Poszukiwanie modelu wody opisującego hydratację biologicznych makromolekuł

• Authors: Jarosław Poznański

Title variants

EN

In quest of a water model describing hydration of biological macromolecules

• Languages of publication: PL EN

Abstracts

EN

The first model of liquid water at atomic resolution was proposed as early as in 1933. Since that time a vast amount of data concerning both microscopic and macroscopic parameters describing hydration phenomena has been collected. Majority of experimental and theoretical studies pointed out that the main driving force of the so called “hydrophobic interactions” is an entropic effect connected with the solute-induced reorganization of solvation shells. Water molecules surrounding apolar solutes were shown to organize in ice-like structures, the properties of which, in particular molecular packing, proton relaxation rates, distribution and strength of intermolecular H-bonds, differ significantly from those determined for the bulk water. Dozens of models were proposed to describe properties of aqueous solutions at different length-scales, but up to 1999 there was no uniform theory of water for the scales varying from nanometers up to millimeters/centimeters, Recently developed LCW model, by K. Lum, D. Chandler and J. D. Weeks, is the first one, which could be applied to a wide range of phenomena including atom hydration, macromolecule solvation, surface wetting, etc.

• Journal: Kosmos
• Year: 2006
• Volume: 55
• Issue: 2-3
• Pages: 149-164

Dates

published

2006

Contributors

author

Jarosław Poznański

• Zakład Biofizyki, Instytut Biochemii i Biofizyki PAN, Pawińskiego 5a, 02-106 Warszawa, Polska

References

• Abraham D. J., Leo A. J., 1987. Extension Of The Fragment Method To Calculate Amino Acid Zwitterion And Side Chain Partition Coefficients. Proteins 2, 130-152.
• Akamatsu M., Katayama T., Kishimoto D., Kurokawa Y., Shibata H., Ueno T., Fujita T., 1994. Quantitative Analyses Of The Structure-hydrophobicity Relationship For N-acetyl Di- And Tripeptide Amides. J. Pharm. Sci. 83, 1026-1033.
• Arrhenius S. A., 1884. Recherches Sur La Conductibilité Galvanique Des électrolytes. Praca Doktorska, Stockholm.
• Ashbaugh H. S., Garde S., Hummer G., Kaler E. W., Paulaitis M. E., 1999. Conformational Equilibria Of Alkanes In Aqueous Solution: Relationship To Water Structure Near Hydrophobic Solutes. Biophys. J. 77, 645-654.
• Ashbaugh H. S., Kaler E. W., Paulaitis M. E., 1999. A “universal” Surface Area Correlation For Molecular Hydrophobic Phenomena. J. Am. Chem. Soc. 121, 9243-9244.
• Ashbaugh H. S., Paulaitis M. E., 1996. Entropy Of Hydrophobic Hydration: Extension To Hydrophobic Chains. J. Phys. Chem. 100, 1900-1913.
• Ashbaugh H. S., Paulaitis M. E., 2001. Effect Of Solute Size And Solute-water Attractive Interactions On Hydration Water Structure Around Hydrophobic Solutes. J. Am. Chem. Soc. 123, 10721-10728.
• Ashbaugh H. S., Truskett T. M., Debenedetti P. G., 2002. A Simple Molecular Thermodynamic Theory Of Hydrophobic Hydration. J. Chem. Phys. 116, 2907-2921.
• Atha D. H., Ingham K. C., 1981. Mechanism Of Precipitation Of Proteins By Polyethylene Glycols. J. Biol. Chem. 256, 12108-12117.
• Barclay I. M., Butler J. A. V., 1938. The Entropy Of Solutions. Trans. Faraday Soc. 34, 1445-1454.
• Ben-Naim A., 2003. Hydrophobic Hydrophilic Phenomena In Biochemical Processes. Biophys. Chem. 105, 183-193.
• Ben-Naim A., Mazo R. M., 1993. Size Dependence Of The Solvation Free Energies Of Large Solutes. J. Phys. Chem. 97, 10829-10834.
• Bernal J. D., Fowler R. H., 1933. A Theory Of Water And Ionic Solutions, With Particular Reference To Hydrogen And Hydroxyl Ions. J. Chem. Phys. 1, 515-548.
• Bowron D. T., Filipponi A., Lobban C., Finney J. L., 1998. Temperature-induced Disordering Of The Hydrophobic Hydration Shell Of Kr And Xe. Chem Phys Lett 293, 33-37.
• Bowron D. T., Filipponi A., Roberts M. A., Finney J. L., 1998. Hydrophobic Hydration And The Formation Of A Clathrate Hydrate. Phys. Rev. Lett. 81, 4164-4167.
• Bowron D. T., Weigel R., Filipponi A., Roberts M. A., Finney J. L., 2001. X-ray Absorption Spectroscopy Investigations Of The Hydrophobic Hydration Of Krypton At High Pressure. Mol. Phys. 99, 761-765.
• Braig K., Menz R. I., Montgomery M. G., Leslie A. G., Walker J. E., 2000. Structure Of Bovine Mitochondrial F1-atpase Inhibited By Mg2+ Adp And Aluminium Fluoride. Structure Fold Des. 8, 567-573.
• Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M., 1983. Charmm: A Program For Macromolecular Energy, Minmimization, And Dynamics Calculations. J. Comp. Chem. 4, 187-217.
• Bull H. B., Breese K., 1974. Surface Tension Of Amino Acid Solutions: A Hydrophobicity Scale Of The Amino Acid Residues. Arch. Biochem. Biophys. 161, 665-670.
• Cabani S., Gianni P., Mollica V., Lepori L., 1981. Group Contributions To The Thermodynamic Properties Of Non-ionic Organic Solutes In Dilute Aqueous-solution. J. Solution Chem. 10, 563-598.
• Carugo O., 2003. Prediction Of Polypeptide Fragments Exposed To The Solvent. In Silico Biology 3, 0035.
• Chothia C., 1974. Hydrophobic Bonding And Accessible Surface Area In Proteins. Nature 248, 338-339.
• Chothia C., 1976. The Nature Of The Accessible And Buried Surfaces In Proteins. J. Mol. Biol. 105, 1-12.
• Clark M., Cramer Iii R. D., Opdenbosch N. V., 1989. Validation Of The General Purpose Tripos 5. 2 Force Field. J. Comput. Chem. 10, 982-1012.
• Dejong P. H. K, Wilson J. E., Neilson G. W., Buckingham A. D., 1997. Hydrophobic Hydration Of Methane. Mol. Phys. 91, 99-103.
• Dill K. A., 1990. Dominant Forces In Protein Folding. Biochemistry 29, 7133-7155.
• Donchev A. G., Ozrin V. D., Subbotin M. V., Tarasov O. V., And Tarasov V. I., 2005. A Quantum Mechanical Polarizable Force Field For Biomolecular Interactions. Pnas 102 7829-7834.
• Eisenberg D., Mclachlan A. D., 1986. Solvation Energy In Protein Folding And Binding. Nature 319, 199-203.
• Ellis R. J., Minton A. P., 2003. Join The Crowd. Nature 425, 27-28.
• Filipponi A., Bowron D. T., Lobban C., Finney J. L., 1997. Structural Determination Of The Hydrophobic Hydration Shell Of Kr. Phys. Rev. Lett. 79, 1293-1296.
• Frank H. S., Evans M. W., 1945. Free Volume And Entropy In Condensed Systems. Iii Entropy In Binary Liquid Mixtures; Partial Molar Entropy In Dilute Solutions; Structure And Thermodynamics In Aqueous Electrolytes. J. Chem. Phys. 13, 507-532.
• Fujita T., Iwasa J., Hansch C., 1964. A New Substituent Constant, π, Derived From Partition Coefficients. J. Am. Chem. Soc. 86, 5175-5180.
• Fulton A., 1987. How Crowded Is Cytoplasm? Cell 30, 345-347.
• Gill S. J., Wadsö I., 1976. An Equation Of State Describing Hydrophobic Interactions. Proc. Nati. Acad. Sci. 73, 2955-2958.
• Grembecka J., Kędzierski P., Sokalski W. A., Leszczyński J., 2001. Electrostatic Models Of Inhibitory Activity. Int. J. Quantum Chem. 83, 180-192.
• Guy H. R., 1985. Amino Acid Side-chain Partition Energies And Distribution Of Residues In Soluble Proteins. Biophys. J. 47, 61-70.
• Hansch C., Fujita T., 1964. ρ-σ-π Analysis - A Method For The Correlation Of Biological-activity And Chemical-structure. J. Am. Chem. Soc. 86, 1616-1626.
• Hansch C., Maloney P. P., Fujita T., Muir R. M., 1962. Correlation Of Biological Activity With Hamnett Substituent Constants And Partition Coefficients. Nature 194, 178-180.
• Hansch C., Muir R. M., Fujita T., Maloney P. P., Geiger F., Streich M., 1963. The Correlation Of Biological Activity Of Plant Growth Regulators And Chloromycetin Derivatives With Hammett Constants And Partition Coefficients. J. Am. Chem. Soc. 83, 2817-2824.
• Hertz H. G., Zeidler M. D., 1964. Kernmagnetische Relaxationszeitmessungen Zur Frage Der Hydratation Unpolarer Gruppen In Wässriger Lösung. Ber. Bunsen. Phys. Chem. 68, 821-837.
• Huang D. M., Chandler D., 2000. Temperature And Length Scale Dependence Of Hydrophobic Effects And Their Possible Implications For Protein Folding. Proc. Natl. Acad. Sci. Usa 97, 8324-8327.
• Huggins M. L., 1922. Atomic Structure. Science 55, 459-460.
• Huggins M. L., 1936. Hydrogen Bridges In Ice And Liquid Water. J. Phys. Chem. 40, 723-731.
• Huggins M. L., 1943. The Structure Of Fibrous Proteins. Chem. Rev. 32, 195-218.
• Jorgensen W. L., Tirado-rives J., 1988. The Opls Potential Functions For Proteins. Energy Minimizations For Crystals Of Cyclic Peptides And Crambin. J. Am. Chem. Soc. 110, 1657-1666.
• Kauzmann W., 1959. Some Factors In The Interpretation Of Protein Denaturation. Advan. Prot. Chem. 14, 1-63.
• Kołos W., 1986. Chemia Kwantowa. Pwn, Warszawa. Laurent T. C., 1971. Enzyme Reactions In Polymer Media. Eur. J. Biochem. 21, 498-506.
• Leo A., Hansch C., Elkins D., 1971. Partition Coefficients And Their Uses. Chem. Rev. 71, 525-616.
• Grochowski P., Bała P., Lesyng B., Mccammon J. A., 1996. Density Functional Based Parametrization Of A Valence Bond Method And Its Applications In Quantum-classical Molecular Dynamics Simulations Of Enzymatic Reactions. Int. J. Quantum Chem. 60, 1143-1164.
• Lifson S., Hagler A. T., Dauber P., 1979. Consistent Force Field Studies Of Intermolecular Forces In Hydrogen-bonded Crystals. 1. Carboxylic Acids, Amides, And The C:o⋅⋅⋅h Hydrogen Bonds. J. Am. Chem. Soc. 101, 5111-5121.
• Lum K., Chandler D., Weeks J. D., 1999. Hydrophobicity At Small And Large Length Scales. J. Phys. Chem. B 103, 4570-4577.
• Mirsky A. E., Pauling L., 1936. On The Structure Of Native, Denatured And Coagulated Proteins. Proc. Natl. Acad. Sci. 22, 439-447.
• Némethy G., Gibson K. D., Palmer K. A., Yoon C. N., Paterlini G., Zagari A., Rumsey S., Scheraga H. A., 1992. Energy Parameters In Polypeptides. 10. Improved Geometrical Parameters And Nonbonded Interactions For Use In The Ecepp/3 Algorithm, With Application To Proline-containing Peptides. J. Phys. Chem. 96, 6472-6484.
• Némethy G., Pottle M. S., Scheraga H. A., 1983. Energy Parameters In Polypeptides. 9. Updating Of Geometrical Parameters, Nonbonded Interactions, And Hydrogen Bond Interactions For The Naturally Occurring Amino Acids. J. Phys. Chem. 87, 1883-1887.
• Némethy G., Scheraga H. A., 1962a. Structure Of Water And Hydrophobic Bonding In Proteins. 1. A Model For The Thermodynamic Properties Of Liquid Water. J. Chem. Phys. 36, 3382-3400.
• Némethy G., Scheraga H. A., 1962b. Structure Of Water And Hydrophobic Bonding In Proteins. Ii. Model For The Thermodynamic Properties Of Aqueous Solutions Of Hydrocarbons. J. Chem. Phys. 36, 3401-3417.
• Némethy G., Scheraga H. A., 1962c. The Structure Of Water And Hydrophobic Bonding In Proteins. Iii. The Thermodynamic Properties Of Hydrophobic Bonds In Proteins. J. Phys. Chem. 66, 1773-1789.
• Pauling L., 1960. Nature Of The Chemical Bond. Cornell Univ. Press, Ithaca. Piela L., 2003. Idee Chemii Kwantowej. PWN, Warszawa.
• Pierotti R. A., 1976. A Scaled Particle Theory Of Aqueous And Nonaqueous Solutions. Chem. Rev. 76, 717-726.
• Pikuła S., 2004. Woda Morska I Dziury W Błonach — Nagroda Nobla Z Chemia Za Rok 2003. Kosmos 53, 243-249.
• Privalov P. L., Gill S. J., 1988. Stability Of Protein Structure And Hydrophobic Interaction. Adv. Protein Chem. 39 191-234.
• Rekker R. F., 1977. The Hydrophobic Fragmental Constant: Its Derivation And Application With A Means Of Characterizing Membrane Systems. Elsevier, Amsterdam.
• Reynolds J. A., Gilbert D. B., Tanford C., 1974. Empirical Correlation Between Hydrophobic Free Energy And Aqueous Cavity Surface Area. Proc. Natl. Acad. Sci. Usa 71, 2925-2927.
• Rose G. D., Geselowitz A. R., Lesser G. J., Lee R. H., Zehfus M. H., 1985. Hydrophobicity Of Amino Acid Residues In Globular Proteins. Science 229, 834-838.
• Sinanoglu O., 1968. Solvent Effects In Molecular Association [w:] Biology, Pullman B. (red.), Academic Press, New York.
• Sokalski W. A., Poirier R., 1983. Cumulative Atomic Multipole Representation Of The Molecular Charge Distribution And Its Basis Set Dependence. Chem. Phys. Lett. 98, 86-92.
• Van Der Waals J. D., 1873. Over De Continuiteit Van Den Gas En Vloeistoftoestand. Praca Doktorska, Uniwersytet W Leiden. Weiner S. J., Kollman P. A., Nguyen D. T., Case D. A., 1986. An All Atom Force Field For Simulations Of Proteins And Nucleic Acids. J. Comp. Chem. 7, 230-252.
• Wolfenden R., Andersson L., Cullis P. M., Southgate C. C., 1981. Affinities Of Amino Acid Side Chains For Solvent Water. Biochemistry 20, 849-855.
• Zhou H., Zhou Y., 2002. Stability Scale And Atomic Solvation Parameters Extracted From 1023 Mutation Experiments. Proteins 49, 483-492.
• Zhou H., Zhou Y., 2004. Quantifying The Effect Of Burial Of Amino Acid Residues On Protein Stability. Proteins 54, 315-322.
• Zielenkiewicz W., Poznański J., 1998. Partial Molar Volumes Of Hydrophobic Compounds — Insight Into The Solvation Shell? J. Solution Chem. 27, 245-254.
• Zielenkiewicz W., Poznański J., Zielenkiewicz A., 1998. Partial Molar Volumes Of Alkylated Uracils — Insight Into The Solvation Shell? Part Ii. J. Solution Chem. 27, 543-551.
• Zimmerman S. B., Minton A. P., 1993. Macromolecular Crowding: Biochemical, Biophysical, And Physiological Consequences. Ann. Rev. Biophys, Biomol. Struct. 22, 27-65.