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. 1997 Jan;72(1):408–415. doi: 10.1016/S0006-3495(97)78681-8

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

O Byron 1
PMCID: PMC1184331  PMID: 8994627

Abstract

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed.

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Selected References

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  1. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  2. Bloomfield V., Dalton W. O., Van Holde K. E. Frictional coefficients of multisubunit structures. I. Theory. Biopolymers. 1967 Feb;5(2):135–148. doi: 10.1002/bip.1967.360050202. [DOI] [PubMed] [Google Scholar]
  3. Brunne R. M., Liepinsh E., Otting G., Wüthrich K., van Gunsteren W. F. 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. 1993 Jun 20;231(4):1040–1048. doi: 10.1006/jmbi.1993.1350. [DOI] [PubMed] [Google Scholar]
  4. Davis K. G., Glennie M., Harding S. E., Burton D. R. A model for the solution conformation of rat IgE. Biochem Soc Trans. 1990 Oct;18(5):935–936. doi: 10.1042/bst0180935. [DOI] [PubMed] [Google Scholar]
  5. Díaz F. G., Iniesta A., García de la Torre J. Hydrodynamic study of flexibility in immunoglobulin IgG1 using Brownian dynamics and the Monte Carlo simulations of a simple model. Biopolymers. 1990;30(5-6):547–554. doi: 10.1002/bip.360300507. [DOI] [PubMed] [Google Scholar]
  6. Eisenberg H. Protein and nucleic acid hydration and cosolvent interactions: establishment of reliable baseline values at high cosolvent concentrations. Biophys Chem. 1994 Dec;53(1-2):57–68. doi: 10.1016/0301-4622(94)00076-x. [DOI] [PubMed] [Google Scholar]
  7. Garcia de la Torre J. G., Bloomfield V. A. Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications. Q Rev Biophys. 1981 Feb;14(1):81–139. doi: 10.1017/s0033583500002080. [DOI] [PubMed] [Google Scholar]
  8. Garcia de la Torre J., Navarro S., Lopez Martinez M. C., Diaz F. G., Lopez Cascales J. J. HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. Biophys J. 1994 Aug;67(2):530–531. doi: 10.1016/S0006-3495(94)80512-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. García de la Torre J., Bloomfield V. A. Conformation of myosin in dilute solution as estimated from hydrodynamic properties. Biochemistry. 1980 Oct 28;19(22):5118–5123. doi: 10.1021/bi00563a028. [DOI] [PubMed] [Google Scholar]
  10. Gregory L., Davis K. G., Sheth B., Boyd J., Jefferis R., Nave C., Burton D. R. The solution conformations of the subclasses of human IgG deduced from sedimentation and small angle X-ray scattering studies. Mol Immunol. 1987 Aug;24(8):821–829. doi: 10.1016/0161-5890(87)90184-2. [DOI] [PubMed] [Google Scholar]
  11. Hester G., Brenner-Holzach O., Rossi F. A., Struck-Donatz M., Winterhalter K. H., Smit J. D., Piontek K. The crystal structure of fructose-1,6-bisphosphate aldolase from Drosophila melanogaster at 2.5 A resolution. FEBS Lett. 1991 Nov 4;292(1-2):237–242. doi: 10.1016/0014-5793(91)80875-4. [DOI] [PubMed] [Google Scholar]
  12. Keown M. B., Ghirlando R., Young R. J., Beavil A. J., Owens R. J., Perkins S. J., Sutton B. J., Gould H. J. Hydrodynamic studies of a complex between the Fc fragment of human IgE and a soluble fragment of the Fc epsilon RI alpha chain. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1841–1845. doi: 10.1073/pnas.92.6.1841. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Perkins S. J. Molecular modelling of human complement subcomponent C1q and its complex with C1r2C1s2 derived from neutron-scattering curves and hydrodynamic properties. Biochem J. 1985 May 15;228(1):13–26. doi: 10.1042/bj2280013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Perkins S. J., Sim R. B. Molecular modelling of human complement component C3 and its fragments by solution scattering. Eur J Biochem. 1986 May 15;157(1):155–168. doi: 10.1111/j.1432-1033.1986.tb09652.x. [DOI] [PubMed] [Google Scholar]
  15. Perkins S. J., Smith K. F., Kilpatrick J. M., Volanakis J. E., Sim R. B. Modelling of the serine-proteinase fold by X-ray and neutron scattering and sedimentation analyses: occurrence of the fold in factor D of the complement system. Biochem J. 1993 Oct 1;295(Pt 1):87–99. doi: 10.1042/bj2950087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Perkins S. J., Smith K. F., Sim R. B. Molecular modelling of the domain structure of factor I of human complement by X-ray and neutron solution scattering. Biochem J. 1993 Oct 1;295(Pt 1):101–108. doi: 10.1042/bj2950101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Quart A. M., Yamane G. Multifocal oral squamous cell carcinoma. Quintessence Int Dent Dig. 1983 Feb;14(2):139–144. [PubMed] [Google Scholar]
  18. Rajan S. S., Ely K. R., Abola E. E., Wood M. K., Colman P. M., Athay R. J., Edmundson A. B. Three-dimensional structure of the Mcg IgG1 immunoglobulin. Mol Immunol. 1983 Jul;20(7):787–799. doi: 10.1016/0161-5890(83)90057-3. [DOI] [PubMed] [Google Scholar]
  19. Rocco M., Aresu O., Zardi L. Conformational state of circulating human plasma fibronectin. FEBS Lett. 1984 Dec 10;178(2):327–330. doi: 10.1016/0014-5793(84)80627-4. [DOI] [PubMed] [Google Scholar]
  20. Rocco M., Infusini E., Daga M. G., Gogioso L., Cuniberti C. Models of fibronectin. EMBO J. 1987 Aug;6(8):2343–2349. doi: 10.1002/j.1460-2075.1987.tb02510.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Rocco M., Spotorno B., Hantgan R. R. Modeling the alpha IIb beta 3 integrin solution conformation. Protein Sci. 1993 Dec;2(12):2154–2166. doi: 10.1002/pro.5560021215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. 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]
  23. Teller D. C., Swanson E., de Haën C. The translational friction coefficient of proteins. Methods Enzymol. 1979;61:103–124. doi: 10.1016/0076-6879(79)61010-8. [DOI] [PubMed] [Google Scholar]
  24. de la Torre J. G. Hydrodynamics of segmentally flexible macromolecules. Eur Biophys J. 1994;23(5):307–322. doi: 10.1007/BF00188655. [DOI] [PubMed] [Google Scholar]

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