Pure Appl Chem
, vol.69
, pp. 2253-2261
-
-
Freire, E.1
-
25
-
-
33646922285
-
A statistical thermodynamic model of the protein ensemble
-
Hilser V.J., Garcia-Moreno B., Oas T.G., Kapp G., Whitten S.T. A statistical thermodynamic model of the protein ensemble. Chem Rev 2006, 106:1545-1558.
-
(2006)
Chem Rev
, vol.106
, pp. 1545-1558
-
-
Hilser, V.J.1
Garcia-Moreno, B.2
Oas, T.G.3
Kapp, G.4
Whitten, S.T.5
-
26
-
-
0036076716
-
Thermodynamic environments in proteins: fundamental determinants of fold specificity
-
Wrabl J.O., Larson S.A., Hilser V.J. Thermodynamic environments in proteins: fundamental determinants of fold specificity. Protein Sci 2002, 11:1945-1957.
-
(2002)
Protein Sci
, vol.11
, pp. 1945-1957
-
-
Wrabl, J.O.1
Larson, S.A.2
Hilser, V.J.3
-
27
-
-
48749084868
-
Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding
-
Wang S., Gu J., Larson S.A., Whitten S.T., Hilser V.J. Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding. J Mol Biol 2008, 381:1184-1201.
-
(2008)
J Mol Biol
, vol.381
, pp. 1184-1201
-
-
Wang, S.1
Gu, J.2
Larson, S.A.3
Whitten, S.T.4
Hilser, V.J.5
-
28
-
-
33748663531
-
Revealing the nature of the native state ensemble through cold denaturation
-
Whitten S.T., Kurtz A.J., Pometun M.S., Wand A.J., Hilser V.J. Revealing the nature of the native state ensemble through cold denaturation. Biochemistry 2006, 45:10163-10173.
-
(2006)
Biochemistry
, vol.45
, pp. 10163-10173
-
-
Whitten, S.T.1
Kurtz, A.J.2
Pometun, M.S.3
Wand, A.J.4
Hilser, V.J.5
-
29
-
-
0034710950
-
Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble
-
Pan H., Lee J.C., Hilser V.J. Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble. Proc Natl Acad Sci USA 2000, 97:12020-12025.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 12020-12025
-
-
Pan, H.1
Lee, J.C.2
Hilser, V.J.3
-
30
-
-
25144442821
-
COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures
-
Vertrees J., Barritt P., Whitten S., Hilser V.J. COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. Bioinformatics 2005, 21:3318-3319.
-
(2005)
Bioinformatics
, vol.21
, pp. 3318-3319
-
-
Vertrees, J.1
Barritt, P.2
Whitten, S.3
Hilser, V.J.4
-
31
-
-
33747133668
-
Kinetics of the Wako-Saitô-Muñoz-Eaton model of protein folding
-
068106, 1-4
-
Zamparo M., Pelizzola A. Kinetics of the Wako-Saitô-Muñoz-Eaton model of protein folding. Phys Rev Lett 2006, 97. 068106, 1-4.
-
(2006)
Phys Rev Lett
, vol.97
-
-
Zamparo, M.1
Pelizzola, A.2
-
32
-
-
42749099473
-
Rigorous results on the local equilibrium kinetics of a protein folding model
-
Zamparo M., Pelizzola A. Rigorous results on the local equilibrium kinetics of a protein folding model. J Stat Mech 2006, 12:1742-5468.
-
(2006)
J Stat Mech
, vol.12
, pp. 1742-5468
-
-
Zamparo, M.1
Pelizzola, A.2
-
33
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz V., Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 1999, 96:11311-11316.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
34
-
-
75749153687
-
Coordinate-dependent diffusion in protein folding
-
Besta R.B., Hummer G. Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci USA 2010, 107:1088-1093.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 1088-1093
-
-
Besta, R.B.1
Hummer, G.2
-
35
-
-
57449106823
-
Chemical, physical, and theoretical kinetics of an ultrafast folding protein
-
Kubelkaa J., Henrya E.R., Cellmera T., Hofrichtera J., Eaton W.A. Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 2008, 105:18655-18662.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 18655-18662
-
-
Kubelkaa, J.1
Henrya, E.R.2
Cellmera, T.3
Hofrichtera, J.4
Eaton, W.A.5
-
36
-
-
0035427398
-
Graph theory predictions of protein flexibility
-
Jacobs D.J., Rader A., Kuhn L.A., Thorpe M.F. Graph theory predictions of protein flexibility. Proteins 2001, 44:150-165.
-
(2001)
Proteins
, vol.44
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.2
Kuhn, L.A.3
Thorpe, M.F.4
-
37
-
-
27744471408
-
Constrained geometric simulation of diffusive motion in proteins
-
Wells S., Menor S., Hespenheide B., Thorpe M.F. Constrained geometric simulation of diffusive motion in proteins. Phys Biol 2005, 2:S127-S136.
-
(2005)
Phys Biol
, vol.2
-
-
Wells, S.1
Menor, S.2
Hespenheide, B.3
Thorpe, M.F.4
-
38
-
-
78149498583
-
-
Thorpe MF:
-
Thorpe MF: http://flexweb.asu.edu/software/first/.
-
-
-
-
39
-
-
77957948190
-
Generating stereochemically acceptable protein pathways
-
Farrell D.W., Speranskiy K., Thorpe M.F. Generating stereochemically acceptable protein pathways. Proteins 2010, 78:2908-2921.
-
(2010)
Proteins
, vol.78
, pp. 2908-2921
-
-
Farrell, D.W.1
Speranskiy, K.2
Thorpe, M.F.3
-
40
-
-
78149499532
-
-
Thorpe MF:
-
Thorpe MF: http://pathways.asu.edu/.
-
-
-
-
41
-
-
0342929614
-
Non-physical sampling distributions in Monte-Carlo free-energy estimation-umbrella sampling
-
Torrie G.M., Valleau J.P. Non-physical sampling distributions in Monte-Carlo free-energy estimation-umbrella sampling. J Comput Phys 1977, 23:187-199.
-
(1977)
J Comput Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
42
-
-
37149025254
-
Roadmap methods for protein folding
-
Humana Press, M. Zaki, C. Bystroff (Eds.)
-
Moll M., Schwarz D., Kavraki L.E. Roadmap methods for protein folding. Protein Structure Prediction: Methods and Protocols 2007, 219-242. Humana Press. M. Zaki, C. Bystroff (Eds.).
-
(2007)
Protein Structure Prediction: Methods and Protocols
, pp. 219-242
-
-
Moll, M.1
Schwarz, D.2
Kavraki, L.E.3
-
43
-
-
34447281773
-
Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values
-
Chiang T.H., Apaydin M.S., Brutlag D.L., Hsu D., Latombe J.C. Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values. J Comput Biol 2007, 14:578-593.
-
(2007)
J Comput Biol
, vol.14
, pp. 578-593
-
-
Chiang, T.H.1
Apaydin, M.S.2
Brutlag, D.L.3
Hsu, D.4
Latombe, J.C.5
-
44
-
-
0036100047
-
Using motion planning to study protein folding pathways
-
Amato N.M., Song G. Using motion planning to study protein folding pathways. J Comput Biol 2002, 9:149-168.
-
(2002)
J Comput Biol
, vol.9
, pp. 149-168
-
-
Amato, N.M.1
Song, G.2
-
45
-
-
34547699008
-
Simulating protein motions with rigidity analysis
-
Thomas S., Tang X., Tapia L., Amato N.M. Simulating protein motions with rigidity analysis. J Comput Biol 2007, 14:839-855.
-
(2007)
J Comput Biol
, vol.14
, pp. 839-855
-
-
Thomas, S.1
Tang, X.2
Tapia, L.3
Amato, N.M.4
-
46
-
-
78149497484
-
-
Amato NM: WEB server.
-
Amato NM: WEB server. http://parasol.tamu.edu/foldingserver/.
-
-
-
-
47
-
-
38549120278
-
Insight into long-range nonadditivity within protein double-mutant cycles
-
Istomin A.Y., Gromiha M.M., Vorov O.K., Jacobs D.J., Livesay D.R. Insight into long-range nonadditivity within protein double-mutant cycles. Proteins 2008, 70:915-924.
-
(2008)
Proteins
, vol.70
, pp. 915-924
-
-
Istomin, A.Y.1
Gromiha, M.M.2
Vorov, O.K.3
Jacobs, D.J.4
Livesay, D.R.5
-
48
-
-
1542285840
-
Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
-
061109, 1-21
-
Jacobs D.J., Dallakayan S., Wood G.G., Heckathorne A. Network rigidity at finite temperature: relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems. Phys Rev E 2003, 68. 061109, 1-21.
-
(2003)
Phys Rev E
, vol.68
-
-
Jacobs, D.J.1
Dallakayan, S.2
Wood, G.G.3
Heckathorne, A.4
-
49
-
-
54749111111
-
Conformational entropy of an ideal cross-linking polymer chain
-
Vorov O.K., Livesay D.R., Jacobs D.J. Conformational entropy of an ideal cross-linking polymer chain. Entropy 2008, 10:285-308.
-
(2008)
Entropy
, vol.10
, pp. 285-308
-
-
Vorov, O.K.1
Livesay, D.R.2
Jacobs, D.J.3
-
50
-
-
21244483843
-
Elucidating protein thermodynamics from the three dimensional structure of the native state using network rigidity
-
Jacobs D.J., Dallakayan S. Elucidating protein thermodynamics from the three dimensional structure of the native state using network rigidity. Biophys J 2005, 88:1-13.
-
(2005)
Biophys J
, vol.88
, pp. 1-13
-
-
Jacobs, D.J.1
Dallakayan, S.2
-
51
-
-
6344223617
-
A flexible approach for understanding protein stability
-
Livesay D.R., Dallakyan S., Wood G.G., Jacobs D.J. A flexible approach for understanding protein stability. FEBS Lett 2004, 576:468-476.
-
(2004)
FEBS Lett
, vol.576
, pp. 468-476
-
-
Livesay, D.R.1
Dallakyan, S.2
Wood, G.G.3
Jacobs, D.J.4
-
52
-
-
30344476409
-
Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair
-
Livesay D.R., Jacobs D.J. Conserved quantitative stability/flexibility relationships (QSFR) in an orthologous RNase H pair. Proteins 2006, 62:130-143.
-
(2006)
Proteins
, vol.62
, pp. 130-143
-
-
Livesay, D.R.1
Jacobs, D.J.2
-
53
-
-
33646033429
-
Elucidating quantitative stability-flexibility relationships within thioredoxin and its fragments using a distance constraint model
-
Jacobs D.J., Livesay D.R., Hules J., Tasayco M.L. Elucidating quantitative stability-flexibility relationships within thioredoxin and its fragments using a distance constraint model. J Mol Biol 2006, 358:882-904.
-
(2006)
J Mol Biol
, vol.358
, pp. 882-904
-
-
Jacobs, D.J.1
Livesay, D.R.2
Hules, J.3
Tasayco, M.L.4
-
54
-
-
51749092455
-
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family
-
Livesay D.R., Huynh D.H., Dallakyan S., Jacobs D.J. Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family. Chem Central J 2008, 2:1-20.
-
(2008)
Chem Central J
, vol.2
, pp. 1-20
-
-
Livesay, D.R.1
Huynh, D.H.2
Dallakyan, S.3
Jacobs, D.J.4
-
55
-
-
66149154705
-
Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family
-
Mottonen J.M., Minli X., Jacobs D.J., Livesay D.R. Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family. Proteins 2009, 75:610-627.
-
(2009)
Proteins
, vol.75
, pp. 610-627
-
-
Mottonen, J.M.1
Minli, X.2
Jacobs, D.J.3
Livesay, D.R.4
-
56
-
-
77958469848
-
Allosteric response is both conserved and variable across three CheY orthologs
-
Mottonen J.M., Jacobs D.J., Livesay D.R. Allosteric response is both conserved and variable across three CheY orthologs. Biophys J 2010, 99:1-10.
-
(2010)
Biophys J
, vol.99
, pp. 1-10
-
-
Mottonen, J.M.1
Jacobs, D.J.2
Livesay, D.R.3
-
57
-
-
0028334097
-
Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies
-
Mark A.E., van Gunsteren W.F. Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies. J Mol Biol 1994, 240:167-176.
-
(1994)
J Mol Biol
, vol.240
, pp. 167-176
-
-
Mark, A.E.1
van Gunsteren, W.F.2
-
58
-
-
0031022887
-
Additivity principles in biochemistry
-
Dill K.A. Additivity principles in biochemistry. J Biol Chem 1997, 272:701-704.
-
(1997)
J Biol Chem
, vol.272
, pp. 701-704
-
-
Dill, K.A.1
-
59
-
-
72549119922
-
Helix/coil nucleation: a local response to global demands
-
Vorov O.K., Livesay D.R., Jacobs D.J. Helix/coil nucleation: a local response to global demands. Biophys J 2009, 97:3000-3009.
-
(2009)
Biophys J
, vol.97
, pp. 3000-3009
-
-
Vorov, O.K.1
Livesay, D.R.2
Jacobs, D.J.3
-
60
-
-
78149501142
-
Thermodynamics of a beta-hairpin to coil transition elucidated by constraint theory
-
Nova Publishers, P.C. Sánchez (Ed.)
-
Jacobs D.J., Fairchild M.J. Thermodynamics of a beta-hairpin to coil transition elucidated by constraint theory. Biopolymer Research Trends 2007, 45-76. Nova Publishers. P.C. Sánchez (Ed.).
-
(2007)
Biopolymer Research Trends
, pp. 45-76
-
-
Jacobs, D.J.1
Fairchild, M.J.2
|