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Volumn 93, Issue 8, 2007, Pages 2791-2804

Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins

Author keywords

[No Author keywords available]

Indexed keywords

NANOTUBE; WATER;

EID: 35349013541     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.104182     Document Type: Article
Times cited : (37)

References (61)
  • 1
    • 0021107512 scopus 로고
    • Interior turns in globular proteins
    • Rose, G. D., and W. B. Young. 1983. Interior turns in globular proteins. Nature. 304:655-657.
    • (1983) Nature , vol.304 , pp. 655-657
    • Rose, G.D.1    Young, W.B.2
  • 2
    • 0027068111 scopus 로고
    • Buried water in homologous serine proteases
    • Sreenivasan, U., and P. H. Axelsen. 1992. Buried water in homologous serine proteases. Biochemistry. 31:12785-12791.
    • (1992) Biochemistry , vol.31 , pp. 12785-12791
    • Sreenivasan, U.1    Axelsen, P.H.2
  • 4
    • 0034024888 scopus 로고    scopus 로고
    • Structural water molecules in the family of fatty acid binding proteins
    • Likic, V. A., N. Juranic, S. Macura, and F. G. Prendergast. 2000. Structural water molecules in the family of fatty acid binding proteins. Protein Sci. 9:497-504.
    • (2000) Protein Sci , vol.9 , pp. 497-504
    • Likic, V.A.1    Juranic, N.2    Macura, S.3    Prendergast, F.G.4
  • 5
    • 0035937261 scopus 로고    scopus 로고
    • Core and surface mutations affect folding kinetics, stability, and cooperativity I IL-1b: Does alteration in buried water play a role?
    • Covalt, J. C., M. Roy, and P. A. Jennings. 2001. Core and surface mutations affect folding kinetics, stability, and cooperativity I IL-1b: does alteration in buried water play a role? J. Mol. Biol. 307:657-669.
    • (2001) J. Mol. Biol , vol.307 , pp. 657-669
    • Covalt, J.C.1    Roy, M.2    Jennings, P.A.3
  • 6
    • 23044435317 scopus 로고    scopus 로고
    • Statistical and molecular dynamics studies of buried waters in globular proteins
    • Park, S., and J. G. Saven. 2005. Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins Struct. Funct. Gen. 60:450-463.
    • (2005) Proteins Struct. Funct. Gen , vol.60 , pp. 450-463
    • Park, S.1    Saven, J.G.2
  • 7
    • 0030696285 scopus 로고    scopus 로고
    • Contribution of water molecules in the interior of a protein to the conformational stability
    • Takano, K., J. Funahashi, Y. Yamagata, S. Fujii, and K. Yutani. 1997. Contribution of water molecules in the interior of a protein to the conformational stability. J. Mol. Biol. 274:132-142.
    • (1997) J. Mol. Biol , vol.274 , pp. 132-142
    • Takano, K.1    Funahashi, J.2    Yamagata, Y.3    Fujii, S.4    Yutani, K.5
  • 8
    • 0034728676 scopus 로고    scopus 로고
    • One water molecule stiffens a protein
    • Mao, Y., M. A. Ratner, and M. F. Jarrold. 2000. One water molecule stiffens a protein. J. Am. Chem. Soc. 122:2950-2951.
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 2950-2951
    • Mao, Y.1    Ratner, M.A.2    Jarrold, M.F.3
  • 9
    • 0033578333 scopus 로고    scopus 로고
    • Binding of buried structural water increases the flexibility of proteins
    • Fischer, S., and C. S. Verma. 1999. Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. USA. 96:9613-9615.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9613-9615
    • Fischer, S.1    Verma, C.S.2
  • 10
    • 0036099192 scopus 로고    scopus 로고
    • a values of buried residues: analysis with continuum methods and role of water penetration. Biophys. J. 82:3289-304.
    • a values of buried residues: analysis with continuum methods and role of water penetration. Biophys. J. 82:3289-304.
  • 11
    • 0035451052 scopus 로고    scopus 로고
    • What are the dielectric "constants" of proteins and how to validate electrostatic models?
    • Schutz, C. N., and A. Warshel. 2002. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins Struct. Funct. Gen. 44:400-417.
    • (2002) Proteins Struct. Funct. Gen , vol.44 , pp. 400-417
    • Schutz, C.N.1    Warshel, A.2
  • 12
    • 0031973948 scopus 로고    scopus 로고
    • Oxygen and proton pathways in cytochrome c oxidase
    • Hofacker, I., and K. Schulten. 1998. Oxygen and proton pathways in cytochrome c oxidase. Proteins Struct. Funct. Gen. 30:100-107.
    • (1998) Proteins Struct. Funct. Gen , vol.30 , pp. 100-107
    • Hofacker, I.1    Schulten, K.2
  • 13
    • 0036225143 scopus 로고    scopus 로고
    • Molecular mechanism of H1 conduction in the single-file water chain of the gramicidin channel
    • Pomès, R., and B. Roux. 2002. Molecular mechanism of H1 conduction in the single-file water chain of the gramicidin channel. Biophys. J. 82:2304-2316.
    • (2002) Biophys. J , vol.82 , pp. 2304-2316
    • Pomès, R.1    Roux, B.2
  • 14
    • 0037379781 scopus 로고    scopus 로고
    • Voltage-gated proton channels and other proton transfer pathways
    • Decoursey, T. E. 2003. Voltage-gated proton channels and other proton transfer pathways. Physiol. Rev. 83:465-579.
    • (2003) Physiol. Rev , vol.83 , pp. 465-579
    • Decoursey, T.E.1
  • 16
    • 1842534583 scopus 로고    scopus 로고
    • MHC-peptide binding is assisted by bound water molecules
    • Petrone, P., and A. E. García. 2004. MHC-peptide binding is assisted by bound water molecules. J. Mol. Biol. 338:419-435.
    • (2004) J. Mol. Biol , vol.338 , pp. 419-435
    • Petrone, P.1    García, A.E.2
  • 17
    • 0027082924 scopus 로고
    • Internal water molecules and H-bonding in biological macro-molecules: A review of structural features with functional implications
    • Meyer, E. 1992. Internal water molecules and H-bonding in biological macro-molecules: a review of structural features with functional implications. Protein Sci. 1:1543-1562.
    • (1992) Protein Sci , vol.1 , pp. 1543-1562
    • Meyer, E.1
  • 19
    • 0037154268 scopus 로고    scopus 로고
    • Protein folding mediated by solvation: Water expelling and formation of the hydrophobic core occur after the structural collapse
    • Cheung, M. S., A. García, and J. N. Onuchic. 2002. Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 685-690
    • Cheung, M.S.1    García, A.2    Onuchic, J.N.3
  • 20
    • 0345133287 scopus 로고    scopus 로고
    • Folding a protein in a computer; an atomic description of the folding/unfolding of protein A
    • García, A., and J. Onuchic. 2003. Folding a protein in a computer; an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA. 100:13898-13903.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13898-13903
    • García, A.1    Onuchic, J.2
  • 21
    • 0037051949 scopus 로고    scopus 로고
    • Relationship between hydrogen-bonding network and reduction potential in c-type cytochromes
    • Garau, G., S. Geremia, and L. Randaccio. 2002. Relationship between hydrogen-bonding network and reduction potential in c-type cytochromes. FEBS Lett. 516:285-286.
    • (2002) FEBS Lett , vol.516 , pp. 285-286
    • Garau, G.1    Geremia, S.2    Randaccio, L.3
  • 22
    • 0036109653 scopus 로고    scopus 로고
    • Water permeation through gramicidin A desformylation and the double helix: A molecular dynamics study
    • de Groot, B. L., D. P. Tieleman, P. Pohl, and H. Grubmüller. 2002. Water permeation through gramicidin A desformylation and the double helix: a molecular dynamics study. Biophys. J. 82:2934-2942.
    • (2002) Biophys. J , vol.82 , pp. 2934-2942
    • de Groot, B.L.1    Tieleman, D.P.2    Pohl, P.3    Grubmüller, H.4
  • 23
    • 2142715470 scopus 로고    scopus 로고
    • Water dynamics and dewetting transitions in the small mechanosensitive channel MscS
    • Anishkin, A., and S. Sukharev. 2004. Water dynamics and dewetting transitions in the small mechanosensitive channel MscS. Biophys. J. 86:2883-2895.
    • (2004) Biophys. J , vol.86 , pp. 2883-2895
    • Anishkin, A.1    Sukharev, S.2
  • 25
  • 26
    • 4143116650 scopus 로고    scopus 로고
    • Computational studies of membrane channels
    • Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure. 12:1343-1351.
    • (2004) Structure , vol.12 , pp. 1343-1351
    • Roux, B.1    Schulten, K.2
  • 27
    • 0028341789 scopus 로고
    • Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme
    • Zhang, X.-J., and B. W. Matthews. 1994. Conservation of solvent-binding sites in 10 crystal forms of T4 lysozyme. Protein Sci. 3:1031-1039.
    • (1994) Protein Sci , vol.3 , pp. 1031-1039
    • Zhang, X.-J.1    Matthews, B.W.2
  • 28
    • 0028105204 scopus 로고
    • Dynamics of the internal and external hydration of globular proteins
    • Denisov, V. P., and B. Halle. 1994. Dynamics of the internal and external hydration of globular proteins. J. Am. Chem. Soc. 116:10324-10325.
    • (1994) J. Am. Chem. Soc , vol.116 , pp. 10324-10325
    • Denisov, V.P.1    Halle, B.2
  • 30
    • 0035943379 scopus 로고    scopus 로고
    • Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions
    • Juers, D. H., and B. W. Matthews. 2001. Reversible lattice repacking illustrates the temperature dependence of macromolecular interactions. J. Mol. Biol. 311:851-862.
    • (2001) J. Mol. Biol , vol.311 , pp. 851-862
    • Juers, D.H.1    Matthews, B.W.2
  • 31
    • 1842687872 scopus 로고    scopus 로고
    • Biomolecular cryocrystallography: Structural changes during flash-cooling
    • Halle, B. 2004. Biomolecular cryocrystallography: structural changes during flash-cooling. Proc. Natl. Acad. Sci. USA. 101:4793-4798.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 4793-4798
    • Halle, B.1
  • 33
    • 0030987236 scopus 로고    scopus 로고
    • Identification of a functional water channel in cytochrome P45 enzymes
    • Oprea, T. I., G. Hummer, and A. E. García. 1997. Identification of a functional water channel in cytochrome P45 enzymes. Proc. Natl. Acad. Sci. USA. 94:2133-2138.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 2133-2138
    • Oprea, T.I.1    Hummer, G.2    García, A.E.3
  • 34
  • 35
    • 0036606442 scopus 로고    scopus 로고
    • Water in protein cavities: A procedure to identify internal water and exchange pathways and application to fatty acid-binding protein
    • Bakowies, D., and W. F. van Gunsteren. 2002. Water in protein cavities: a procedure to identify internal water and exchange pathways and application to fatty acid-binding protein. Proteins Struct. Funct. Gen. 47:534-545.
    • (2002) Proteins Struct. Funct. Gen , vol.47 , pp. 534-545
    • Bakowies, D.1    van Gunsteren, W.F.2
  • 36
    • 0036306105 scopus 로고    scopus 로고
    • Simulations of apo and holo-fatty acid binding protein: Structure and dynamics of protein, ligand and internal water
    • Bakowies, D., and W. F. van Gunsteren. 2002. Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water. J. Mol. Biol. 315:713-736.
    • (2002) J. Mol. Biol , vol.315 , pp. 713-736
    • Bakowies, D.1    van Gunsteren, W.F.2
  • 37
    • 41349092888 scopus 로고    scopus 로고
    • Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry and polaron model study
    • Damjanović, A., I. Kosztin, U. Kleinekathoefer, and K. Schulten. 2002. Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry and polaron model study. Phys. Rev. E. 65:031919.
    • (2002) Phys. Rev. E , vol.65 , pp. 031919
    • Damjanović, A.1    Kosztin, I.2    Kleinekathoefer, U.3    Schulten, K.4
  • 38
    • 0026189146 scopus 로고
    • A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins
    • Wade, R. C., M. Mazor, J. A. McCammon, and F. A. Quiocho. 1991. A molecular dynamics study of thermodynamic and structural aspects of the hydration of cavities in proteins. Biopolymers. 31:919-931.
    • (1991) Biopolymers , vol.31 , pp. 919-931
    • Wade, R.C.1    Mazor, M.2    McCammon, J.A.3    Quiocho, F.A.4
  • 39
    • 0029757992 scopus 로고    scopus 로고
    • Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel - a molecular dynamics free energy perturbation study
    • Roux, B., M. Nina, R. Pomes, and J. Smith. 1996. Thermodynamics stability of water molecules in the bacteriorhodopsin proton channel - a molecular dynamics free energy perturbation study. Biophys. J. 71:670-681.
    • (1996) Biophys. J , vol.71 , pp. 670-681
    • Roux, B.1    Nina, M.2    Pomes, R.3    Smith, J.4
  • 40
    • 3042592839 scopus 로고    scopus 로고
    • Hydration free energies and entropies for water in protein interiors
    • Olano, L. R., and S. W. Rick. 2004. Hydration free energies and entropies for water in protein interiors. J. Am. Chem. Soc. 126:7991-8000.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 7991-8000
    • Olano, L.R.1    Rick, S.W.2
  • 41
    • 0029126354 scopus 로고
    • A comparison of neutron diffraction and molecular dynamics structures: Hydroxyl group and water molecule orientations in trypsin
    • McDowell, R. S., and A. A. Kossiakoff. 1995. A comparison of neutron diffraction and molecular dynamics structures: hydroxyl group and water molecule orientations in trypsin. J. Mol. Biol. 250:553-570.
    • (1995) J. Mol. Biol , vol.250 , pp. 553-570
    • McDowell, R.S.1    Kossiakoff, A.A.2
  • 42
    • 0035839052 scopus 로고    scopus 로고
    • Dynamics of hydration in hen egg white lysozyme
    • Sterpone, F., M. Ceccarelli, and M. Marchi. 2001. Dynamics of hydration in hen egg white lysozyme. J. Mol. Biol. 311:409-419.
    • (2001) J. Mol. Biol , vol.311 , pp. 409-419
    • Sterpone, F.1    Ceccarelli, M.2    Marchi, M.3
  • 43
    • 0001520216 scopus 로고
    • Computation of the mean residence time of water in the hydration shells of biomolecules
    • García, A. E., and L. Stiller. 1993. Computation of the mean residence time of water in the hydration shells of biomolecules. J. Comput. Chem. 14:1396-1406.
    • (1993) J. Comput. Chem , vol.14 , pp. 1396-1406
    • García, A.E.1    Stiller, L.2
  • 44
    • 4344601490 scopus 로고    scopus 로고
    • Solvation thermodynamics of protein studied by the 3D-RISM theory
    • Imai, T., A. Kovalenko, and F. Hirata. 2004. Solvation thermodynamics of protein studied by the 3D-RISM theory. Chem. Phys. Lett. 395:1-6.
    • (2004) Chem. Phys. Lett , vol.395 , pp. 1-6
    • Imai, T.1    Kovalenko, A.2    Hirata, F.3
  • 45
    • 0033850087 scopus 로고    scopus 로고
    • Dwyer, J. J., A. G. Gittis, D. A. Karp, E. E. Lattman, D. S. Spencer, W. E. Stites, and B. García-Moreno E. 2000. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys. J. 79:1610-1620.
    • Dwyer, J. J., A. G. Gittis, D. A. Karp, E. E. Lattman, D. S. Spencer, W. E. Stites, and B. García-Moreno E. 2000. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys. J. 79:1610-1620.
  • 46
    • 3342908886 scopus 로고    scopus 로고
    • X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: Insights into polarity of the protein interior
    • Nguyen, D. M., R. L. Reynald, A. G. Gittis, and E. E. Lattman. 2004. X-ray and thermodynamic studies of staphylococcal nuclease variants I92E and I92K: insights into polarity of the protein interior. J. Mol. Biol. 341:565-574.
    • (2004) J. Mol. Biol , vol.341 , pp. 565-574
    • Nguyen, D.M.1    Reynald, R.L.2    Gittis, A.G.3    Lattman, E.E.4
  • 47
    • 33947683393 scopus 로고    scopus 로고
    • Karp, D. A., A. G. Gittis, M. A. Stahley, C. A. Fitch, W. E. Stites, E. E. Lattman, and B. García-Moreno E. 2007. Molecular determinants of the abnormal pKa value of an internal aspartic acid: contributions by local unfolding and water penetration. Biophys. J. 92:2041-2053.
    • Karp, D. A., A. G. Gittis, M. A. Stahley, C. A. Fitch, W. E. Stites, E. E. Lattman, and B. García-Moreno E. 2007. Molecular determinants of the abnormal pKa value of an internal aspartic acid: contributions by local unfolding and water penetration. Biophys. J. 92:2041-2053.
  • 48
    • 33745685012 scopus 로고    scopus 로고
    • Using a charging coordinate in studies of ionization induced partial unfolding
    • Kato, M., and A. Warshel. 2006. Using a charging coordinate in studies of ionization induced partial unfolding. J. Phys. Chem. B. 110:11566-11570.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 11566-11570
    • Kato, M.1    Warshel, A.2
  • 49
    • 10044267947 scopus 로고    scopus 로고
    • Stabilization of internal charges in a protein: Water penetration or conformational change?
    • Denisov, V. P., J. L. Schlessman, B. García-Moreno E., and B. Halle. 2004. Stabilization of internal charges in a protein: water penetration or conformational change? Biophys. J. 87:3982-3994.
    • (2004) Biophys. J , vol.87 , pp. 3982-3994
    • Denisov, V.P.J.L.1    Schlessman, B.2    García-Moreno, E.3    Halle, B.4
  • 50
    • 0040321024 scopus 로고    scopus 로고
    • García-Moreno E., B., J. J. Dwyer, A. G. Gittis, E. E. Lattman, D. S. Spencer, and W. E. Stites. 1997. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys. Chem. 64:211-224.
    • García-Moreno E., B., J. J. Dwyer, A. G. Gittis, E. E. Lattman, D. S. Spencer, and W. E. Stites. 1997. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys. Chem. 64:211-224.
  • 52
    • 0029937870 scopus 로고    scopus 로고
    • Hydrophilicity of cavities in proteins
    • Zhang, L., and J. Hermans. 1996. Hydrophilicity of cavities in proteins. Proteins Struct. Funct. Gen.. 24:433-438.
    • (1996) Proteins Struct. Funct. Gen , vol.24 , pp. 433-438
    • Zhang, L.1    Hermans, J.2
  • 53
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J. Phys. Chem. B. 102:3586-3616.
    • MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, I. W. E. Reiher, B. Roux, M. Schlenkrich, J. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-hydrogen empirical potential for molecular modeling and dynamics studies of proteins using the CHARMM22 force field. J. Phys. Chem. B. 102:3586-3616.
  • 54
    • 36449007836 scopus 로고
    • Constant pressure molecular dynamics simulation - the Langevin piston method
    • Feller, S. E., Y. H. Zhang, R. W. Pastor, and B. R. Brooks. 1995. Constant pressure molecular dynamics simulation - the Langevin piston method. J. Chem. Phys. 103:4613-4621.
    • (1995) J. Chem. Phys , vol.103 , pp. 4613-4621
    • Feller, S.E.1    Zhang, Y.H.2    Pastor, R.W.3    Brooks, B.R.4
  • 56
    • 0041814016 scopus 로고    scopus 로고
    • MMTSB NIH Research Resource, The Scripps Research Institute, La Jolla, CA
    • Feig, M., J. Karanicolas, and C. L. Brooks III. 2001. MMTSB tool set. MMTSB NIH Research Resource, The Scripps Research Institute, La Jolla, CA.
    • (2001) MMTSB tool set
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 58
    • 0035829539 scopus 로고    scopus 로고
    • Water conduction through the hydrophobic channel of a carbon nanotube
    • Hummer, G., J. C. Rasaiah, and J. P. Noworyta. 2001. Water conduction through the hydrophobic channel of a carbon nanotube. Nature. 414:188-190.
    • (2001) Nature , vol.414 , pp. 188-190
    • Hummer, G.1    Rasaiah, J.C.2    Noworyta, J.P.3
  • 60
    • 32644473051 scopus 로고    scopus 로고
    • Effect of flexibility on hydrophobic behavior of nanotube water channels
    • Andreev, S., D. Reichman, and G. Hummer. 2005. Effect of flexibility on hydrophobic behavior of nanotube water channels. J. Chem. Phys. 123:194502.
    • (2005) J. Chem. Phys , vol.123 , pp. 194502
    • Andreev, S.1    Reichman, D.2    Hummer, G.3
  • 61
    • 85030585339 scopus 로고    scopus 로고
    • DeLano Scientific, San Carlos, CA
    • DeLano, W. L. 2002. The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA. http://www.pymol.org.
    • (2002)
    • DeLano, W.L.1


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