-
1
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14:1-63.
-
(1959)
Adv Protein Chem
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
2
-
-
84876039950
-
-
W. H. Freeman, New York, 5th Ed
-
Lehninger A-L, Cox M-M, Nelson D-L (2008) Lehninger Principles of Biochemistry (W. H. Freeman, New York), 5th Ed, pp 140-142.
-
(2008)
Lehninger Principles of Biochemistry
, pp. 140-142
-
-
Lehninger, A.-L.1
Cox, M.-M.2
Nelson, D.-L.3
-
3
-
-
79953759344
-
Role of solvation effects in protein denaturation: From thermodynamics to single molecules and back
-
England JL, Haran G (2011) Role of solvation effects in protein denaturation: From thermodynamics to single molecules and back. Annu Rev Phys Chem 62:257-277.
-
(2011)
Annu Rev Phys Chem
, vol.62
, pp. 257-277
-
-
England, J.L.1
Haran, G.2
-
4
-
-
34848916114
-
Anatomy of energetic changes accompanying urea-induced protein denaturation
-
Auton M, Holthauzen LM, Bolen DW (2007) Anatomy of energetic changes accompanying urea-induced protein denaturation. Proc Natl Acad Sci USA 104(39):15317-15322.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.39
, pp. 15317-15322
-
-
Auton, M.1
Holthauzen, L.M.2
Bolen, D.W.3
-
5
-
-
6944241424
-
Aqueous urea solution destabilizes Abeta (16-22) oligomers
-
Klimov DK, Straub JE, Thirumalai D (2004) Aqueous urea solution destabilizes Abeta (16-22) oligomers. Proc Natl Acad Sci USA 101(41):14760-14765.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.41
, pp. 14760-14765
-
-
Klimov, D.K.1
Straub, J.E.2
Thirumalai, D.3
-
6
-
-
79953858621
-
Backbone and side-chain contributions in protein denaturation by urea
-
Canchi DR, García AE (2011) Backbone and side-chain contributions in protein denaturation by urea. Biophys J 100(6):1526-1533.
-
(2011)
Biophys J
, vol.100
, Issue.6
, pp. 1526-1533
-
-
Canchi, D.R.1
García, A.E.2
-
7
-
-
34250869055
-
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
-
O'Brien EP, Dima RI, Brooks B, Thirumalai D (2007) Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism. J Am Chem Soc 129(23):7346-7353.
-
(2007)
J Am Chem Soc
, vol.129
, Issue.23
, pp. 7346-7353
-
-
O'Brien, E.P.1
Dima, R.I.2
Brooks, B.3
Thirumalai, D.4
-
8
-
-
37549043949
-
Interaction of urea with amino acids: Implications for urea-induced protein denaturation
-
Stumpe MC, Grubmüller H (2007) Interaction of urea with amino acids: Implications for urea-induced protein denaturation. J Am Chem Soc 129(51):16126-16131.
-
(2007)
J Am Chem Soc
, vol.129
, Issue.51
, pp. 16126-16131
-
-
Stumpe, M.C.1
Grubmüller, H.2
-
9
-
-
57149110439
-
Polar or apolar-The role of polarity for urea-induced protein denaturation
-
Stumpe MC, Grubmüller H (2008) Polar or apolar-The role of polarity for urea-induced protein denaturation. PLOS Comput Biol 4(11):e1000221.
-
(2008)
PLOS Comput Biol
, vol.4
, Issue.11
-
-
Stumpe, M.C.1
Grubmüller, H.2
-
10
-
-
67650363919
-
Urea impedes the hydrophobic collapse of partially unfolded proteins
-
Stumpe MC, Grubmüller H (2009) Urea impedes the hydrophobic collapse of partially unfolded proteins. Biophys J 96(9):3744-3752.
-
(2009)
Biophys J
, vol.96
, Issue.9
, pp. 3744-3752
-
-
Stumpe, M.C.1
Grubmüller, H.2
-
11
-
-
0037442337
-
Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution
-
Mountain RD, Thirumalai D (2003) Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc 125(7):1950-1957.
-
(2003)
J Am Chem Soc
, vol.125
, Issue.7
, pp. 1950-1957
-
-
Mountain, R.D.1
Thirumalai, D.2
-
12
-
-
62449341938
-
Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group
-
Lim WK, Rösgen J, Englander SW (2009) Urea, but not guanidinium, destabilizes proteins by forming hydrogen bonds to the peptide group. Proc Natl Acad Sci USA 106(8):2595-2600.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.8
, pp. 2595-2600
-
-
Lim, W.K.1
Rösgen, J.2
Englander, S.W.3
-
13
-
-
80054991841
-
Effect of urea on the p-hairpin conformational ensemble and protein denaturation mechanism
-
Berteotti A, Barducci A, Parrinello M (2011) Effect of urea on the p-hairpin conformational ensemble and protein denaturation mechanism. J Am Chem Soc 133(43):17200-17206.
-
(2011)
J Am Chem Soc
, vol.133
, Issue.43
, pp. 17200-17206
-
-
Berteotti, A.1
Barducci, A.2
Parrinello, M.3
-
14
-
-
55949131241
-
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
-
Hua L, Zhou R, Thirumalai D, Berne BJ (2008) Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding. Proc Natl Acad Sci USA 105(44):16928-16933.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.44
, pp. 16928-16933
-
-
Hua, L.1
Zhou, R.2
Thirumalai, D.3
Berne, B.J.4
-
15
-
-
77955365355
-
On the stability of chymotrypsin inhibitor 2 in a 10 M urea solution. The role of interaction energies for urea-induced protein denaturation
-
Lindgren M, Westlund PO (2010) On the stability of chymotrypsin inhibitor 2 in a 10 M urea solution. The role of interaction energies for urea-induced protein denaturation. Phys Chem Chem Phys 12(32):9358-9366.
-
(2010)
Phys Chem Chem Phys
, vol.12
, Issue.32
, pp. 9358-9366
-
-
Lindgren, M.1
Westlund, P.O.2
-
16
-
-
33845488514
-
Effect of urea on the structural dynamics of water
-
Rezus YL, Bakker HJ (2006) Effect of urea on the structural dynamics of water. Proc Natl Acad Sci USA 103(49):18417-18420.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.49
, pp. 18417-18420
-
-
Rezus, Y.L.1
Bakker, H.J.2
-
17
-
-
33947088873
-
Nuclear magnetic resonance studies of aqueous urea solutions
-
Finer E, Franks F, Tait M (1972) Nuclear magnetic resonance studies of aqueous urea solutions. J Am Chem Soc 94(13):4424-4429.
-
(1972)
J Am Chem Soc
, vol.94
, Issue.13
, pp. 4424-4429
-
-
Finer, E.1
Franks, F.2
Tait, M.3
-
18
-
-
34250723399
-
Aqueous urea solutions: Structure, energetics, and urea aggregation
-
Stumpe MC, Grubmüller H (2007) Aqueous urea solutions: Structure, energetics, and urea aggregation. J Phys Chem B 111(22):6220-6228.
-
(2007)
J Phys Chem B
, vol.111
, Issue.22
, pp. 6220-6228
-
-
Stumpe, M.C.1
Grubmüller, H.2
-
19
-
-
0032556206
-
Effect of the protein denaturants urea and guanidinium on water structure: A structural and thermodynamic study
-
Vanzi F, Madan B, Sharp K (1998) Effect of the protein denaturants urea and guanidinium on water structure: A structural and thermodynamic study. J Am Chem Soc 120(41):10748-10753.
-
(1998)
J Am Chem Soc
, vol.120
, Issue.41
, pp. 10748-10753
-
-
Vanzi, F.1
Madan, B.2
Sharp, K.3
-
20
-
-
0141560450
-
Impact of urea on water structure: A clue to its properties as a denaturant?
-
Soper AK, Castner EW, Luzar A (2003) Impact of urea on water structure: A clue to its properties as a denaturant? Biophys Chem 105(2-3):649-666.
-
(2003)
Biophys Chem
, vol.105
, Issue.2-3
, pp. 649-666
-
-
Soper, A.K.1
Castner, E.W.2
Luzar, A.3
-
21
-
-
0021764813
-
Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure
-
Pardi A, Billeter M, Wüthrich K (1984) Calibration of the angular dependence of the amide proton-C alpha proton coupling constants, 3JHN alpha, in a globular protein. Use of 3JHN alpha for identification of helical secondary structure. J Mol Biol 180(3):741-751.
-
(1984)
J Mol Biol
, vol.180
, Issue.3
, pp. 741-751
-
-
Pardi, A.1
Billeter, M.2
Wüthrich, K.3
-
22
-
-
80054717093
-
Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer
-
Guinn EJ, Pegram LM, Capp MW, Pollock MN, Record MT, Jr. (2011) Quantifying why urea is a protein denaturant, whereas glycine betaine is a protein stabilizer. Proc Natl Acad Sci USA 108(41):16932-16937.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.41
, pp. 16932-16937
-
-
Guinn, E.J.1
Pegram, L.M.2
Capp, M.W.3
Pollock, M.N.4
Record Jr., M.T.5
-
23
-
-
0037007485
-
Fifty years of solvent denaturation
-
Schellman JA (2002) Fifty years of solvent denaturation. Biophys Chem 96(2-3):91-101.
-
(2002)
Biophys Chem
, vol.96
, Issue.2-3
, pp. 91-101
-
-
Schellman, J.A.1
-
24
-
-
27744555656
-
Protein folding, stability, and solvation structure in osmolyte solutions
-
Rösgen J, Pettitt BM, Bolen DW (2005) Protein folding, stability, and solvation structure in osmolyte solutions. Biophys J 89(5):2988-2997.
-
(2005)
Biophys J
, vol.89
, Issue.5
, pp. 2988-2997
-
-
Rösgen, J.1
Pettitt, B.M.2
Bolen, D.W.3
-
25
-
-
84863236979
-
Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering data
-
Huang JR, Gabel F, Jensen MR, Grzesiek S, Blackledge M (2012) Sequence-specific mapping of the interaction between urea and unfolded ubiquitin from ensemble analysis of NMR and small angle scattering data. J Am Chem Soc 134(9):4429-4436.
-
(2012)
J Am Chem Soc
, vol.134
, Issue.9
, pp. 4429-4436
-
-
Huang, J.R.1
Gabel, F.2
Jensen, M.R.3
Grzesiek, S.4
Blackledge, M.5
-
26
-
-
72049093998
-
A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering
-
Bernadó P, Blackledge M (2009) A self-consistent description of the conformational behavior of chemically denatured proteins from NMR and small angle scattering. Biophys J 97(10):2839-2845.
-
(2009)
Biophys J
, vol.97
, Issue.10
, pp. 2839-2845
-
-
Bernadó, P.1
Blackledge, M.2
-
27
-
-
0038370011
-
The molecular basis for the chemical denaturation of proteins by urea
-
Bennion BJ, Daggett V (2003) The molecular basis for the chemical denaturation of proteins by urea. Proc Natl Acad Sci USA 100(9):5142-5147.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, Issue.9
, pp. 5142-5147
-
-
Bennion, B.J.1
Daggett, V.2
-
28
-
-
0030939289
-
Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea
-
Tirado-Rives J, Orozco M, Jorgensen WL (1997) Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea. Biochemistry 36(24):7313-7329.
-
(1997)
Biochemistry
, vol.36
, Issue.24
, pp. 7313-7329
-
-
Tirado-Rives, J.1
Orozco, M.2
Jorgensen, W.L.3
-
29
-
-
77749285768
-
Equilibrium study of protein denaturation by urea
-
Canchi DR, Paschek D, García AE (2010) Equilibrium study of protein denaturation by urea. J Am Chem Soc 132(7):2338-2344.
-
(2010)
J Am Chem Soc
, vol.132
, Issue.7
, pp. 2338-2344
-
-
Canchi, D.R.1
Paschek, D.2
García, A.E.3
-
30
-
-
77950831084
-
Refinement of ensembles describing unstructured proteins using NMR residual dipolar couplings
-
Esteban-Martín S, Fenwick RB, Salvatella X (2010) Refinement of ensembles describing unstructured proteins using NMR residual dipolar couplings. J Am Chem Soc 132(13):4626-4632.
-
(2010)
J Am Chem Soc
, vol.132
, Issue.13
, pp. 4626-4632
-
-
Esteban-Martín, S.1
Fenwick, R.B.2
Salvatella, X.3
-
31
-
-
24944542708
-
Statistical coil model of the unfolded state: Resolving the reconciliation problem
-
Jha AK, Colubri A, Freed KF, Sosnick TR (2005) Statistical coil model of the unfolded state: Resolving the reconciliation problem. Proc Natl Acad Sci USA 102(37):13099-13104.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.37
, pp. 13099-13104
-
-
Jha, A.K.1
Colubri, A.2
Freed, K.F.3
Sosnick, T.R.4
-
32
-
-
84860456767
-
MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations
-
Hospital A, et al. (2012) MDWeb and MDMoby: An integrated web-based platform for molecular dynamics simulations. Bioinformatics 28(9):1278-1279.
-
(2012)
Bioinformatics
, vol.28
, Issue.9
, pp. 1278-1279
-
-
Hospital, A.1
-
33
-
-
0039232743
-
Keeping the shape but changing the charge: A simulation study of urea and its iso-steric analogues
-
Tsai J, Gerstein M, Levitt M (1996) Keeping the shape but changing the charge: A simulation study of urea and its iso-steric analogues. J Chem Phys 104(23):9417-9430.
-
(1996)
J Chem Phys
, vol.104
, Issue.23
, pp. 9417-9430
-
-
Tsai, J.1
Gerstein, M.2
Levitt, M.3
-
34
-
-
2942555203
-
Importance of excluded volume on the solvation of urea in water
-
Mountain RD, Thirumalai D (2004) Importance of excluded volume on the solvation of urea in water. J Phys Chem B 108(21):6826-6831.
-
(2004)
J Phys Chem B
, vol.108
, Issue.21
, pp. 6826-6831
-
-
Mountain, R.D.1
Thirumalai, D.2
-
35
-
-
79953059618
-
Urea-induced drying of hydrophobic nanotubes: Comparison of different urea models
-
Xiu P, et al. (2011) Urea-induced drying of hydrophobic nanotubes: Comparison of different urea models. J Phys Chem B 115(12):2988-2994.
-
(2011)
J Phys Chem B
, vol.115
, Issue.12
, pp. 2988-2994
-
-
Xiu, P.1
-
36
-
-
6944251055
-
Note in an approximation treatment for many-electron system
-
Møller C, Plesset MS (1934) Note in an approximation treatment for many-electron system. Phys Rev 46(7):618-622.
-
(1934)
Phys Rev
, vol.46
, Issue.7
, pp. 618-622
-
-
Møller, C.1
Plesset, M.S.2
-
37
-
-
70450206724
-
-
Revision A.1, Inc., Wallingford CT
-
Frisch MJ, et al. (2009) Gaussian 09, (Revision A.1, Inc., Wallingford CT). Available at http://www.gaussian. com/g-tech/g-ur/m-citation. htm.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.1
-
38
-
-
84986513726
-
Calculation of the average properties of atoms in molecules. II
-
Biegler-König FW, Bader R F W, Tang TH (1982) Calculation of the average properties of atoms in molecules. II. J Comput Chem 13(2):317-328.
-
(1982)
J Comput Chem
, vol.13
, Issue.2
, pp. 317-328
-
-
Biegler-König, F.W.1
Bader, R.F.W.2
Tang, T.H.3
-
39
-
-
0029878720
-
VMD: Visual molecular dynamics
-
27-28
-
Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. J Mol Graph 14(1):33-38, 27-28.
-
(1996)
J Mol Graph
, vol.14
, Issue.1
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
40
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23(4):566-579.
-
(1995)
Proteins
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
41
-
-
0037189885
-
Physical interpretation of residual dipolar couplings in neutral aligned media
-
Almond A, Axelsen JB (2002) Physical interpretation of residual dipolar couplings in neutral aligned media. J Am Chem Soc 124(34):9986-9987.
-
(2002)
J Am Chem Soc
, vol.124
, Issue.34
, pp. 9986-9987
-
-
Almond, A.1
Axelsen, J.B.2
-
42
-
-
0029185933
-
CRYSOL-A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
-
Svergun DI, Barberato C, Koch M H J (1995) CRYSOL-A program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl Cryst 28(6):768-773.
-
(1995)
J. Appl Cryst
, vol.28
, Issue.6
, pp. 768-773
-
-
Svergun, D.I.1
Barberato, C.2
Koch, M.H.J.3
-
43
-
-
33846512402
-
A consensus view of protein dynamics
-
Rueda M, et al. (2007) A consensus view of protein dynamics. Proc Natl Acad Sci USA 104(3):796-801.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.3
, pp. 796-801
-
-
Rueda, M.1
-
44
-
-
84857463877
-
Systematic validation of protein force fields against experimental data
-
Lindorff-Larsen K, et al. (2012) Systematic validation of protein force fields against experimental data. PLoS ONE 7(2):e32131.
-
(2012)
PLoS ONE
, vol.7
, Issue.2
-
-
Lindorff-Larsen, K.1
-
45
-
-
33846564097
-
Direct observation of dipolar couplings and hydrogen bonds across a beta-hairpin in 8 M urea
-
Meier S, Strohmeier M, Blackledge M, Grzesiek S (2007) Direct observation of dipolar couplings and hydrogen bonds across a beta-hairpin in 8 M urea. J Am Chem Soc 129(4):754-755.
-
(2007)
J Am Chem Soc
, vol.129
, Issue.4
, pp. 754-755
-
-
Meier, S.1
Strohmeier, M.2
Blackledge, M.3
Grzesiek, S.4
-
46
-
-
76749109966
-
Hydrogen bonding progressively strengthens upon transfer of the protein urea-denatured state to water and protecting osmolytes
-
Holthauzen LM, Rösgen J, Bolen DW (2010) Hydrogen bonding progressively strengthens upon transfer of the protein urea-denatured state to water and protecting osmolytes. Biochemistry 49(6):1310-1318.
-
(2010)
Biochemistry
, vol.49
, Issue.6
, pp. 1310-1318
-
-
Holthauzen, L.M.1
Rösgen, J.2
Bolen, D.W.3
-
47
-
-
0345401784
-
A quantum theory of molecular structure and its applications
-
Bader R (1991) A quantum theory of molecular structure and its applications. Chem Rev 91(5):893-928.
-
(1991)
Chem Rev
, vol.91
, Issue.5
, pp. 893-928
-
-
Bader, R.1
-
48
-
-
31344444913
-
Hydrogen bonds: Relation between lengths and electron densities at bond critical points
-
Tang TH, Deretey E, Knak Jensen SJ, Csizmadia IG (2006) Hydrogen bonds: Relation between lengths and electron densities at bond critical points. Eur Phys J D 37:217-222.
-
(2006)
Eur Phys J D
, vol.37
, pp. 217-222
-
-
Tang, T.H.1
Deretey, E.2
Knak Jensen, S.J.3
Csizmadia, I.G.4
-
49
-
-
0030320442
-
The concept of a random coil. Residual structure in peptides and denatured proteins
-
Smith LJ, Fiebig KM, Schwalbe H, Dobson CM (1996) The concept of a random coil. Residual structure in peptides and denatured proteins. Fold Des 1(5):R95-R106.
-
(1996)
Fold des
, vol.1
, Issue.5
-
-
Smith, L.J.1
Fiebig, K.M.2
Schwalbe, H.3
Dobson, C.M.4
|