-
1
-
-
0026320508
-
Protein stability and molecular adaptation to extreme conditons
-
Jaenicke R. Protein stability and molecular adaptation to extreme conditons. Eur J Biochem 1991; 202: 715-728.
-
(1991)
Eur J Biochem
, vol.202
, pp. 715-728
-
-
Jaenicke, R.1
-
2
-
-
20144369761
-
Stability of proteins: Temperature, pressure and the role of the solvent
-
Scharnagl C, Reif M, Friedrich J. Stability of proteins: Temperature, pressure and the role of the solvent. Biochim Biophys Acta 2005; 1749: 187-213.
-
(2005)
Biochim Biophys Acta
, vol.1749
, pp. 187-213
-
-
Scharnagl, C.1
Reif, M.2
Friedrich, J.3
-
3
-
-
33645960997
-
Protein stability and dynamics in the pressure-temperature plane
-
Meersman F, Smeller L, Heremans K. Protein stability and dynamics in the pressure-temperature plane. Biochim Biophys Acta 2006; 1764: 346-354.
-
(2006)
Biochim Biophys Acta
, vol.1764
, pp. 346-354
-
-
Meersman, F.1
Smeller, L.2
Heremans, K.3
-
4
-
-
0037437224
-
On the temperature-pressure free-energy landscape of proteins
-
Ravindra R, Winter R. On the temperature-pressure free-energy landscape of proteins. ChemPhysChem 2003; 4: 359-365.
-
(2003)
ChemPhysChem
, vol.4
, pp. 359-365
-
-
Ravindra, R.1
Winter, R.2
-
5
-
-
0027762355
-
Pressure stability of proteins
-
Silva JL, Weber G. Pressure stability of proteins. Annu Rev Phys Chem 1993; 44: 89-113.
-
(1993)
Annu Rev Phys Chem
, vol.44
, pp. 89-113
-
-
Silva, J.L.1
Weber, G.2
-
7
-
-
0037171124
-
High pressure simulations of biomolecules
-
Paci E. High pressure simulations of biomolecules. Biochim Biophys Acta 2002; 1595: 185-200.
-
(2002)
Biochim Biophys Acta
, vol.1595
, pp. 185-200
-
-
Paci, E.1
-
8
-
-
69949130768
-
Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution
-
Ortore MG, Spinozzi F, Mariani P, Paciaroni A, Barbosa LRS, Amenitsch H, Steinhart M, Ollivier J, Russo D. Combining structure and dynamics: non-denaturing high-pressure effect on lysozyme in solution. J R Soc Interface 2009; 6: S619-S634.
-
(2009)
J R Soc Interface
, vol.6
-
-
Ortore, M.G.1
Spinozzi, F.2
Mariani, P.3
Paciaroni, A.4
Barbosa, L.R.S.5
Amenitsch, H.6
Steinhart, M.7
Ollivier, J.8
Russo, D.9
-
9
-
-
0026785575
-
Molecular dynamics simulation of solvated protein at high pressure
-
Kitchen DB, Reed LH, Levy RM. Molecular dynamics simulation of solvated protein at high pressure. Biochemistry 1992; 31: 10083-10093.
-
(1992)
Biochemistry
, vol.31
, pp. 10083-10093
-
-
Kitchen, D.B.1
Reed, L.H.2
Levy, R.M.3
-
10
-
-
28944435120
-
Effect of pressure on the conformation of proteins. A molecular dynamics simulation of lysozyme
-
McCarthy AN, Grigera JR. Effect of pressure on the conformation of proteins. A molecular dynamics simulation of lysozyme. J Mol Graph Model 2006; 24: 254-261.
-
(2006)
J Mol Graph Model
, vol.24
, pp. 254-261
-
-
McCarthy, A.N.1
Grigera, J.R.2
-
11
-
-
41849146789
-
Relaxation dynamics of lysozyme in solution under pressure: combining molecular dynamics simulations and quasielastic neutron scattering
-
Calandrini V, Hamon V, Hinsen K, Calligari P, Bellissent-Funel M-C, Kneller GR. Relaxation dynamics of lysozyme in solution under pressure: combining molecular dynamics simulations and quasielastic neutron scattering. Chem Phys 2008; 345: 289-297.
-
(2008)
Chem Phys
, vol.345
, pp. 289-297
-
-
Calandrini, V.1
Hamon, V.2
Hinsen, K.3
Calligari, P.4
Bellissent-Funel, M.-C.5
Kneller, G.R.6
-
12
-
-
37648998898
-
A high pressure cell for small angle neutron scattering up to 500 MPa in combination with light scattering to investigate liquid samples
-
Kohlbrecher J, Bollhalder A, Vavrin R, Meier G. A high pressure cell for small angle neutron scattering up to 500 MPa in combination with light scattering to investigate liquid samples. Rev Sci Instrum 2007; 78: 125101.
-
(2007)
Rev Sci Instrum
, vol.78
, pp. 125101
-
-
Kohlbrecher, J.1
Bollhalder, A.2
Vavrin, R.3
Meier, G.4
-
13
-
-
25444479429
-
The influence of a medium pressure on the structure and dynamics of a bovine pancreatic trypsin inhibitor protein
-
Appavou MS, Gibrat G, Bellissent-Funel M-C, Plazanet M, Pieper J, Buchsteiner A, Annighöfer B. The influence of a medium pressure on the structure and dynamics of a bovine pancreatic trypsin inhibitor protein. J Phys: Condens Matter 2005; 17: S3093-S3099.
-
(2005)
J Phys: Condens Matter
, vol.17
-
-
Appavou, M.S.1
Gibrat, G.2
Bellissent-Funel, M.-C.3
Plazanet, M.4
Pieper, J.5
Buchsteiner, A.6
Annighöfer, B.7
-
14
-
-
0344406172
-
Pressure-dependent changes in the solution structure of hen egg-white lysozyme
-
Refaee M, Tezuka T, Akasaka K, Williamson MP. Pressure-dependent changes in the solution structure of hen egg-white lysozyme. J Mol Biol 2003; 327: 857-865.
-
(2003)
J Mol Biol
, vol.327
, pp. 857-865
-
-
Refaee, M.1
Tezuka, T.2
Akasaka, K.3
Williamson, M.P.4
-
15
-
-
0033932840
-
Protein compressibility, dynamics, and pressure
-
Kharakoz DP. Protein compressibility, dynamics, and pressure. Biophys J 2000; 79: 511-525.
-
(2000)
Biophys J
, vol.79
, pp. 511-525
-
-
Kharakoz, D.P.1
-
16
-
-
33244458851
-
Pressure-dependent transition in protein dynamics at about 4kbar revealed by molecular dynamics simulation
-
Meinhold L, Smith JC. Pressure-dependent transition in protein dynamics at about 4kbar revealed by molecular dynamics simulation. Phys Rev E 2005; 72: 061908.
-
(2005)
Phys Rev E
, vol.72
, pp. 061908
-
-
Meinhold, L.1
Smith, J.C.2
-
18
-
-
0035478292
-
Pressure provides new insights into protein folding, dynamics and structure
-
Silva JL, Foguel D, Royer CA. Pressure provides new insights into protein folding, dynamics and structure. Trends Biochem Sci 2001; 26: 612-618.
-
(2001)
Trends Biochem Sci
, vol.26
, pp. 612-618
-
-
Silva, J.L.1
Foguel, D.2
Royer, C.A.3
-
19
-
-
79958163072
-
Analysis of the mechanism of lysozyme pressure denaturation from Raman spectroscopy investigations, and comparison with thermal denaturation
-
Hédoux A, Guinet Y, Paccou L. Analysis of the mechanism of lysozyme pressure denaturation from Raman spectroscopy investigations, and comparison with thermal denaturation. J Phys Chem B 2011; 115: 6740-6748.
-
(2011)
J Phys Chem B
, vol.115
, pp. 6740-6748
-
-
Hédoux, A.1
Guinet, Y.2
Paccou, L.3
-
20
-
-
0031837399
-
Determination of the volume changes for pressure-induced transitions of apomyoglobin between the native, molten globule, and unfolded states
-
Vidugiris GJA, Royer CA. Determination of the volume changes for pressure-induced transitions of apomyoglobin between the native, molten globule, and unfolded states. Biophys J 1998; 75: 463-470.
-
(1998)
Biophys J
, vol.75
, pp. 463-470
-
-
Vidugiris, G.J.A.1
Royer, C.A.2
-
21
-
-
0032539604
-
The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins
-
Hummer G, Garde S, Garcia AE, Paulaitis ME, Pratt LR. The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. Proc Natl Acad Sci USA 1998; 95: 1552-1555.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 1552-1555
-
-
Hummer, G.1
Garde, S.2
Garcia, A.E.3
Paulaitis, M.E.4
Pratt, L.R.5
-
22
-
-
77951232650
-
Studying pressure denaturation of a protein by molecular dynamics simulations
-
Sarupria S, Ghosh T, García AE, Garde S. Studying pressure denaturation of a protein by molecular dynamics simulations. Proteins 2010; 78: 1641-1651.
-
(2010)
Proteins
, vol.78
, pp. 1641-1651
-
-
Sarupria, S.1
Ghosh, T.2
García, A.E.3
Garde, S.4
-
23
-
-
33845422105
-
Decomposition of protein experimental compressibility into intrinsic and hydration shell contributions
-
Dadarlat VM, Post CB. Decomposition of protein experimental compressibility into intrinsic and hydration shell contributions. Biophys J 2006; 91: 4544-4554.
-
(2006)
Biophys J
, vol.91
, pp. 4544-4554
-
-
Dadarlat, V.M.1
Post, C.B.2
-
24
-
-
56649083699
-
Computing the stability diagram of the Trp-cage miniprotein
-
Paschek D, Hempel S, Garcia AE. Computing the stability diagram of the Trp-cage miniprotein. Proc Natl Acad Sci USA 2008; 105: 17754-17759.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17754-17759
-
-
Paschek, D.1
Hempel, S.2
Garcia, A.E.3
-
25
-
-
0000170769
-
Structures of high-density and low-density water
-
K
-
Soper AK, Ricci MA. Structures of high-density and low-density water. Phys Rev Lett 2000; 84: 2881-2884.
-
(2000)
Phys Rev Lett
, vol.84
, pp. 2881-2884
-
-
Soper, A.1
Ricci, M.A.2
-
26
-
-
0037120451
-
Pressure evolution of the high-frequency sound velocity in liquid water
-
Krisch M, Loubeyre P, Ruocco G, Sette F, Cunsolo A, D'Astuto M, LeToullec R, Lorenzen M, Mermet A, Monaco G, Verbeni R. Pressure evolution of the high-frequency sound velocity in liquid water. Phys Rev Lett 2002; 89: 125502.
-
(2002)
Phys Rev Lett
, vol.89
, pp. 125502
-
-
Krisch, M.1
Loubeyre, P.2
Ruocco, G.3
Sette, F.4
Cunsolo, A.5
D'Astuto, M.6
LeToullec, R.7
Lorenzen, M.8
Mermet, A.9
Monaco, G.10
Verbeni, R.11
-
27
-
-
0027732618
-
Effect of solvent on collective motions in globular protein
-
Hayward S, Kitao A, Hirata F, Go N. Effect of solvent on collective motions in globular protein. J Mol Biol 1993; 234: 1207-1217.
-
(1993)
J Mol Biol
, vol.234
, pp. 1207-1217
-
-
Hayward, S.1
Kitao, A.2
Hirata, F.3
Go, N.4
-
28
-
-
0025357111
-
Protein secondary structures in water from second-derivative amide I infrared spectra
-
Dong A, Huang P, Caughey WS. Protein secondary structures in water from second-derivative amide I infrared spectra. Biochemistry 1990; 29: 3303-3308.
-
(1990)
Biochemistry
, vol.29
, pp. 3303-3308
-
-
Dong, A.1
Huang, P.2
Caughey, W.S.3
-
29
-
-
6444222991
-
Use of glass electrodes to measure acidities in deuterium oxide
-
Glasoe PK, Long FA. Use of glass electrodes to measure acidities in deuterium oxide. J Phys Chem 1960; 64: 188-190.
-
(1960)
J Phys Chem
, vol.64
, pp. 188-190
-
-
Glasoe, P.K.1
Long, F.A.2
-
30
-
-
23144457576
-
H++: a server for estimating pKas and adding missing hydrogens to macromolecules
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, Onufriev A. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 2005; 33: W368-W371.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
31
-
-
0043194670
-
Evolution of the internal dynamics of two globular proteins from dry powder to solution
-
Pérez J, Zanotti J-M, Durand D. Evolution of the internal dynamics of two globular proteins from dry powder to solution. Biophys J 1999; 77: 454-469.
-
(1999)
Biophys J
, vol.77
, pp. 454-469
-
-
Pérez, J.1
Zanotti, J.-M.2
Durand, D.3
-
32
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks BR, Brooks CL, MacKerell AD, 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, C.L.2
MacKerell, 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..
-
33
-
-
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, Wiórkiewicz-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
Bellott3
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
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
34
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
MacKerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 2004; 25: 1400-1415.
-
(2004)
J Comput Chem
, vol.25
, pp. 1400-1415
-
-
MacKerell, A.D.1
Feig, M.2
Brooks, C.L.3
-
36
-
-
0037067102
-
Water rotational relaxation and diffusion in hydrated lysozyme
-
Marchi M, Sterpone F, Ceccarelli M. Water rotational relaxation and diffusion in hydrated lysozyme. J Am Chem Soc 2002; 124: 6787-6791.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 6787-6791
-
-
Marchi, M.1
Sterpone, F.2
Ceccarelli, M.3
-
37
-
-
84857817727
-
Magnitude and molecular origin of water slowdown next to a protein
-
Sterpone F, Stirnemann G, Laage D. Magnitude and molecular origin of water slowdown next to a protein. J Am Chem Soc 2012; 134: 4116-4119.
-
(2012)
J Am Chem Soc
, vol.134
, pp. 4116-4119
-
-
Sterpone, F.1
Stirnemann, G.2
Laage, D.3
-
38
-
-
0035526029
-
Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K
-
Mark P, Nilsson L. Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. J Phys Chem A 2001; 105: 9954-9960.
-
(2001)
J Phys Chem A
, vol.105
, pp. 9954-9960
-
-
Mark, P.1
Nilsson, L.2
-
39
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
-
Ryckaert J-P, 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
-
40
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995; 23: 566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
41
-
-
0029004611
-
The volume of atoms on the protein surface: calculated from simulation, using Voronoi Polyhedra
-
Gerstein M, Tsai J, Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi Polyhedra. J Mol Biol 1995; 249: 955-966.
-
(1995)
J Mol Biol
, vol.249
, pp. 955-966
-
-
Gerstein, M.1
Tsai, J.2
Levitt, M.3
-
42
-
-
39749155117
-
Water penetration in the low and high pressure native states of ubiquitin
-
Day R, García AE. Water penetration in the low and high pressure native states of ubiquitin. Proteins 2008; 70: 1175-1184.
-
(2008)
Proteins
, vol.70
, pp. 1175-1184
-
-
Day, R.1
García, A.E.2
-
43
-
-
36749116946
-
Molecular motions in compressed liquid water
-
Jonas J, DeFries T, Wilbur DJ. Molecular motions in compressed liquid water. J Chem Phys 1976; 65: 582-588.
-
(1976)
J Chem Phys
, vol.65
, pp. 582-588
-
-
Jonas, J.1
DeFries, T.2
Wilbur, D.J.3
-
44
-
-
78650655036
-
Entropy and dynamics of water in hydration layers of a bilayer
-
Debnath A, Mukherjee B, Ayappa KG, Maiti PK, Lin S-T. Entropy and dynamics of water in hydration layers of a bilayer. J Chem Phys 2010; 133: 174704.
-
(2010)
J Chem Phys
, vol.133
, pp. 174704
-
-
Debnath, A.1
Mukherjee, B.2
Ayappa, K.G.3
Maiti, P.K.4
Lin, S.-T.5
-
45
-
-
48549083172
-
Conformational entropy of biomolecules: beyond the quasi-harmonic approximation
-
Numata J, Wan M, Knapp E-W. Conformational entropy of biomolecules: beyond the quasi-harmonic approximation. Genome Inform 2007; 18: 192-205.
-
(2007)
Genome Inform
, vol.18
, pp. 192-205
-
-
Numata, J.1
Wan, M.2
Knapp, E.-W.3
-
46
-
-
0030057862
-
The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation
-
Abseher R, Schreiber H, Steinhauser O. The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation. Proteins 1996; 25: 366-378.
-
(1996)
Proteins
, vol.25
, pp. 366-378
-
-
Abseher, R.1
Schreiber, H.2
Steinhauser, O.3
-
47
-
-
0000866097
-
Hydrogen bonds in water
-
Rapaport DC. Hydrogen bonds in water. Mol Phys 1983; 50: 1151-1162.
-
(1983)
Mol Phys
, vol.50
, pp. 1151-1162
-
-
Rapaport, D.C.1
-
48
-
-
0035905815
-
Relationship between structural order and the anomalies of liquid water
-
Errington JR, Debenedetti PG. Relationship between structural order and the anomalies of liquid water. Nature 2001; 409: 318-321.
-
(2001)
Nature
, vol.409
, pp. 318-321
-
-
Errington, J.R.1
Debenedetti, P.G.2
-
50
-
-
0025333959
-
Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering
-
Cusack S, Doster W. Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering. Biophys J 1990; 58: 243-251.
-
(1990)
Biophys J
, vol.58
, pp. 243-251
-
-
Cusack, S.1
Doster, W.2
-
51
-
-
4043156208
-
Direct determination of vibrational density of states change on ligand binding to a protein
-
Balog E, Becker T, Oettl M, Lechner R, Daniel R, Finney J, Smith J. Direct determination of vibrational density of states change on ligand binding to a protein. Phys Rev Lett 2004; 93: 028103.
-
(2004)
Phys Rev Lett
, vol.93
, pp. 028103
-
-
Balog, E.1
Becker, T.2
Oettl, M.3
Lechner, R.4
Daniel, R.5
Finney, J.6
Smith, J.7
-
52
-
-
33749590375
-
Picosecond dynamics of T and R forms of aspartate transcarbamylase: A neutron scattering study
-
Zanotti J-M, Hervé G, Bellissent-Funel M-C. Picosecond dynamics of T and R forms of aspartate transcarbamylase: A neutron scattering study. Biochim Biophys Acta 2006; 1764: 1527-1535.
-
(2006)
Biochim Biophys Acta
, vol.1764
, pp. 1527-1535
-
-
Zanotti, J.-M.1
Hervé, G.2
Bellissent-Funel, M.-C.3
-
53
-
-
0041320758
-
Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy
-
Giraud G, Karolin J, Wynne K. Low-frequency modes of peptides and globular proteins in solution observed by ultrafast OHD-RIKES spectroscopy. Biophys J 2003; 85: 1903-1913.
-
(2003)
Biophys J
, vol.85
, pp. 1903-1913
-
-
Giraud, G.1
Karolin, J.2
Wynne, K.3
-
54
-
-
0001611784
-
Analysis of calculated normal modes of a set of native and partially unfolded proteins
-
van Vlijmen HWT, Karplus M. Analysis of calculated normal modes of a set of native and partially unfolded proteins. J Phys Chem B 1999; 103: 3009-3021.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3009-3021
-
-
van Vlijmen, H.W.T.1
Karplus, M.2
-
55
-
-
33751534910
-
Conformational heterogeneity and low-frequency vibrational modes of proteins
-
Balog E, Smith JC, Perahia D. Conformational heterogeneity and low-frequency vibrational modes of proteins. Phys Chem Chem Phys 2006; 8: 5543-5548.
-
(2006)
Phys Chem Chem Phys
, vol.8
, pp. 5543-5548
-
-
Balog, E.1
Smith, J.C.2
Perahia, D.3
-
56
-
-
73649096212
-
Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: a Raman scattering and molecular dynamics simulation study
-
Lerbret A, Affouard F, Bordat P, Hédoux A, Guinet Y, Descamps M. Low-frequency vibrational properties of lysozyme in sugar aqueous solutions: a Raman scattering and molecular dynamics simulation study. J Chem Phys 2009; 131: 245103.
-
(2009)
J Chem Phys
, vol.131
, pp. 245103
-
-
Lerbret, A.1
Affouard, F.2
Bordat, P.3
Hédoux, A.4
Guinet, Y.5
Descamps, M.6
-
57
-
-
71649083072
-
The protein-solvent glass transition
-
Doster W. The protein-solvent glass transition. Biochim Biophys Acta 2010; 1804: 3-14.
-
(2010)
Biochim Biophys Acta
, vol.1804
, pp. 3-14
-
-
Doster, W.1
-
58
-
-
36849074084
-
Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation
-
Meinhold L, Smith JC, Kitao A, Zewail AH. Picosecond fluctuating protein energy landscape mapped by pressure-temperature molecular dynamics simulation. Proc Natl Acad Sci USA 2007; 104: 17261-17265.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 17261-17265
-
-
Meinhold, L.1
Smith, J.C.2
Kitao, A.3
Zewail, A.H.4
-
59
-
-
0031554921
-
Pressure-induced changes in the folded structure of lysozyme
-
Akasaka K, Tezuka T, Yamada H. Pressure-induced changes in the folded structure of lysozyme. J Mol Biol 1997; 271: 671-678.
-
(1997)
J Mol Biol
, vol.271
, pp. 671-678
-
-
Akasaka, K.1
Tezuka, T.2
Yamada, H.3
-
60
-
-
78249233614
-
Normal mode analysis and applications in biological physics
-
Dykeman EC, Sankey OF. Normal mode analysis and applications in biological physics. J Phys Condens Matter 2010; 22: 423202.
-
(2010)
J Phys Condens Matter
, vol.22
, pp. 423202
-
-
Dykeman, E.C.1
Sankey, O.F.2
-
61
-
-
78649784550
-
Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit
-
Skjaerven L, Martinez A, Reuter N. Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit. Proteins 2011; 79: 232-243.
-
(2011)
Proteins
, vol.79
, pp. 232-243
-
-
Skjaerven, L.1
Martinez, A.2
Reuter, N.3
-
62
-
-
0000129552
-
Single-particle dynamics of water molecules in confined space
-
Bellissent-Funel M-C, Chen SH, Zanotti J-M. Single-particle dynamics of water molecules in confined space. Phys Rev E 1995; 51: 4558-4569.
-
(1995)
Phys Rev E
, vol.51
, pp. 4558-4569
-
-
Bellissent-Funel, M.-C.1
Chen, S.H.2
Zanotti, J.-M.3
-
63
-
-
2742571585
-
Slow dynamics of water molecules on the surface of a globular protein
-
Bellissent-Funel M-C, Zanotti J-M, Chen SH. Slow dynamics of water molecules on the surface of a globular protein. Faraday Discuss 1996; 103: 281-294.
-
(1996)
Faraday Discuss
, vol.103
, pp. 281-294
-
-
Bellissent-Funel, M.-C.1
Zanotti, J.-M.2
Chen, S.H.3
-
64
-
-
36849125881
-
Raman spectral studies of water structure
-
Walrafen GE. Raman spectral studies of water structure. J Chem Phys 1964; 40: 3249-3256.
-
(1964)
J Chem Phys
, vol.40
, pp. 3249-3256
-
-
Walrafen, G.E.1
-
66
-
-
79953026819
-
Short-range structural transformations in water at high pressures
-
Khusnutdinoff RM, Mokshin AV. Short-range structural transformations in water at high pressures. J Non-Cryst Solids 2011; 357: 1677-1684.
-
(2011)
J Non-Cryst Solids
, vol.357
, pp. 1677-1684
-
-
Khusnutdinoff, R.M.1
Mokshin, A.V.2
-
67
-
-
0037117502
-
Is the first hydration shell of lysozyme of higher density than bulk water?
-
Merzel F, Smith JC. Is the first hydration shell of lysozyme of higher density than bulk water? Proc Natl Acad Sci USA 2002; 99: 5378-5383.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 5378-5383
-
-
Merzel, F.1
Smith, J.C.2
-
68
-
-
34547485422
-
How protein surfaces induce anomalous dynamics of hydration water
-
Pizzitutti F, Marchi M, Sterpone F, Rossky PJ. How protein surfaces induce anomalous dynamics of hydration water. J Phys Chem B 2007; 111: 7584-7590.
-
(2007)
J Phys Chem B
, vol.111
, pp. 7584-7590
-
-
Pizzitutti, F.1
Marchi, M.2
Sterpone, F.3
Rossky, P.J.4
-
69
-
-
0032478214
-
Protein hydration in solution: experimental observation by x-ray and neutron scattering
-
Svergun DI, Richard S, Koch MHJ, Sayers Z, Kuprin S, Zaccai G. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc Natl Acad Sci USA 1998; 95: 2267-2272.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2267-2272
-
-
Svergun, D.I.1
Richard, S.2
Koch, M.H.J.3
Sayers, Z.4
Kuprin, S.5
Zaccai, G.6
-
70
-
-
73949137828
-
Tetrahedral ordering in water: Raman profiles and their temperature dependence
-
Paolantoni M, Faginas Lago N, Albertí M, Laganà A. Tetrahedral ordering in water: Raman profiles and their temperature dependence. J Phys Chem A 2009; 113: 15100-15105.
-
(2009)
J Phys Chem A
, vol.113
, pp. 15100-15105
-
-
Paolantoni, M.1
Faginas Lago, N.2
Albertí, M.3
Laganà, A.4
-
71
-
-
0001156416
-
The effects of pressure on structural and dynamical properties of associated liquids: molecular dynamics calculations for the extended simple point charge model of water
-
Bagchi K, Balasubramanian S, Klein ML. The effects of pressure on structural and dynamical properties of associated liquids: molecular dynamics calculations for the extended simple point charge model of water. J Chem Phys 1997; 107: 8561-8567.
-
(1997)
J Chem Phys
, vol.107
, pp. 8561-8567
-
-
Bagchi, K.1
Balasubramanian, S.2
Klein, M.L.3
-
73
-
-
0037899660
-
Polarizable atomic multipole water model for molecular mechanics simulation
-
Ren P, Ponder JW. Polarizable atomic multipole water model for molecular mechanics simulation. J Phys Chem B 2003; 107: 5933-5947.
-
(2003)
J Phys Chem B
, vol.107
, pp. 5933-5947
-
-
Ren, P.1
Ponder, J.W.2
-
74
-
-
33144482975
-
Relation between rotational and translational dynamic heterogeneities in water
-
Mazza MG, Giovambattista N, Starr FW, Stanley HE. Relation between rotational and translational dynamic heterogeneities in water. Phys Rev Lett 2006; 96: 057803.
-
(2006)
Phys Rev Lett
, vol.96
, pp. 057803
-
-
Mazza, M.G.1
Giovambattista, N.2
Starr, F.W.3
Stanley, H.E.4
-
76
-
-
0345498055
-
Anomalous diffusion of adsorbed water: a neutron scattering study of hydrated myoglobin
-
Settles M, Doster W. Anomalous diffusion of adsorbed water: a neutron scattering study of hydrated myoglobin. Faraday Discuss 1996; 103: 269-279.
-
(1996)
Faraday Discuss
, vol.103
, pp. 269-279
-
-
Settles, M.1
Doster, W.2
-
77
-
-
36549103625
-
Temperature dependence of the low- and high-frequency Raman scattering from liquid water
-
Walrafen GE, Fisher MR, Hokmabadi MS, Yang W-H. Temperature dependence of the low- and high-frequency Raman scattering from liquid water. J Chem Phys 1986; 85: 6970-6982.
-
(1986)
J Chem Phys
, vol.85
, pp. 6970-6982
-
-
Walrafen, G.E.1
Fisher, M.R.2
Hokmabadi, M.S.3
Yang, W.-H.4
-
78
-
-
0037257527
-
An interpretation of the low-frequency spectrum of liquid water
-
Padró JA, Martí J. An interpretation of the low-frequency spectrum of liquid water. J Chem Phys 2003; 118: 452-453.
-
(2003)
J Chem Phys
, vol.118
, pp. 452-453
-
-
Padró, J.A.1
Martí, J.2
-
79
-
-
77956209545
-
Combining THz spectroscopy and MD simulations to study protein-hydration coupling
-
Heyden M, Havenith M. Combining THz spectroscopy and MD simulations to study protein-hydration coupling. Methods 2010; 52: 74-83.
-
(2010)
Methods
, vol.52
, pp. 74-83
-
-
Heyden, M.1
Havenith, M.2
-
80
-
-
37249045537
-
Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study
-
Chakraborty S, Sinha SK, Bandyopadhyay S. Low-frequency vibrational spectrum of water in the hydration layer of a protein: a molecular dynamics simulation study. J Phys Chem B 2007; 111: 13626-13631.
-
(2007)
J Phys Chem B
, vol.111
, pp. 13626-13631
-
-
Chakraborty, S.1
Sinha, S.K.2
Bandyopadhyay, S.3
-
81
-
-
57049116557
-
On the molecular mechanism of water reorientation
-
Laage D, Hynes JT. On the molecular mechanism of water reorientation. J Phys Chem B 2008; 112: 14230-14242.
-
(2008)
J Phys Chem B
, vol.112
, pp. 14230-14242
-
-
Laage, D.1
Hynes, J.T.2
-
82
-
-
38949207174
-
Effect of temperature, pressure, and cosolvents on structural and dynamic properties of the hydration shell of SNase: a molecular dynamics computer simulation study
-
Smolin N, Winter R. Effect of temperature, pressure, and cosolvents on structural and dynamic properties of the hydration shell of SNase: a molecular dynamics computer simulation study. J Phy Chem B 2008; 112: 997-1006.
-
(2008)
J Phy Chem B
, vol.112
, pp. 997-1006
-
-
Smolin, N.1
Winter, R.2
-
83
-
-
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
-
85
-
-
33845561444
-
Compressibility of globular proteins in water at 25°C
-
Gekko K, Noguchi H. Compressibility of globular proteins in water at 25°C. J Phys Chem 1979; 83: 2706-2714.
-
(1979)
J Phys Chem
, vol.83
, pp. 2706-2714
-
-
Gekko, K.1
Noguchi, H.2
-
87
-
-
0030892956
-
NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules
-
Otting G, Liepinsh E, Halle B, Frey U. NMR identification of hydrophobic cavities with low water occupancies in protein structures using small gas molecules. Nature Struct Biol 1997; 4: 396-404.
-
(1997)
Nature Struct Biol
, vol.4
, pp. 396-404
-
-
Otting, G.1
Liepinsh, E.2
Halle, B.3
Frey, U.4
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