-
1
-
-
0019889036
-
Calculations of enzymatic-reactions-calculations of pKa, proton-transfer reactions, and general acid catalysis reactions in enzymes
-
Warshel A. Calculations of enzymatic-reactions-calculations of pKa, proton-transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 1981;20:3167-3177.
-
(1981)
Biochemistry
, vol.20
, pp. 3167-3177
-
-
Warshel, A.1
-
2
-
-
0036001159
-
Structural basis of perturbed pKa values of catalytic groups in enzyme active sites
-
Harris TK, Turner GJ. Structural basis of perturbed pKa values of catalytic groups in enzyme active sites. IUBMB Life 2002;53:85-98.
-
(2002)
IUBMB Life
, vol.53
, pp. 85-98
-
-
Harris, T.K.1
Turner, G.J.2
-
3
-
-
0042011188
-
Calculating pKa values in enzyme active sites
-
Nielsen JE, Mccammon JA. Calculating pKa values in enzyme active sites. Protein Sci 2003;12:1894-1901.
-
(2003)
Protein Sci
, vol.12
, pp. 1894-1901
-
-
Nielsen, J.E.1
Mccammon, J.A.2
-
4
-
-
0034620544
-
Protonation states and pH titration in the photocycle of photoactive yellow protein
-
Demchuk E, Genick UK, Woo TT, Getzoff ED, Bashford D. Protonation states and pH titration in the photocycle of photoactive yellow protein. Biochemistry 2000;39:1100-1113.
-
(2000)
Biochemistry
, vol.39
, pp. 1100-1113
-
-
Demchuk, E.1
Genick, U.K.2
Woo, T.T.3
Getzoff, E.D.4
Bashford, D.5
-
5
-
-
0032516494
-
Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin
-
Dillet V, Dyson HJ, Bashford D. Calculations of electrostatic interactions and pKas in the active site of Escherichia coli thioredoxin. Biochemistry 1998;37:10298-10306.
-
(1998)
Biochemistry
, vol.37
, pp. 10298-10306
-
-
Dillet, V.1
Dyson, H.J.2
Bashford, D.3
-
6
-
-
80155168200
-
Charged nucleobases and their potential for RNA catalysis
-
Wilcox JL, Ahluwalia AK, Bevilacqua PC. Charged nucleobases and their potential for RNA catalysis. Acc Chem Res 2011;44:1270-1279.
-
(2011)
Acc Chem Res
, vol.44
, pp. 1270-1279
-
-
Wilcox, J.L.1
Ahluwalia, A.K.2
Bevilacqua, P.C.3
-
7
-
-
84871308282
-
Role of pK(a) of nucleobases in the origins of chemical evolution
-
Krishnamurthy R. Role of pK(a) of nucleobases in the origins of chemical evolution. Acc Chem Res 2012;45:2035-2044.
-
(2012)
Acc Chem Res
, vol.45
, pp. 2035-2044
-
-
Krishnamurthy, R.1
-
8
-
-
0035852640
-
Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage
-
Proc Natl Acad Sci USA
-
Shih IH, Been MD. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc Natl Acad Sci USA 2001;98:1489-1494.
-
(2001)
, vol.98
, pp. 1489-1494
-
-
Shih, I.H.1
Been, M.D.2
-
9
-
-
2442641641
-
A conformational switch controls hepatitis delta virus ribozyme catalysis
-
Ke A, Zhou K, Ding F, Cate JH, Doudna JA. A conformational switch controls hepatitis delta virus ribozyme catalysis. Nature 2004;429:201-205.
-
(2004)
Nature
, vol.429
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.4
Doudna, J.A.5
-
10
-
-
0034719109
-
Adenine protonation in domain B of the hairpin ribozyme
-
Ravindranathan S, Butcher SE, Feigon J. Adenine protonation in domain B of the hairpin ribozyme. Biochemistry 2000;39:16026-16032.
-
(2000)
Biochemistry
, vol.39
, pp. 16026-16032
-
-
Ravindranathan, S.1
Butcher, S.E.2
Feigon, J.3
-
11
-
-
0034757632
-
Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping
-
Ryder SP, Oyelere AK, Padilla JL, Klostermeier D, Millar DP, Strobel SA. Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA 2001;7:1454-1463.
-
(2001)
RNA
, vol.7
, pp. 1454-1463
-
-
Ryder, S.P.1
Oyelere, A.K.2
Padilla, J.L.3
Klostermeier, D.4
Millar, D.P.5
Strobel, S.A.6
-
12
-
-
0020119906
-
A salt bridge stabilizes the helix formed by isolated C-peptide of Rnase-A
-
Bierzynski A, Kim PS, Baldwin RL. A salt bridge stabilizes the helix formed by isolated C-peptide of Rnase-A. Proc Natl Acad Sci USA 1982;79:2470-2474.
-
(1982)
Proc Natl Acad Sci USA
, vol.79
, pp. 2470-2474
-
-
Bierzynski, A.1
Kim, P.S.2
Baldwin, R.L.3
-
13
-
-
0000640899
-
Nature of the charged-group effect on the stability of the C-peptide helix
-
Shoemaker KR, Kim PS, Brems DN, Marqusee S, York EJ, Chaiken IM, Stewart JM, Baldwin RL. Nature of the charged-group effect on the stability of the C-peptide helix. Proc Natl Acad Sci USA 1985;82:2349-2353.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 2349-2353
-
-
Shoemaker, K.R.1
Kim, P.S.2
Brems, D.N.3
Marqusee, S.4
York, E.J.5
Chaiken, I.M.6
Stewart, J.M.7
Baldwin, R.L.8
-
14
-
-
0031776357
-
Electrostatic contributions to molecular free energies in solution
-
Schaefer M, Van Vlijmen HWT, Karplus M. Electrostatic contributions to molecular free energies in solution. Adv Protein Chem 1998;51:1-57.
-
(1998)
Adv Protein Chem
, vol.51
, pp. 1-57
-
-
Schaefer, M.1
Van Vlijmen, H.W.T.2
Karplus, M.3
-
15
-
-
0029981197
-
Alternative conformations of amyloidogenic proteins govern their behavior
-
Kelly JW. Alternative conformations of amyloidogenic proteins govern their behavior. Curr Opin Struct Biol 1996;6:11-17.
-
(1996)
Curr Opin Struct Biol
, vol.6
, pp. 11-17
-
-
Kelly, J.W.1
-
17
-
-
0000467270
-
Electrostatic basis of structure-function correlation in proteins
-
Warshel A. Electrostatic basis of structure-function correlation in proteins. Acc Chem Res 1981;14:284-290.
-
(1981)
Acc Chem Res
, vol.14
, pp. 284-290
-
-
Warshel, A.1
-
18
-
-
0038833031
-
Determinants of ligand binding to cAMP-dependent protein kinase
-
Hunenberger PH, Helms V, Narayana N, Taylor SS, McCammon JA. Determinants of ligand binding to cAMP-dependent protein kinase. Biochemistry 1999;38:2358-2366.
-
(1999)
Biochemistry
, vol.38
, pp. 2358-2366
-
-
Hunenberger, P.H.1
Helms, V.2
Narayana, N.3
Taylor, S.S.4
McCammon, J.A.5
-
19
-
-
84355161447
-
An equilibrium-dependent retroviral mRNA switch regulates translational recoding
-
561-U193
-
Houck-Loomis B, Durney MA, Salguero C, Shankar N, Nagle JM, Goff SP, D'Souza VM. An equilibrium-dependent retroviral mRNA switch regulates translational recoding. Nature 2011;480:561-U193.
-
(2011)
Nature
, vol.480
-
-
Houck-Loomis, B.1
Durney, M.A.2
Salguero, C.3
Shankar, N.4
Nagle, J.M.5
Goff, S.P.6
D'Souza, V.M.7
-
21
-
-
0022546047
-
Functional-role of aspartic acid-27 in dihydrofolate-reductase revealed by mutagenesis
-
Howell EE, Villafranca JE, Warren MS, Oatley SJ, Kraut J. Functional-role of aspartic acid-27 in dihydrofolate-reductase revealed by mutagenesis. Science 1986;231:1123-1128.
-
(1986)
Science
, vol.231
, pp. 1123-1128
-
-
Howell, E.E.1
Villafranca, J.E.2
Warren, M.S.3
Oatley, S.J.4
Kraut, J.5
-
22
-
-
0033581879
-
Structural changes linked to proton translocation by subunit c of the ATP synthase
-
Rastogi VK, Girvin ME. Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature 1999;402:263-268.
-
(1999)
Nature
, vol.402
, pp. 263-268
-
-
Rastogi, V.K.1
Girvin, M.E.2
-
23
-
-
7244254183
-
Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change
-
Reiter NJ, Blad H, Abildgaard F, Butcher SE. Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change. Biochemistry 2004;43:13739-13747.
-
(2004)
Biochemistry
, vol.43
, pp. 13739-13747
-
-
Reiter, N.J.1
Blad, H.2
Abildgaard, F.3
Butcher, S.E.4
-
24
-
-
0028023726
-
Structure of influenza hemagglutinin at the pH of membrane-fusion
-
Bullough PA, Hughson FM, Skehel JJ, Wiley DC. Structure of influenza hemagglutinin at the pH of membrane-fusion. Nature 1994;371:37-43.
-
(1994)
Nature
, vol.371
, pp. 37-43
-
-
Bullough, P.A.1
Hughson, F.M.2
Skehel, J.J.3
Wiley, D.C.4
-
27
-
-
77950390113
-
Modulation of buried ionizable groups in proteins with engineered surface charge
-
Pey AL, Rodriguez-Larrea D, Gavira JA, Garcia-Moreno B, Sanchez-Ruiz JM. Modulation of buried ionizable groups in proteins with engineered surface charge. J Am Chem Soc 2010;132:1218-1219.
-
(2010)
J Am Chem Soc
, vol.132
, pp. 1218-1219
-
-
Pey, A.L.1
Rodriguez-Larrea, D.2
Gavira, J.A.3
Garcia-Moreno, B.4
Sanchez-Ruiz, J.M.5
-
28
-
-
56649102324
-
High tolerance for ionizable residues in the hydrophobic interior of proteins
-
Isom DG, Cannon BR, Castaneda CA, Robinson A, Garcia-Moreno B. High tolerance for ionizable residues in the hydrophobic interior of proteins. Proc Natl Acad Sci USA 2008;105:17784-17788.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17784-17788
-
-
Isom, D.G.1
Cannon, B.R.2
Castaneda, C.A.3
Robinson, A.4
Garcia-Moreno, B.5
-
29
-
-
81055156704
-
The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins
-
Nielsen JE, Gunner MR, Garcia-Moreno BE. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 2011;79:3249-3259.
-
(2011)
Proteins
, vol.79
, pp. 3249-3259
-
-
Nielsen, J.E.1
Gunner, M.R.2
Garcia-Moreno, B.E.3
-
30
-
-
81055157643
-
Progress in the prediction of pKa values in proteins
-
Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y, Milletti F, Nielsen JE, Farrell D, Carstensen T, Olsson MH, Shen JK, Warwicker J, Williams S, Word JM. Progress in the prediction of pKa values in proteins. Proteins 2011;79:3260-3275.
-
(2011)
Proteins
, vol.79
, pp. 3260-3275
-
-
Alexov, E.1
Mehler, E.L.2
Baker, N.3
Baptista, A.M.4
Huang, Y.5
Milletti, F.6
Nielsen, J.E.7
Farrell, D.8
Carstensen, T.9
Olsson, M.H.10
Shen, J.K.11
Warwicker, J.12
Williams, S.13
Word, J.M.14
-
31
-
-
2442693239
-
Macroscopic electrostatic models for protonation states in proteins
-
Bashford D. Macroscopic electrostatic models for protonation states in proteins. Front Biosci 2004;9:1082-1099.
-
(2004)
Front Biosci
, vol.9
, pp. 1082-1099
-
-
Bashford, D.1
-
33
-
-
0028859420
-
Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility
-
You TJ, Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J 1995;69:1721-1733.
-
(1995)
Biophys J
, vol.69
, pp. 1721-1733
-
-
You, T.J.1
Bashford, D.2
-
34
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
-
Georgescu RE, Alexov EG, Gunner MR. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys J 2002;83:1731-1748.
-
(2002)
Biophys J
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
35
-
-
0022248941
-
Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor
-
Russell ST, Warshel A. Calculations of electrostatic energies in proteins. The energetics of ionized groups in bovine pancreatic trypsin inhibitor. J Mol Biol 1985;185:389-404.
-
(1985)
J Mol Biol
, vol.185
, pp. 389-404
-
-
Russell, S.T.1
Warshel, A.2
-
36
-
-
0000728542
-
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the polaris and enzymix programs
-
Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the polaris and enzymix programs. J Comput Chem 1993;14:161-185.
-
(1993)
J Comput Chem
, vol.14
, pp. 161-185
-
-
Lee, F.S.1
Chu, Z.T.2
Warshel, A.3
-
37
-
-
0023060081
-
Free-energy of charges in solvated proteins-microscopic calculations using a reversible charging process
-
Warshel A, Sussman F, King G. Free-energy of charges in solvated proteins-microscopic calculations using a reversible charging process. Biochemistry 1986;25:8368-8372.
-
(1986)
Biochemistry
, vol.25
, pp. 8368-8372
-
-
Warshel, A.1
Sussman, F.2
King, G.3
-
38
-
-
0000671518
-
Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches
-
Sham YY, Chu ZT, Warshel A. Consistent calculations of pKa's of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 1997;101:4458-4472.
-
(1997)
J Phys Chem B
, vol.101
, pp. 4458-4472
-
-
Sham, Y.Y.1
Chu, Z.T.2
Warshel, A.3
-
39
-
-
17044422037
-
Biomolecular simulations at constant pH
-
Mongan J, Case DA. Biomolecular simulations at constant pH. Curr Opin Struct Biol 2005;15:157-163.
-
(2005)
Curr Opin Struct Biol
, vol.15
, pp. 157-163
-
-
Mongan, J.1
Case, D.A.2
-
40
-
-
0036606101
-
Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation
-
Burgi R, Kollman PA, van Gunsteren WF. Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation. Proteins 2002;47:469-480.
-
(2002)
Proteins
, vol.47
, pp. 469-480
-
-
Burgi, R.1
Kollman, P.A.2
van Gunsteren, W.F.3
-
41
-
-
0036732086
-
Constant-pH molecular dynamics using stochastic titration
-
Baptista AM, Teixeira VH, Soares CM. Constant-pH molecular dynamics using stochastic titration. J Chem Phys 2002;117:4184-4200.
-
(2002)
J Chem Phys
, vol.117
, pp. 4184-4200
-
-
Baptista, A.M.1
Teixeira, V.H.2
Soares, C.M.3
-
42
-
-
33644745556
-
Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine
-
Machuqueiro M, Baptista AM. Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine. J Phys Chem B 2006;110:2927-2933.
-
(2006)
J Phys Chem B
, vol.110
, pp. 2927-2933
-
-
Machuqueiro, M.1
Baptista, A.M.2
-
43
-
-
44949173075
-
Acidic range titration of HEWL using a constant-pH molecular dynamics method
-
Baptista AM, Machuqueiro M. Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins 2008;72:289-298.
-
(2008)
Proteins
, vol.72
, pp. 289-298
-
-
Baptista, A.M.1
Machuqueiro, M.2
-
44
-
-
0141956090
-
Generalized born model with a simple smoothing function
-
Im WP, Lee MS, Brooks CL, III. Generalized born model with a simple smoothing function. J Comput Chem 2003;24:1691-1702.
-
(2003)
J Comput Chem
, vol.24
, pp. 1691-1702
-
-
Im, W.P.1
Lee, M.S.2
Brooks III, C.L.3
-
45
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field
-
Chen JH, Im WP, Brooks CL, III. Balancing solvation and intramolecular interactions: Toward a consistent generalized born force field. J Am Chem Soc 2006;128:3728-3736.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 3728-3736
-
-
Chen, J.H.1
Im, W.P.2
Brooks III, C.L.3
-
46
-
-
2942737233
-
Constant-pH molecular dynamics simulations: a test case of succinic acid
-
Dlugosz M, Antosiewicz JM. Constant-pH molecular dynamics simulations: a test case of succinic acid. Chem Phys 2004;302:161-170.
-
(2004)
Chem Phys
, vol.302
, pp. 161-170
-
-
Dlugosz, M.1
Antosiewicz, J.M.2
-
47
-
-
42749101264
-
Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain
-
Dlugosz M, Antosiewicz JM, Robertson AD. Constant-pH molecular dynamics study of protonation-structure relationship in a heptapeptide derived from ovomucoid third domain. Phys Rev E 2004;69:021915.
-
(2004)
Phys Rev E
, vol.69
, pp. 021915
-
-
Dlugosz, M.1
Antosiewicz, J.M.2
Robertson, A.D.3
-
48
-
-
9244223045
-
Constant pH molecular dynamics in generalized born implicit solvent
-
Mongan J, Case DA, McCammon JA. Constant pH molecular dynamics in generalized born implicit solvent. J Comput Chem 2004;25:2038-2048.
-
(2004)
J Comput Chem
, vol.25
, pp. 2038-2048
-
-
Mongan, J.1
Case, D.A.2
McCammon, J.A.3
-
49
-
-
77950113751
-
Coupling constant pH molecular dynamics with accelerated molecular dynamics
-
Williams SL, de Oliveira CA, McCammon JA. Coupling constant pH molecular dynamics with accelerated molecular dynamics. J Chem Theory Comput 2010;6:560-568.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 560-568
-
-
Williams, S.L.1
de Oliveira, C.A.2
McCammon, J.A.3
-
50
-
-
77951139956
-
Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model
-
Meng Y, Roitberg AE. Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model. J Chem Theory Comput 2010;6:1401-1412.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 1401-1412
-
-
Meng, Y.1
Roitberg, A.E.2
-
51
-
-
84869051811
-
Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics
-
Swails JM, Roitberg AE. Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics. J Chem Theory Comput 2012;8:4393-4404.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 4393-4404
-
-
Swails, J.M.1
Roitberg, A.E.2
-
52
-
-
84864742236
-
pH-replica exchange molecular dynamics in proteins using a discrete protonation method
-
Sabri Dashti D, Meng Y, Roitberg AE. pH-replica exchange molecular dynamics in proteins using a discrete protonation method. J Phys Chem B 2012;116:8805-8811.
-
(2012)
J Phys Chem B
, vol.116
, pp. 8805-8811
-
-
Sabri Dashti, D.1
Meng, Y.2
Roitberg, A.E.3
-
53
-
-
77951241004
-
Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models
-
Messer BM, Roca M, Chu ZT, Vicatos S, Kilshtain AV, Warshel A. Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models. Proteins 2010;78:1212-1227.
-
(2010)
Proteins
, vol.78
, pp. 1212-1227
-
-
Messer, B.M.1
Roca, M.2
Chu, Z.T.3
Vicatos, S.4
Kilshtain, A.V.5
Warshel, A.6
-
54
-
-
33646268674
-
Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase
-
Olsson MHM, Warshel A. Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proc Natl Acad Sci USA 2006;103:6500-6505.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 6500-6505
-
-
Olsson, M.H.M.1
Warshel, A.2
-
55
-
-
4243810035
-
Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches
-
Aaqvist J, Warshel A. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chem Rev 1993;93:2523-2544.
-
(1993)
Chem Rev
, vol.93
, pp. 2523-2544
-
-
Aaqvist, J.1
Warshel, A.2
-
56
-
-
0030970305
-
Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration
-
Baptista AM, Martel PJ, Petersen SB. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins 1997;27:523.
-
(1997)
Proteins
, vol.27
, pp. 523
-
-
Baptista, A.M.1
Martel, P.J.2
Petersen, S.B.3
-
57
-
-
0035827113
-
Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines
-
Borjesson U, Hunenberger PH. Explicit-solvent molecular dynamics simulation at constant pH: Methodology and application to small amines. J Chem Phys 2001;114:9706-9719.
-
(2001)
J Chem Phys
, vol.114
, pp. 9706-9719
-
-
Borjesson, U.1
Hunenberger, P.H.2
-
58
-
-
0001692244
-
Lambda-dynamics-a new approach to free-energy calculations
-
Kong X, Brooks CL, III. Lambda-dynamics-a new approach to free-energy calculations. J Chem Phys 1996;105:2414-2423.
-
(1996)
J Chem Phys
, vol.105
, pp. 2414-2423
-
-
Kong, X.1
Brooks III, C.L.2
-
59
-
-
67650495212
-
Lambda-dynamics free energy simulation methods
-
Knight JL, Brooks CL, III. Lambda-dynamics free energy simulation methods. J Comput Chem 2009;30:1692-1700.
-
(2009)
J Comput Chem
, vol.30
, pp. 1692-1700
-
-
Knight, J.L.1
Brooks III, C.L.2
-
60
-
-
0000381173
-
Efficient and flexible algorithm for free energy calculations using the λ-dynamics approach
-
Guo Z, Brooks CL, III, Kong X. Efficient and flexible algorithm for free energy calculations using the λ-dynamics approach. J Phys Chem B 1998;102:2032-2036.
-
(1998)
J Phys Chem B
, vol.102
, pp. 2032-2036
-
-
Guo, Z.1
Brooks III, C.L.2
Kong, X.3
-
61
-
-
4043132337
-
Constant-pH molecular dynamics using continuous titration coordinates
-
Lee MS, Salsbury FR, Brooks CL, III. Constant-pH molecular dynamics using continuous titration coordinates. Proteins 2004;56:738-752.
-
(2004)
Proteins
, vol.56
, pp. 738-752
-
-
Lee, M.S.1
Salsbury, F.R.2
Brooks III, C.L.3
-
62
-
-
23244440384
-
Constant pH molecular dynamics with proton tautomerism
-
Khandogin J, Brooks CL, III. Constant pH molecular dynamics with proton tautomerism. Biophys J 2005;89:141-157.
-
(2005)
Biophys J
, vol.89
, pp. 141-157
-
-
Khandogin, J.1
Brooks III, C.L.2
-
63
-
-
33747131772
-
Toward the accurate first-principles prediction of ionization equilibria in proteins
-
Khandogin J, Brooks CL, III. Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry 2006;45:9363-9373.
-
(2006)
Biochemistry
, vol.45
, pp. 9363-9373
-
-
Khandogin, J.1
Brooks III, C.L.2
-
64
-
-
33845478722
-
Exploring atomistic details of pH-dependent peptide folding
-
Khandogin J, Chen J, Brooks CL, III. Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci USA 2006;103:18546-18550.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 18546-18550
-
-
Khandogin, J.1
Chen, J.2
Brooks III, C.L.3
-
65
-
-
33947410754
-
Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network
-
Khandogin J, Raleigh DP, Brooks CL, III. Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. J Am Chem Soc 2007;129:3056-3057.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 3056-3057
-
-
Khandogin, J.1
Raleigh, D.P.2
Brooks III, C.L.3
-
66
-
-
36749079289
-
Linking folding with aggregation in Alzheimer's beta-amyloid peptides
-
Khandogin J, Brooks CL, III. Linking folding with aggregation in Alzheimer's beta-amyloid peptides. Proc Natl Acad Sci USA 2007;104:16880-16885.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 16880-16885
-
-
Khandogin, J.1
Brooks III, C.L.2
-
67
-
-
82555187203
-
Probing pH-dependent dissociation of HdeA dimers
-
Zhang BW, Brunetti L, Brooks CL, III. Probing pH-dependent dissociation of HdeA dimers. J Am Chem Soc 2011;133:19393-19398.
-
(2011)
J Am Chem Soc
, vol.133
, pp. 19393-19398
-
-
Zhang, B.W.1
Brunetti, L.2
Brooks III, C.L.3
-
68
-
-
77955691787
-
Uncovering specific electrostatic interactions in the denatured states of proteins
-
Shen JK. Uncovering specific electrostatic interactions in the denatured states of proteins. Biophys J 2010;99:924-932.
-
(2010)
Biophys J
, vol.99
, pp. 924-932
-
-
Shen, J.K.1
-
69
-
-
84857744963
-
Unraveling a trap-and-trigger mechanism in the pH-sensitive self-assembly of spider silk proteins
-
Wallace JA, Shen JK. Unraveling a trap-and-trigger mechanism in the pH-sensitive self-assembly of spider silk proteins. J Phys Chem Lett 2012;3:658-662.
-
(2012)
J Phys Chem Lett
, vol.3
, pp. 658-662
-
-
Wallace, J.A.1
Shen, J.K.2
-
70
-
-
84878282275
-
pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability
-
Law SM, Zhang BW, Brooks CL, III. pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability. Protein Sci 2013;22:595-604.
-
(2013)
Protein Sci
, vol.22
, pp. 595-604
-
-
Law, S.M.1
Zhang, B.W.2
Brooks III, C.L.3
-
71
-
-
23144435711
-
Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study
-
Dlugosz M, Antosiewicz JM. Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study. J Phys Chem B 2005;109:13777-13784.
-
(2005)
J Phys Chem B
, vol.109
, pp. 13777-13784
-
-
Dlugosz, M.1
Antosiewicz, J.M.2
-
72
-
-
33947640091
-
The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study
-
Machuqueiro M, Baptista AM. The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study. Biophys J 2007;92:1836-1845.
-
(2007)
Biophys J
, vol.92
, pp. 1836-1845
-
-
Machuqueiro, M.1
Baptista, A.M.2
-
73
-
-
77957317648
-
Constant-pH molecular dynamics simulations reveal a beta-rich form of the human prion protein
-
Campos SR, Machuqueiro M, Baptista AM. Constant-pH molecular dynamics simulations reveal a beta-rich form of the human prion protein. J Phys Chem B 2010;114:12692-12700.
-
(2010)
J Phys Chem B
, vol.114
, pp. 12692-12700
-
-
Campos, S.R.1
Machuqueiro, M.2
Baptista, A.M.3
-
74
-
-
81055155927
-
Predicting extreme pK(a) shifts in staphylococcal nuclease mutants with constant pH molecular dynamics
-
Arthur EJ, Yesselman JD, Brooks CL, III. Predicting extreme pK(a) shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. Proteins 2011;79:3276-3286.
-
(2011)
Proteins
, vol.79
, pp. 3276-3286
-
-
Arthur, E.J.1
Yesselman, J.D.2
Brooks III, C.L.3
-
75
-
-
80051643867
-
Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange
-
Wallace JA, Shen JK. Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange. J Chem Theory Comput 2011;7:2617-2629.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2617-2629
-
-
Wallace, J.A.1
Shen, J.K.2
-
76
-
-
33749380313
-
Modulation of acid-sensing ion channel currents, acid-induced increase of intracellular Ca2+, and acidosis-mediated neuronal injury by intracellular pH
-
Wang WZ, Chu XP, Li MH, Seeds J, Simon RP, Xiong ZG. Modulation of acid-sensing ion channel currents, acid-induced increase of intracellular Ca2+, and acidosis-mediated neuronal injury by intracellular pH. J Biol Chem 2006;281:29369-29378.
-
(2006)
J Biol Chem
, vol.281
, pp. 29369-29378
-
-
Wang, W.Z.1
Chu, X.P.2
Li, M.H.3
Seeds, J.4
Simon, R.P.5
Xiong, Z.G.6
-
77
-
-
1642524428
-
pH dependency and desensitization kinetics of heterologously expressed combinations of acid-sensing ion channel subunits
-
Hesselager M, Timmermann DB, Ahring PK. pH dependency and desensitization kinetics of heterologously expressed combinations of acid-sensing ion channel subunits. J Biol Chem 2004;279:11006-11015.
-
(2004)
J Biol Chem
, vol.279
, pp. 11006-11015
-
-
Hesselager, M.1
Timmermann, D.B.2
Ahring, P.K.3
-
78
-
-
0035914378
-
pH alterations "reset" Ca2+ sensitivity of brain Na+ channel 2, a degenerin/epithelial Na+ ion channel, in planar lipid bilayers
-
Berdiev BK, Mapstone TB, Markert JM, Gillespie GY, Lockhart J, Fuller CM, Benos DJ. pH alterations "reset" Ca2+ sensitivity of brain Na+ channel 2, a degenerin/epithelial Na+ ion channel, in planar lipid bilayers. J Biol Chem 2001;276:38755-38761.
-
(2001)
J Biol Chem
, vol.276
, pp. 38755-38761
-
-
Berdiev, B.K.1
Mapstone, T.B.2
Markert, J.M.3
Gillespie, G.Y.4
Lockhart, J.5
Fuller, C.M.6
Benos, D.J.7
-
79
-
-
77950021500
-
pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG
-
Damaghi M, Bippes C, Koster S, Yildiz O, Mari SA, Kuhlbrandt W, Muller DJ. pH-dependent interactions guide the folding and gate the transmembrane pore of the beta-barrel membrane protein OmpG. J Mol Biol 2010;397:878-882.
-
(2010)
J Mol Biol
, vol.397
, pp. 878-882
-
-
Damaghi, M.1
Bippes, C.2
Koster, S.3
Yildiz, O.4
Mari, S.A.5
Kuhlbrandt, W.6
Muller, D.J.7
-
81
-
-
80052811290
-
Applying efficient implicit non-geometric constraints in alchemical free energy simulations
-
Knight JL, Brooks CL, III. Applying efficient implicit non-geometric constraints in alchemical free energy simulations. J Comput Chem 2011;32:3423-3432.
-
(2011)
J Comput Chem
, vol.32
, pp. 3423-3432
-
-
Knight, J.L.1
Brooks III, C.L.2
-
82
-
-
80052805166
-
Multisite λ dynamics for simulated structure-activity relationship studies
-
Knight JL, Brooks CL, III. Multisite λ dynamics for simulated structure-activity relationship studies. J Chem Theory Comput 2011;7:2728-2739.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2728-2739
-
-
Knight, J.L.1
Brooks III, C.L.2
-
83
-
-
84855710487
-
Constant pH molecular dynamics simulations of nucleic acids in explicit solvent
-
Goh GB, Knight JL, Brooks CL, III. Constant pH molecular dynamics simulations of nucleic acids in explicit solvent. J Chem Theory Comput 2012;8:36-46.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 36-46
-
-
Goh, G.B.1
Knight, J.L.2
Brooks III, C.L.3
-
85
-
-
84874876112
-
Toward accurate prediction of the protonation equilibrium of nucleic acids
-
Goh GB, Knight JL, Brooks CL, III. Toward accurate prediction of the protonation equilibrium of nucleic acids. J Phys Chem Lett 2013;4:760-766.
-
(2013)
J Phys Chem Lett
, vol.4
, pp. 760-766
-
-
Goh, G.B.1
Knight, J.L.2
Brooks III, C.L.3
-
86
-
-
58149512801
-
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
-
Zheng L, Chen M, Yang W. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems. Proc Natl Acad Sci USA 2008;105:20227-20232.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 20227-20232
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
87
-
-
84859416849
-
Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation
-
Shi CY, Wallace JA, Shen JK. Thermodynamic coupling of protonation and conformational equilibria in proteins: theory and simulation. Biophys J 2012;102:1590-1597.
-
(2012)
Biophys J
, vol.102
, pp. 1590-1597
-
-
Shi, C.Y.1
Wallace, J.A.2
Shen, J.K.3
-
88
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks BR, Brooks CL, III, Mackerell AD, Jr., Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem 2009;30:1545-1614.
-
(2009)
J Comput Chem
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
89
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
90
-
-
1942423619
-
MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology
-
Feig M, Karanicolas J, Brooks CL, III. MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graphics Modell 2004;22:377-395.
-
(2004)
J Mol Graphics Modell
, vol.22
, pp. 377-395
-
-
Feig, M.1
Karanicolas, J.2
Brooks III, C.L.3
-
91
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
92
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 1977;23:327-341.
-
(1977)
J Comput Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
93
-
-
0029170114
-
Molecular-dynamics simulations on solvated biomolecular systems-the particle mesh ewald method leads to stable trajectories of DNA, RNA, and Proteins
-
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA. Molecular-dynamics simulations on solvated biomolecular systems-the particle mesh ewald method leads to stable trajectories of DNA, RNA, and Proteins. J Am Chem Soc 1995;117:4193-4194.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
94
-
-
0026755515
-
Cutoff size does strongly influence molecular-dynamics results on solvated polypeptides
-
Schreiber H, Steinhauser O. Cutoff size does strongly influence molecular-dynamics results on solvated polypeptides. Biochemistry 1992;31:5856-5860.
-
(1992)
Biochemistry
, vol.31
, pp. 5856-5860
-
-
Schreiber, H.1
Steinhauser, O.2
-
95
-
-
84986534166
-
New spherical-cutoff methods for long-range forces in macromolecular simulation
-
Steinbach PJ, Brooks BR. New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem 1994;15:667-683.
-
(1994)
J Comput Chem
, vol.15
, pp. 667-683
-
-
Steinbach, P.J.1
Brooks, B.R.2
-
96
-
-
12144275299
-
Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides
-
Beck DAC, Armen RS, Daggett V. Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. Biochemistry 2005;44:609-616.
-
(2005)
Biochemistry
, vol.44
, pp. 609-616
-
-
Beck, D.A.C.1
Armen, R.S.2
Daggett, V.3
-
97
-
-
0033850287
-
On the truncation of long-range electrostatic interactions in DNA
-
Norberg J, Nilsson L. On the truncation of long-range electrostatic interactions in DNA. Biophys J 2000;79:1537-1553.
-
(2000)
Biophys J
, vol.79
, pp. 1537-1553
-
-
Norberg, J.1
Nilsson, L.2
-
98
-
-
0035957234
-
A novel view of pH titration in biomolecules
-
Onufriev A, Case DA, Ullmann GM. A novel view of pH titration in biomolecules. Biochemistry 2001;40:3413-3419.
-
(2001)
Biochemistry
, vol.40
, pp. 3413-3419
-
-
Onufriev, A.1
Case, D.A.2
Ullmann, G.M.3
-
99
-
-
0001461682
-
Examination of titration behavior
-
Nozaki Y, Tanford C. Examination of titration behavior. Methods Enzymol 1967;11:715-734.
-
(1967)
Methods Enzymol
, vol.11
, pp. 715-734
-
-
Nozaki, Y.1
Tanford, C.2
-
100
-
-
0027219184
-
Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines
-
Bashford D, Case DA, Dalvit C, Tennant L, Wright PE. Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines. Biochemistry 1993;32:8045-8056.
-
(1993)
Biochemistry
, vol.32
, pp. 8045-8056
-
-
Bashford, D.1
Case, D.A.2
Dalvit, C.3
Tennant, L.4
Wright, P.E.5
-
101
-
-
0015522917
-
Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength
-
Parsons SM, Raftery MA. Ionization behavior of the catalytic carboxyls of lysozyme. Effects of ionic strength. Biochemistry 1972;11:1623-1629.
-
(1972)
Biochemistry
, vol.11
, pp. 1623-1629
-
-
Parsons, S.M.1
Raftery, M.A.2
-
102
-
-
0016198076
-
Ionization constants of Glu 35 and Asp 52 in hen, turkey, and human lysozymes
-
Kuramitsu S, Ikeda K, Hamaguchi K, Fujio H, Amano T. Ionization constants of Glu 35 and Asp 52 in hen, turkey, and human lysozymes. J Biochem 1974;76:671-683.
-
(1974)
J Biochem
, vol.76
, pp. 671-683
-
-
Kuramitsu, S.1
Ikeda, K.2
Hamaguchi, K.3
Fujio, H.4
Amano, T.5
-
103
-
-
0016669682
-
Participation of the catalytic carboxyls, Asp 52 and Glu 35, and Asp 101 in the binding of substrate analogues to hen lysozyme
-
Kuramitsu S, Ikeda K, Hamaguchi K. Participation of the catalytic carboxyls, Asp 52 and Glu 35, and Asp 101 in the binding of substrate analogues to hen lysozyme. J Biochem 1975;77:291-301.
-
(1975)
J Biochem
, vol.77
, pp. 291-301
-
-
Kuramitsu, S.1
Ikeda, K.2
Hamaguchi, K.3
-
104
-
-
0026910551
-
Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values
-
Takahashi T, Nakamura H, Wada A. Electrostatic forces in two lysozymes: calculations and measurements of histidine pKa values. Biopolymers 1992;32:897-909.
-
(1992)
Biopolymers
, vol.32
, pp. 897-909
-
-
Takahashi, T.1
Nakamura, H.2
Wada, A.3
-
105
-
-
0028178465
-
Measurement of the individual Pk(a) values of acidic residues of hen and turkey lysozymes by 2-dimensional H-1-Nmr
-
Bartik K, Redfield C, Dobson CM. Measurement of the individual Pk(a) values of acidic residues of hen and turkey lysozymes by 2-dimensional H-1-Nmr. Biophys J 1994;66:1180-1184.
-
(1994)
Biophys J
, vol.66
, pp. 1180-1184
-
-
Bartik, K.1
Redfield, C.2
Dobson, C.M.3
-
106
-
-
79551502607
-
Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations
-
Webb H, Tynan-Connolly BM, Lee GM, Farrell D, O'Meara F, Søndergaard CR, Teilum K, Hewage C, McIntosh LP, Nielsen JE. Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations. Proteins 2011;79:685-702.
-
(2011)
Proteins
, vol.79
, pp. 685-702
-
-
Webb, H.1
Tynan-Connolly, B.M.2
Lee, G.M.3
Farrell, D.4
O'Meara, F.5
Søndergaard, C.R.6
Teilum, K.7
Hewage, C.8
McIntosh, L.P.9
Nielsen, J.E.10
-
107
-
-
81055140448
-
Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?
-
Machuqueiro M, Baptista AM. Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems? Proteins 2011;79:3437-3447.
-
(2011)
Proteins
, vol.79
, pp. 3437-3447
-
-
Machuqueiro, M.1
Baptista, A.M.2
-
108
-
-
84870174327
-
Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH
-
Wallace JA, Shen JK. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. J Chem Phys 2012;137:184105.
-
(2012)
J Chem Phys
, vol.137
, pp. 184105
-
-
Wallace, J.A.1
Shen, J.K.2
-
109
-
-
62649119756
-
Downhill versus barrier-limited folding of BBL 1: energetic and structural perturbation effects upon protonation of a histidine of unusually low pK(a)
-
Arbely E, Rutherford TJ, Sharpe TD, Ferguson N, Fersht AR. Downhill versus barrier-limited folding of BBL 1: energetic and structural perturbation effects upon protonation of a histidine of unusually low pK(a). J Mol Biol 2009;387:986-992.
-
(2009)
J Mol Biol
, vol.387
, pp. 986-992
-
-
Arbely, E.1
Rutherford, T.J.2
Sharpe, T.D.3
Ferguson, N.4
Fersht, A.R.5
-
110
-
-
0033551039
-
pK(a) values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions
-
Kuhlman B, Luisi DL, Young P, Raleigh DP. pK(a) values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions. Biochemistry 1999;38:4896-4903.
-
(1999)
Biochemistry
, vol.38
, pp. 4896-4903
-
-
Kuhlman, B.1
Luisi, D.L.2
Young, P.3
Raleigh, D.P.4
|