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Volumn 100, Issue 1-3, 2002, Pages 221-237

A microscopic view of peptide and protein solvation

Author keywords

Hydrophobic effect; Molecular dynamics; Peptide hydration; Protein hydration; Solvation; Water structure

Indexed keywords

AMINO ACID; CHYMOTRYPSIN INHIBITOR; MEMBRANE PROTEIN; PEPTIDE; PROTEIN; TRIPEPTIDE; WATER;

EID: 0037438967     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(02)00283-1     Document Type: Article
Times cited : (44)

References (49)
  • 1
    • 0017869404 scopus 로고
    • Water and proteins. I. The significance and structure of water; Its interaction with electrolytes and non-electrolytes
    • Edsall J.T., McKenzie H.A. Water and proteins. I. The significance and structure of water; its interaction with electrolytes and non-electrolytes. Adv. Biophys. 10:1978;137-207.
    • (1978) Adv. Biophys. , vol.10 , pp. 137-207
    • Edsall, J.T.1    McKenzie, H.A.2
  • 2
    • 0034662899 scopus 로고    scopus 로고
    • The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 440 MPa
    • Soper A.K. The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 440 MPa. Chem. Phys. 258:2000;121-137.
    • (2000) Chem. Phys. , vol.258 , pp. 121-137
    • Soper, A.K.1
  • 3
    • 4243089023 scopus 로고
    • Solvent structure and perturbations in solutions of chemical and biological importance
    • Finney J.L., Soper A.K. Solvent structure and perturbations in solutions of chemical and biological importance. Chem. Soc. Rev. 23:1994;1-10.
    • (1994) Chem. Soc. Rev. , vol.23 , pp. 1-10
    • Finney, J.L.1    Soper, A.K.2
  • 4
    • 33751145001 scopus 로고    scopus 로고
    • Orientation of water molecules around small polar and non-polar groups in solution: A neutron diffraction and computer simulation study
    • Soper A.K., Luzar A. Orientation of water molecules around small polar and non-polar groups in solution: a neutron diffraction and computer simulation study. J. Phys. Chem. 100:1996;1357-1367.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1357-1367
    • Soper, A.K.1    Luzar, A.2
  • 5
    • 0033906678 scopus 로고    scopus 로고
    • Probing the structure of water around biological molecules: Concepts, constructs and consequences
    • Soper A.K. Probing the structure of water around biological molecules: concepts, constructs and consequences. Physica B. 276-278:2000;12-16.
    • (2000) Physica B , vol.276-278 , pp. 12-16
    • Soper, A.K.1
  • 6
    • 0029746155 scopus 로고    scopus 로고
    • Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid
    • Pertsemlidis A., Saxena A.M., Soper A.K., Head-Gordon T., Glaesar R.M. Direct evidence for modified solvent structure within the hydration shell of a hydrophobic amino acid. Proc. Natl. Acad. Sci. USA. 93:1996;10769-10774.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 10769-10774
    • Pertsemlidis, A.1    Saxena, A.M.2    Soper, A.K.3    Head-Gordon, T.4    Glaesar, R.M.5
  • 7
    • 0030568435 scopus 로고    scopus 로고
    • Testing the modified hydration-shell hydrogen-bond model of hydrophobic effects using molecular dynamics simulation
    • Laidig K.E., Daggett V. Testing the modified hydration-shell hydrogen-bond model of hydrophobic effects using molecular dynamics simulation. J. Phys. Chem. 100:1996;5616-5619.
    • (1996) J. Phys. Chem. , vol.100 , pp. 5616-5619
    • Laidig, K.E.1    Daggett, V.2
  • 8
    • 0030822464 scopus 로고    scopus 로고
    • Differences in hydration structure near hydrophobic and hydrophilic amino acids
    • Head-Gordon T., Sorenson J.M., Pertsemlidis A., Glaeser R.M. Differences in hydration structure near hydrophobic and hydrophilic amino acids. Biophys. J. 73:1997;2106-2115.
    • (1997) Biophys. J. , vol.73 , pp. 2106-2115
    • Head-Gordon, T.1    Sorenson, J.M.2    Pertsemlidis, A.3    Glaeser, R.M.4
  • 9
    • 0031853128 scopus 로고    scopus 로고
    • The hydrophobic effect. 3. A key ingredient in predicting n-octanol-water partition coefficients
    • Kesselring R.P. The hydrophobic effect. 3. A key ingredient in predicting n-octanol-water partition coefficients. J. Pharm. Sci. 87:1998;1015-1024.
    • (1998) J. Pharm. Sci. , vol.87 , pp. 1015-1024
    • Kesselring, R.P.1
  • 10
    • 0036154172 scopus 로고    scopus 로고
    • Apolar and polar solvation thermodynamics related to the protein unfolding process
    • Bakk A., Hoye J.S., Hansen A. Apolar and polar solvation thermodynamics related to the protein unfolding process. Biophys. J. 82:2002;713-719.
    • (2002) Biophys. J. , vol.82 , pp. 713-719
    • Bakk, A.1    Hoye, J.S.2    Hansen, A.3
  • 11
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins. 35:1999;133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 12
    • 0030038545 scopus 로고    scopus 로고
    • Direct observation of protein solvation and discrete disorder with experimental crystallographic phases
    • Burling F.T., Weis W.I., Flaherty K.M., Brunger A.T. Direct observation of protein solvation and discrete disorder with experimental crystallographic phases. Science. 271:1996;72-77.
    • (1996) Science , vol.271 , pp. 72-77
    • Burling, F.T.1    Weis, W.I.2    Flaherty, K.M.3    Brunger, A.T.4
  • 13
    • 0032533454 scopus 로고    scopus 로고
    • Crystallographic water sites from a theoretical prospective
    • Feig M., Pettitt B.M. Crystallographic water sites from a theoretical prospective. Structure. 6:1998;1351-1354.
    • (1998) Structure , vol.6 , pp. 1351-1354
    • Feig, M.1    Pettitt, B.M.2
  • 14
    • 0031807764 scopus 로고    scopus 로고
    • Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study
    • Makarov V.A., Feigh M., Andrews K., Pettitt B.M. Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophys. J. 75:1998;150-158.
    • (1998) Biophys. J. , vol.75 , pp. 150-158
    • Makarov, V.A.1    Feigh, M.2    Andrews, K.3    Pettitt, B.M.4
  • 15
    • 0033636839 scopus 로고    scopus 로고
    • Residence times of water molecules in the hydration sites of myoglobin
    • Makarov V.A., Andrews B.K., Smith P.E., Pettitt B.M. Residence times of water molecules in the hydration sites of myoglobin. Biophys. J. 79:2000;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
  • 16
    • 0003233568 scopus 로고    scopus 로고
    • NMR studies of water bound to biological molecules
    • Otting G. NMR studies of water bound to biological molecules. Prog. NMR Spectrosc. 31:1997;259-285.
    • (1997) Prog. NMR Spectrosc. , vol.31 , pp. 259-285
    • Otting, G.1
  • 17
    • 0033012840 scopus 로고    scopus 로고
    • Hydration of denatured and molten globule proteins
    • Denisov V.P., Jonsson B.H., Halle B. Hydration of denatured and molten globule proteins. Nat. Struct. Biol. 6:1999;253-260.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 253-260
    • Denisov, V.P.1    Jonsson, B.H.2    Halle, B.3
  • 19
    • 0035909921 scopus 로고    scopus 로고
    • The free energy landscape for β-hairpin folding in explicit water
    • Zhou R., Berne B., Germain R. The free energy landscape for β-hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA. 98:2001;14931-14936.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 14931-14936
    • Zhou, R.1    Berne, B.2    Germain, R.3
  • 20
    • 0003104284 scopus 로고    scopus 로고
    • Transition States in Protein Folding
    • Frontiers in Molecular Biology Series, R.H. Pain (Ed.), Oxford University Press, Oxford, UK, Chapter 7
    • V. Daggett, A.R. Fersht, Transition States in Protein Folding. In Mechanisms of Protein Folding, 2nd Edition, Frontiers in Molecular Biology Series, R.H. Pain (Ed.), Oxford University Press, Oxford, UK, Chapter 7, 2000, pp. 175-211.
    • (2000) Mechanisms of Protein Folding, 2nd Edition , pp. 175-211
    • Daggett, V.1    Fersht, A.R.2
  • 21
    • 0031965674 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the hydrophobic collapse of ubiquitin
    • Alonso D.O.V., Daggett V. Molecular dynamics simulations of the hydrophobic collapse of ubiquitin. Protein Sci. 7:1998;860-874.
    • (1998) Protein Sci. , vol.7 , pp. 860-874
    • Alonso, D.O.V.1    Daggett, V.2
  • 22
    • 0028965968 scopus 로고
    • Molecular dynamics simulations of protein unfolding and limited refolding - Characterization of partially unfolded states of ubiquitin in 60% methanol and in water
    • Alonso D.O.V., Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding - characterization of partially unfolded states of ubiquitin in 60% methanol and in water. J. Mol. Biol. 247:1995;501-520.
    • (1995) J. Mol. Biol. , vol.247 , pp. 501-520
    • Alonso, D.O.V.1    Daggett, V.2
  • 23
    • 0032544002 scopus 로고    scopus 로고
    • The early stage of folding of villain headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation
    • Duan Y., Wang L., Kollman P.A. The early stage of folding of villain headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc. Natl. Acad. Sci. USA. 95:1998;9897-9902.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 9897-9902
    • Duan, Y.1    Wang, L.2    Kollman, P.A.3
  • 24
    • 0035814373 scopus 로고    scopus 로고
    • Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers
    • Li B., Alonso D.O.V., Bennion B.J., Daggett V. Hydrophobic hydration is an important source of elasticity in elastin-based biopolymers. J. Am. Chem. Soc. 123:2001;11991-11998.
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 11991-11998
    • Li, B.1    Alonso, D.O.V.2    Bennion, B.J.3    Daggett, V.4
  • 26
    • 0036286851 scopus 로고    scopus 로고
    • Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
    • Makarov V., Pettitt B.M., Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Acc. Chem. Res. 35:2002;376-384.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 376-384
    • Makarov, V.1    Pettitt, B.M.2    Feig, M.3
  • 27
    • 0000125216 scopus 로고    scopus 로고
    • Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M., Hirshberg M., Sharon R., Laiding K.E., Daggett V. Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem. B. 101:1997;5051-5061.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5051-5061
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Laiding, K.E.4    Daggett, V.5
  • 28
    • 0024094768 scopus 로고
    • Accurate simulation of protein dynamics in solution
    • Levitt M., Sharon R. Accurate simulation of protein dynamics in solution. Proc. Natl. Acad. Sci. USA. 85:1988;7557-7561.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 7557-7561
    • Levitt, M.1    Sharon, R.2
  • 29
    • 0032538064 scopus 로고    scopus 로고
    • Altering diffusivity in biological solutions through modification of solution structure and dynamics
    • Laidig K.E., Gainer J.L., Daggett V. Altering diffusivity in biological solutions through modification of solution structure and dynamics. J. Am. Chem. Soc. 120:1998;9394-9395.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9394-9395
    • Laidig, K.E.1    Gainer, J.L.2    Daggett, V.3
  • 30
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • Day R., Bennion B.J., Ham S., Daggett V. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J. Mol. Biol. 322:2002;189-203.
    • (2002) J. Mol. Biol. , vol.322 , pp. 189-203
    • Day, R.1    Bennion, B.J.2    Ham, S.3    Daggett, V.4
  • 33
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M., Hirshberg M., Sharon R., Daggett V. Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Comp. Phys. Commun. 91:1995;215-231.
    • (1995) Comp. Phys. Commun. , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 34
    • 0009979659 scopus 로고
    • Precise representation of volume properties of water at 1 atmosphere
    • Kell G.S. Precise representation of volume properties of water at 1 atmosphere. J. Chem. Eng. Data. 12:1967;66.
    • (1967) J. Chem. Eng. Data , vol.12 , pp. 66
    • Kell, G.S.1
  • 37
    • 0002404088 scopus 로고
    • On the orthogonal transformation used for structural comparisons
    • Kearsley S.K. On the orthogonal transformation used for structural comparisons. Acta Cryst. A. 5:1989;208-210.
    • (1989) Acta Cryst. A , vol.5 , pp. 208-210
    • Kearsley, S.K.1
  • 38
    • 0026244229 scopus 로고
    • MOLSCRIPT - A program to produce both detailed and schematic plots of protein structures
    • Kaulis P.J. MOLSCRIPT - a program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst. 24:1991;946-950.
    • (1991) J. Appl. Cryst. , vol.24 , pp. 946-950
    • Kaulis, P.J.1
  • 39
    • 0027092679 scopus 로고
    • The solution structure of Eglin-C based on measurements of many NOEs and coupling constants and its comparison with X-ray structures
    • Hyberts S.G., Goldberg M.S., Havel T.F., Wagner G. The solution structure of Eglin-C based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci. 1:1992;736-751.
    • (1992) Protein Sci. , vol.1 , pp. 736-751
    • Hyberts, S.G.1    Goldberg, M.S.2    Havel, T.F.3    Wagner, G.4
  • 41
    • 0037117502 scopus 로고    scopus 로고
    • Is the first hydration shell of lysozyme of higher density than bulk water?
    • Merzel F., Smith J.C. Is the first hydration shell of lysozyme of higher density than bulk water? Proc. Natl. Acad. Sci. USA. 99:2002;5378-5383.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5378-5383
    • Merzel, F.1    Smith, J.C.2
  • 43
    • 0037133342 scopus 로고    scopus 로고
    • Biological water at the protein surface: Dynamics solvation probed directly with femtosecond resolution
    • Pal S.K., Peon J., Zewail A. Biological water at the protein surface: dynamics solvation probed directly with femtosecond resolution. Proc. Natl. Acad. Sci. USA. 99:2002;1763-1768.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1763-1768
    • Pal, S.K.1    Peon, J.2    Zewail, A.3
  • 44
    • 37049095962 scopus 로고
    • Pressure and temperature dependence of self-diffusion in water
    • Krynicki K., Green C.D., Sawyer D.W. Pressure and temperature dependence of self-diffusion in water. Discuss. Faraday Soc. 66:1978;199-208.
    • (1978) Discuss. Faraday Soc. , vol.66 , pp. 199-208
    • Krynicki, K.1    Green, C.D.2    Sawyer, D.W.3
  • 45
    • 0035526029 scopus 로고    scopus 로고
    • 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. 105:2001;9954-9960.
    • (2001) J. Phys. Chem. A , vol.105 , pp. 9954-9960
    • Mark, P.1    Nilsson, L.2
  • 47
    • 37049247339 scopus 로고
    • Observed diffraction pattern and proposed models of liquid water
    • Narten A.H., Levy H.A. Observed diffraction pattern and proposed models of liquid water. Science. 165:1969;447-454.
    • (1969) Science , vol.165 , pp. 447-454
    • Narten, A.H.1    Levy, H.A.2
  • 48
    • 0037171737 scopus 로고    scopus 로고
    • Molecular segregation observed in a concentrated alcohol-water solution
    • Dixit S., Crain J., Poon W.C.K., Finney J.L., Soper A.K. Molecular segregation observed in a concentrated alcohol-water solution. Nature. 416:2002;829-832.
    • (2002) Nature , vol.416 , pp. 829-832
    • Dixit, S.1    Crain, J.2    Poon, W.C.K.3    Finney, J.L.4    Soper, A.K.5


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