-
1
-
-
33645983232
-
Water structure and interactions with protein surfaces
-
Raschke, T. M. 2006. Water structure and interactions with protein surfaces. Curr. Opin. Struct. Biol. 16:152-159.
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, pp. 152-159
-
-
Raschke, T.M.1
-
2
-
-
0020094523
-
Increase in apparent compressibility of cytochrome c upon oxidation
-
Eden, D., J. B. Matthew, J. J. Rosa, and F. M. Richards. 1982. Increase in apparent compressibility of cytochrome c upon oxidation. Proc. Natl. Acad. Sci. USA. 79:815-819.
-
(1982)
Proc. Natl. Acad. Sci. USA
, vol.79
, pp. 815-819
-
-
Eden, D.1
Matthew, J.B.2
Rosa, J.J.3
Richards, F.M.4
-
3
-
-
0029619776
-
A novel basis for capsid stabilization by antiviral compounds
-
Phelps, D. K., and C. B. Post. 1995. A novel basis for capsid stabilization by antiviral compounds. J. Mol. Biol. 254:544-551.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 544-551
-
-
Phelps, D.K.1
Post, C.B.2
-
4
-
-
0027993455
-
Hydration and partial compressibility of biological compounds
-
Chalikian, T. V., A. P. Sarvazyan, and K. J. Breslauer. 1994. Hydration and partial compressibility of biological compounds. Biophys. Chem. 51:89-109.
-
(1994)
Biophys. Chem.
, vol.51
, pp. 89-109
-
-
Chalikian, T.V.1
Sarvazyan, A.P.2
Breslauer, K.J.3
-
5
-
-
0030034601
-
Compressibility as a means to detect and characterize globular protein states
-
Chalikian, T. V., and K. J. Breslauer. 1996. Compressibility as a means to detect and characterize globular protein states. Proc. Natl. Acad. Sci. USA. 93:1012-1014.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 1012-1014
-
-
Chalikian, T.V.1
Breslauer, K.J.2
-
6
-
-
0037171121
-
Compressibility gives new insight into protein dynamics and enzyme function
-
Gekko, K. 2002. Compressibility gives new insight into protein dynamics and enzyme function. Biochim. Biophys. Acta. 1595:382-386.
-
(2002)
Biochim. Biophys. Acta
, vol.1595
, pp. 382-386
-
-
Gekko, K.1
-
8
-
-
0344845411
-
Effects of disulfide bonds on compactness of protein molecules revealed by volume, compressibility, and expansibility changes during reduction
-
Gekko, K., A. Kimoto, and T. Kamiyama. 2003. Effects of disulfide bonds on compactness of protein molecules revealed by volume, compressibility, and expansibility changes during reduction. Biochemistry. 42:13746-13753.
-
(2003)
Biochemistry
, vol.42
, pp. 13746-13753
-
-
Gekko, K.1
Kimoto, A.2
Kamiyama, T.3
-
9
-
-
30444461405
-
Compressibility changes accompanying conformational transitions of apomyoglobin
-
Taulier, N., I. V. Beletskaya, and T. V. Chalikian. 2005. Compressibility changes accompanying conformational transitions of apomyoglobin. Biopolymers. 79:218-229.
-
(2005)
Biopolymers
, vol.79
, pp. 218-229
-
-
Taulier, N.1
Beletskaya, I.V.2
Chalikian, T.V.3
-
10
-
-
0041846677
-
Volume and compressibility changes accompanying thermally induced native-to-unfolded and molten globule-to-unfolded transitions of cytochrome c: A high pressure study
-
Dubins, D. N., R. Filfil, R. B. Macgregor, and T. V. Chalikian. 2003. Volume and compressibility changes accompanying thermally induced native-to-unfolded and molten globule-to-unfolded transitions of cytochrome c: A high pressure study. Biochemistry. 42:8671-8678.
-
(2003)
Biochemistry
, vol.42
, pp. 8671-8678
-
-
Dubins, D.N.1
Filfil, R.2
Macgregor, R.B.3
Chalikian, T.V.4
-
11
-
-
0037470558
-
The thermodynamics of protein-protein recognition as characterized by a combination of volumetric and calorimetric techniques: The binding of turkey ovomucoid third domain to alpha-chymotrypsin
-
Chalikian, T. V., and R. Filfil. 2003. The thermodynamics of protein-protein recognition as characterized by a combination of volumetric and calorimetric techniques: the binding of turkey ovomucoid third domain to alpha-chymotrypsin. J. Mol. Biol. 326:1271-1288.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 1271-1288
-
-
Chalikian, T.V.1
Filfil, R.2
-
12
-
-
0037171134
-
Cytochrome p-450-co and substrates: Lessons from ligand binding under high pressure
-
Jung, C. 2002. Cytochrome p-450-co and substrates: lessons from ligand binding under high pressure. Biochim. Biophys. Acta. 1595:309-328.
-
(2002)
Biochim. Biophys. Acta
, vol.1595
, pp. 309-328
-
-
Jung, C.1
-
13
-
-
0008047756
-
The hydration of globular proteins as derived from volume and compressibility measurements: Cross correlating thermodynamic and structural data
-
Chalikian, T. V., M. Totrov, R. Abagyan, and K. J. Breslauer. 1996. The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol. 260:588-603.
-
(1996)
J. Mol. Biol.
, vol.260
, pp. 588-603
-
-
Chalikian, T.V.1
Totrov, M.2
Abagyan, R.3
Breslauer, K.J.4
-
14
-
-
0345598919
-
Adhesive-cohesive model for protein compressibility: An alternative perspective on stability
-
Dadarlat, V. M., and C. B. Post. 2003. Adhesive-cohesive model for protein compressibility: an alternative perspective on stability. Proc. Natl. Acad. Sci. USA. 100:14778-14783.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 14778-14783
-
-
Dadarlat, V.M.1
Post, C.B.2
-
15
-
-
0027431378
-
Protein hydration elucidated by molecular dynamics simulation
-
Steinbach, P., and B. Brooks. 1993. Protein hydration elucidated by molecular dynamics simulation. Proc. Natl. Acad. Sci. USA. 90:9135-9139.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 9135-9139
-
-
Steinbach, P.1
Brooks, B.2
-
16
-
-
33745326750
-
Simulation studies of the protein-water interface. I. Properties at the molecular resolution
-
Schroder, C., T. Rudas, S. Boresch, and O. Steinhauser. 2006. Simulation studies of the protein-water interface. I. Properties at the molecular resolution. J. Chem. Phys. 124:234907.
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 234907
-
-
Schroder, C.1
Rudas, T.2
Boresch, S.3
Steinhauser, O.4
-
17
-
-
33745293234
-
Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution
-
Rudas, T., C. Schroder, S. Boresch, and O. Steinhauser. 2006. Simulation studies of the protein-water interface. II. Properties at the mesoscopic resolution. J. Chem. Phys. 124:234908.
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 234908
-
-
Rudas, T.1
Schroder, C.2
Boresch, S.3
Steinhauser, O.4
-
18
-
-
0033988125
-
Solvent mobility and the protein "glass" transition
-
Vitkup, D., D. Ringe, G. A. Petsko, and M. Karplus. 2000. Solvent mobility and the protein "glass" transition. Nat. Struct. Biol. 7:34-38.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 34-38
-
-
Vitkup, D.1
Ringe, D.2
Petsko, G.A.3
Karplus, M.4
-
19
-
-
0025877453
-
Protein hydration and function
-
Rupley, J. A., and G. Careri. 1991. Protein hydration and function. Adv. Protein Chem. 41:37-172.
-
(1991)
Adv. Protein Chem.
, vol.41
, pp. 37-172
-
-
Rupley, J.A.1
Careri, G.2
-
20
-
-
0035726161
-
Is the cell a gel - And why does it matter?
-
Pollack, G. H. 2001. Is the cell a gel - and why does it matter? Jpn. J. Physiol. 51:649-660.
-
(2001)
Jpn. J. Physiol.
, vol.51
, pp. 649-660
-
-
Pollack, G.H.1
-
21
-
-
0037466515
-
The role of aqueous interfaces in the cell
-
Pollack, G. H. 2003. The role of aqueous interfaces in the cell. Adv. Colloid Interface Sci. 103:173-196.
-
(2003)
Adv. Colloid Interface Sci.
, vol.103
, pp. 173-196
-
-
Pollack, G.H.1
-
22
-
-
0027304152
-
Hydration of proteins: A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations
-
Brunne, R. M., E. Liepinsh, G. Otting, K. Wuthrich, and W. F. van Gunsteren. 1993. Hydration of proteins: a comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations. J. Mol. Biol. 231:1040-1048.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 1040-1048
-
-
Brunne, R.M.1
Liepinsh, E.2
Otting, G.3
Wuthrich, K.4
Van Gunsteren, W.F.5
-
23
-
-
0027369863
-
Multiple hydration layers in cubic insulin crystals
-
Badger, J. 1993. Multiple hydration layers in cubic insulin crystals. Biophys. J. 65:1656-1659.
-
(1993)
Biophys. J.
, vol.65
, pp. 1656-1659
-
-
Badger, J.1
-
24
-
-
0032478214
-
Protein hydration in solution: Experimental observation by x-ray and neutron scattering
-
Svergun, D. I., S. M. Richard, H. J. Koch, Z. Sayers, S. Kuprin, and G. Zaccai. 1998. Protein hydration in solution: experimental observation by x-ray and neutron scattering. Proc. Natl. Acad. Sci. USA. 95:2267-2272.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 2267-2272
-
-
Svergun, D.I.1
Richard, S.M.2
Koch, H.J.3
Sayers, Z.4
Kuprin, S.5
Zaccai, G.6
-
25
-
-
0032809455
-
Orientational order and dynamics of hydration water in a single crystal of bovine pancreatic trypsin inhibitor
-
Venu, K., L. A. Svensson, and B. Halle. 1999. Orientational order and dynamics of hydration water in a single crystal of bovine pancreatic trypsin inhibitor. Biophys. J. 77:1074-1085.
-
(1999)
Biophys. J.
, vol.77
, pp. 1074-1085
-
-
Venu, K.1
Svensson, L.A.2
Halle, B.3
-
26
-
-
1542375172
-
Hydration dynamics near a model protein surface
-
Russo, D., G. Hura, and T. Head-Gordon. 2005. Hydration dynamics near a model protein surface. Biophys. J. 86:1852-1862.
-
(2005)
Biophys. J.
, vol.86
, pp. 1852-1862
-
-
Russo, D.1
Hura, G.2
Head-Gordon, T.3
-
27
-
-
0024094768
-
Accurate simulation of protein dynamics in solution
-
Levitt, M., and R. Sharon. 1988. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA. 85:7557-7561.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 7557-7561
-
-
Levitt, M.1
Sharon, R.2
-
28
-
-
0032054168
-
Protein hydration density: Theory, simulation and crystallography
-
Makarov, V. A., K. A. Andrews, and B. M. Pettitt. 1998a. Protein hydration density: theory, simulation and crystallography. Curr. Opin. Struct. Biol. 8:218-221.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 218-221
-
-
Makarov, V.A.1
Andrews, K.A.2
Pettitt, B.M.3
-
29
-
-
0032104775
-
Reconstructing the protein-water interface
-
Makarov, V. A., K. A. Andrews, and B. M. Pettitt. 1998b. Reconstructing the protein-water interface. Biopolymers. 45:469-478.
-
(1998)
Biopolymers
, vol.45
, pp. 469-478
-
-
Makarov, V.A.1
Andrews, K.A.2
Pettitt, B.M.3
-
30
-
-
0033636839
-
Residence times of water molecules in the hydration sites of myoglobin
-
Makarov, V. A., B. K. Andrews, P. E. Smith, and B. M. Pettitt. 2000. Residence times of water molecules in the hydration sites of myoglobin. Biophys. J. 79:2966-2974.
-
(2000)
Biophys. J.
, vol.79
, pp. 2966-2974
-
-
Makarov, V.A.1
Andrews, B.K.2
Smith, P.E.3
Pettitt, B.M.4
-
31
-
-
0036707992
-
Structural and dynamic properties of water around acetylcholinesterase
-
Henchman, R. H., and J. A. McCammon. 2002. Structural and dynamic properties of water around acetylcholinesterase. Protein Sci. 11:2080-2090.
-
(2002)
Protein Sci.
, vol.11
, pp. 2080-2090
-
-
Henchman, R.H.1
McCammon, J.A.2
-
32
-
-
0142123115
-
Biomolecular hydration: From water dynamics to hydrodynamics
-
Halle, B., and M. Davidovic. 2003. Biomolecular hydration: from water dynamics to hydrodynamics. Proc. Natl. Acad. Sci. USA. 100:12135-12140.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12135-12140
-
-
Halle, B.1
Davidovic, M.2
-
33
-
-
36749120002
-
Theory of the hydrophobic effect
-
Pratt, L. R., and D. Chandler. 1977. Theory of the hydrophobic effect. J. Chem. Phys. 67:3683-3704.
-
(1977)
J. Chem. Phys.
, vol.67
, pp. 3683-3704
-
-
Pratt, L.R.1
Chandler, D.2
-
34
-
-
0009150541
-
Entropy of hydrophobic hydration: A new statistical mechanical formulation
-
Lazaridis, T., and M. E. Paulaitis. 1992. Entropy of hydrophobic hydration: a new statistical mechanical formulation. J. Chem. Phys. 96:3847.
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 3847
-
-
Lazaridis, T.1
Paulaitis, M.E.2
-
35
-
-
33751157739
-
Simulation studies of the hydration entropy of simple, hydrophobic solutes
-
Lazaridis, T., and M. E. Paulaitis. 1994. Simulation studies of the hydration entropy of simple, hydrophobic solutes. J. Phys. Chem. 98:635.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 635
-
-
Lazaridis, T.1
Paulaitis, M.E.2
-
36
-
-
0034662849
-
New perspectives on hydrophobic effects
-
Hummer, G., S. Garde, A. E. García, and L. R. Pratt. 2000. New perspectives on hydrophobic effects. Chem. Phys. 258:349-370.
-
(2000)
Chem. Phys.
, vol.258
, pp. 349-370
-
-
Hummer, G.1
Garde, S.2
García, A.E.3
Pratt, L.R.4
-
37
-
-
0020688832
-
Calculation of volume fluctuation for globular protein models
-
Lee, B. 1983. Calculation of volume fluctuation for globular protein models. Proc. Natl. Acad. Sci. USA. 80:622-626.
-
(1983)
Proc. Natl. Acad. Sci. USA
, vol.80
, pp. 622-626
-
-
Lee, B.1
-
38
-
-
0022999267
-
Compressibility structure relationship of globular-proteins
-
Gekko, K., and Y. Hasegawa. 1986. Compressibility structure relationship of globular-proteins. Biochemistry. 25:6563-6571.
-
(1986)
Biochemistry
, vol.25
, pp. 6563-6571
-
-
Gekko, K.1
Hasegawa, Y.2
-
39
-
-
0027535729
-
Hydrational and intrinsic compressibilities of globular proteins
-
Kharakoz, D. P., and A. P. Sarvazyan. 1993. Hydrational and intrinsic compressibilities of globular proteins. Biopolymers. 33:11-26.
-
(1993)
Biopolymers
, vol.33
, pp. 11-26
-
-
Kharakoz, D.P.1
Sarvazyan, A.P.2
-
40
-
-
0031790423
-
Thermodynamic analysis of biomolecules: A volumetric approach
-
Chalikian, T. V., and K. J. Breslauer. 1998. Thermodynamic analysis of biomolecules: a volumetric approach. Curr. Opin. Struct. Biol. 8:657-664.
-
(1998)
Curr. Opin. Struct. Biol.
, vol.8
, pp. 657-664
-
-
Chalikian, T.V.1
Breslauer, K.J.2
-
41
-
-
0035924822
-
Structural thermodynamics of hydration
-
Chalikian, T. V. 2001. Structural thermodynamics of hydration. J. Phys. Chem. B. 105:12566-12578.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 12566-12578
-
-
Chalikian, T.V.1
-
42
-
-
0037703765
-
Compressibility of cavities and biological water from Voronoi volumes in hydrated proteins
-
Marchi, M. 2003. Compressibility of cavities and biological water from Voronoi volumes in hydrated proteins. J. Phys. Chem. B. 107:6598-6602.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 6598-6602
-
-
Marchi, M.1
-
43
-
-
0030038545
-
Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
-
Burling, F. T., W. I. Weis, K. M. Flaherty, and A. T. Brünger. 1996. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science. 271:72-77.
-
(1996)
Science
, vol.271
, pp. 72-77
-
-
Burling, F.T.1
Weis, W.I.2
Flaherty, K.M.3
Brünger, A.T.4
-
44
-
-
20644465398
-
Insights into protein compressibility from molecular dynamics simulations
-
Dadarlat, V. M., and C. B. Post. 2001. Insights into protein compressibility from molecular dynamics simulations. J. Phys. Chem. B. 105:715-724.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 715-724
-
-
Dadarlat, V.M.1
Post, C.B.2
-
46
-
-
0029859688
-
Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulations at high pressure
-
Paci, E., and M. Marchi. 1996. Intrinsic compressibility and volume compression in solvated proteins by molecular dynamics simulations at high pressure. Proc. Natl. Acad. Sci. USA. 93:11609-11614.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 11609-11614
-
-
Paci, E.1
Marchi, M.2
-
47
-
-
33846823909
-
Particle mesh Ewald: An nlog(n) method for Ewald sums in large systems
-
Darden, T. A., D. M. York, and L. G. Pedersen. 1993. Particle mesh Ewald: An nlog(n) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.G.3
-
48
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization and dynamics calculations
-
Brooks, B., R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaminathan, S.5
Karplus, M.6
-
49
-
-
24144440918
-
Potentials of mean force (PMFs) for the interaction of blocked alanine dipeptide molecules in water and vacuum from MD simulations
-
Dadarlat, V. M. 2005. Potentials of mean force (PMFs) for the interaction of blocked alanine dipeptide molecules in water and vacuum from MD simulations. Biophys. J. 89:1433-1445.
-
(2005)
Biophys. J.
, vol.89
, pp. 1433-1445
-
-
Dadarlat, V.M.1
-
50
-
-
0015222647
-
The interpretation of protein structures: Estimation of static accessibility
-
Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
51
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 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
-
54
-
-
0022448585
-
Oxygen-17 and deuterium nuclear magnetic resonance studies of lysozyme hydration
-
Lioutas, T. S., I. C. Baianu, and M. P. Steinberg. 1986. Oxygen-17 and deuterium nuclear magnetic resonance studies of lysozyme hydration. Arch. Biochem. Biophys. 247:68-75.
-
(1986)
Arch. Biochem. Biophys.
, vol.247
, pp. 68-75
-
-
Lioutas, T.S.1
Baianu, I.C.2
Steinberg, M.P.3
-
55
-
-
0001689633
-
Volumetric properties of aqueous solutions of bovine serum albumin, human serum albumin, and human hemoglobin
-
Iqbal, M., and R. E. Verrall. 1987. Volumetric properties of aqueous solutions of bovine serum albumin, human serum albumin, and human hemoglobin. J. Phys. Chem. 91:1935-1941.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 1935-1941
-
-
Iqbal, M.1
Verrall, R.E.2
-
56
-
-
0034604175
-
Functional group contributions to partial molar compressibilities of alcohols in water
-
Lockwood, D. M., P. J. Rossky, and R. M. Levy. 2000. Functional group contributions to partial molar compressibilities of alcohols in water. J. Phys. Chem. B. 104:4210-4217.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 4210-4217
-
-
Lockwood, D.M.1
Rossky, P.J.2
Levy, R.M.3
|