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. 1995 Dec;69(6):2298–2303. doi: 10.1016/S0006-3495(95)80100-1

Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins.

X Z Zhou 1
PMCID: PMC1236468  PMID: 8599637

Abstract

The translational friction coefficients and intrinsic viscosities of four proteins (ribonuclease A, lysozyme, myoglobin, and chymotrypsinogen A) are calculated using atomic-level structural details. Inclusion of a 0.9-A-thick hydration shell allows calculated results for both hydrodynamic properties of each protein to reproduce experimental data. The use of detailed protein structures is made possible by relating translational friction and intrinsic viscosity to capacitance and polarizability, which can be calculated easily. The 0.9-A hydration shell corresponds to a hydration level of 0.3-0.4 g water/g protein. Hydration levels within this narrow range are also found by a number of other techniques such as nuclear magnetic resonance spectroscopy, infrared spectroscopy, calorimetry, and computer simulation. The use of detailed protein structures in predicting hydrodynamic properties thus allows hydrodynamic measurement to join the other techniques in leading to a unified picture of protein hydration. In contrast, earlier interpretations of hydrodynamic data based on modeling proteins as ellipsoids gave hydration levels that varied widely from protein to protein and thus challenged the existence of a unified picture of protein hydration.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allison S. A., Tran V. T. Modeling the electrophoresis of rigid polyions: application to lysozyme. Biophys J. 1995 Jun;68(6):2261–2270. doi: 10.1016/S0006-3495(95)80408-X. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bull H. B., Breese K. Protein hydration. II. Specific heat of egg albumin. Arch Biochem Biophys. 1968 Nov;128(2):497–502. doi: 10.1016/0003-9861(68)90056-8. [DOI] [PubMed] [Google Scholar]
  3. Diamond R. Real-space refinement of the structure of hen egg-white lysozyme. J Mol Biol. 1974 Jan 25;82(3):371–391. doi: 10.1016/0022-2836(74)90598-1. [DOI] [PubMed] [Google Scholar]
  4. Kuntz I. D. Hydration of macromolecules. IV. Polypeptide conformation in frozen solutions. J Am Chem Soc. 1971 Jan 27;93(2):516–518. doi: 10.1021/ja00731a037. [DOI] [PubMed] [Google Scholar]
  5. Kuntz I. D., Jr, Kauzmann W. Hydration of proteins and polypeptides. Adv Protein Chem. 1974;28:239–345. doi: 10.1016/s0065-3233(08)60232-6. [DOI] [PubMed] [Google Scholar]
  6. LUZZATI V., WITZ J., NICOLAIEFF A. [Determination of the weight and dimensions of proteins in solution by central diffusion of x-rays measured by the absolute scale: the example of lysozyme]. J Mol Biol. 1961 Aug;3:362–378. [PubMed] [Google Scholar]
  7. Norberg J., Nilsson L. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates. Biophys J. 1995 Dec;69(6):2277–2285. doi: 10.1016/S0006-3495(95)80098-6. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Rupley J. A., Careri G. Protein hydration and function. Adv Protein Chem. 1991;41:37–172. doi: 10.1016/s0065-3233(08)60197-7. [DOI] [PubMed] [Google Scholar]
  9. SCHWERT G. W. The molecular size and shape of the pancreatic proteases. II. Chymotrypsinogen. J Biol Chem. 1951 Jun;190(2):799–806. [PubMed] [Google Scholar]
  10. SOPHIANOPOULOS A. J., RHODES C. K., HOLCOMB D. N., VAN HOLDE K. E. Physical studies of lysozyme. I. Characterization. J Biol Chem. 1962 Apr;237:1107–1112. [PubMed] [Google Scholar]
  11. Squire P. G., Himmel M. E. Hydrodynamics and protein hydration. Arch Biochem Biophys. 1979 Aug;196(1):165–177. doi: 10.1016/0003-9861(79)90563-0. [DOI] [PubMed] [Google Scholar]
  12. Steinbach P. J., Brooks B. R. Protein hydration elucidated by molecular dynamics simulation. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):9135–9139. doi: 10.1073/pnas.90.19.9135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Tanford C. Protein denaturation. Adv Protein Chem. 1968;23:121–282. doi: 10.1016/s0065-3233(08)60401-5. [DOI] [PubMed] [Google Scholar]
  14. Venable R. M., Pastor R. W. Frictional models for stochastic simulations of proteins. Biopolymers. 1988 Jun;27(6):1001–1014. doi: 10.1002/bip.360270609. [DOI] [PubMed] [Google Scholar]
  15. WILCOX P. E., KRAUT J., WADE R. D., NEURATH H. The molecular weight of alpha-chymotrypsinogen. Biochim Biophys Acta. 1957 Apr;24(1):72–78. doi: 10.1016/0006-3002(57)90147-6. [DOI] [PubMed] [Google Scholar]
  16. Wang D., Bode W., Huber R. Bovine chymotrypsinogen A X-ray crystal structure analysis and refinement of a new crystal form at 1.8 A resolution. J Mol Biol. 1985 Oct 5;185(3):595–624. doi: 10.1016/0022-2836(85)90074-9. [DOI] [PubMed] [Google Scholar]
  17. Wlodawer A., Svensson L. A., Sjölin L., Gilliland G. L. Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry. 1988 Apr 19;27(8):2705–2717. doi: 10.1021/bi00408a010. [DOI] [PubMed] [Google Scholar]
  18. Zhou H. X. Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. Biophys J. 1993 Aug;65(2):955–963. doi: 10.1016/S0006-3495(93)81094-4. [DOI] [PMC free article] [PubMed] [Google Scholar]

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