The packing density in proteins: Standard radii and volumes

Journal of Molecular Biology

Volumn 290, Issue 1, 1999, Pages 253-266

  Tsai, Jerry ^a   Taylor, Robin ^b   Chothia, Cyrus ^c   Gerstein, Mark ^d  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

^c MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^d YALE UNIVERSITY   (United States)

Author keywords

Atomic group radii and volumes; Packing efficiency; Protein interior; Voronoi polyhedra

Indexed keywords

HYDROGEN; WATER;

ARTICLE; CALCULATION; COVALENT BOND; CRYSTAL STRUCTURE; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0033516705     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2829     Document Type: Article

References (36)

1. Abola E. E., Sussman J. L., Prilusky J., Manning N. O. Protein Data Bank archives of three-dimensional macromolecular structures. Methods Enzymol. 277:1997;556-571.
2. Allen F. H., Davies J. E., Gallo J. J., Johnson O., Kennard O., Macrae C. F., Mitchell E. M., Mitchell G. F., Smith J. M., Watson D. The development of versions 3 and 4 of the Cambridge Structural Database System. J. Chem. Inf. Comput. Sci. 31:1991;187-204.
3. Allen F. H., Baalham C. A., Lommerse J. P. M., Raithby P. R. Carbonyl-carbonyl interactions can be competitive with hydrogen bonds. Acta Crystallog. sect. B. 54:1998;320-329.
4. Bernal J. D., Finney J. L. Random close-packed hard-sphere model II. Geometry of random packing of hard spheres. Discus. Faraday Soc. 43:1967;62-69.
5. Bernstein F. C., Koetzle T. F., Williams G. J. B., Meyer E. F., Brice M. D. j., Rodgers J. R., Kennard O., Shimanouchi O., Tasumi M. Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
6. Bolton W. Intermolecular carbonyl carbon-oxygen interactions in organic crystals. Nature. 201:1964;987-989.
7. Bondi A. VDW volumes and radii. J. Phys. Chem. 68:1964;441-451.
8. Chothia C. Structural invariants in protein folding. Nature. 254:1975;304-308.
9. Cohn E. J., Edsall J. T. Proteins, Amino Acids and Peptides as Ions and Dipolar Ions. 1943;Reinhold, New York. p. 370-381.
10. Connolly M. Analytical molecular surface calculation. J. Appl. Crystallog. 16:1983;548-558.
11. Delaunay B. Sur la sphére vide. Bull. Acad. Sci USSR (VII), Classe Sci. Mat. Nat. 1934;. p. 783-800.
12. Gekko K., Noguchi H. Compressibility of globular proteins in water at 25 °C. J. Phys. Chem. 83:1979;2706-2714.
13. Gerstein M., Chothia C. Packing at the protein-water interface. Proc. Natl Acad. Sci. USA. 93:1996;10167-10172.
14. Gerstein M., Tsai J., Levitt M. The volume of atoms on the protein surface: calculated from simulation, using Voronoi polyhedra. J. Mol. Biol. 249:1995;955-966.
15. Harpaz Y., Gerstein M., Chothia C. Volume changes on protein folding. Structure. 2:1994;641-649.
16. Kocher J. P., Prevost M., Wodak S. J., Lee B. Properties of the protein matrix revealed by the free energy of cavity formation. Structure. 4:1996;1517-1529.
17. Kuhn L. A., Siani M. A., Pique M. E., Fisher C. L., Getzhoff E. D., Tainer J. A. The interdependence of protein surface-topography and bound water-molecules revealed by surface accessibility and fractal density measures. J. Mol. Biol. 228:1992;12-22.
18. Kuntz I. D. Tertiary structure in carboxypeptidase. J. Am. Chem. Soc. 94:1972;8568-8572.
19. Lee B., Richards F. M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
20. Li A. J., Nussinov R. A set of VDW and columbic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking. Proteins: Struct. Funct. Genet. 32:1998;111-127.
21. Liang J., Edelsbrunner E., Wodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications of ligand design. Protein Sci. 7:1998;1884-1887.
22. Lo Conte L., Chothia C., Janin J. Atomic structure of protein-protein recognition sites. J. Mol. Biol. 285:1999;2177-2198.
23. Maccallum P. H., Poet R., Milner-White E. J. Columbic attractions between partially charged main-chain atoms stabilise the right-handed twist found in most beta-strands. J. Mol. Biol. 248:1995a;374-384.
24. Maccallum P. H., Poet R., Milner-White E. J. Columbic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of alpha-helices and antiparallel beta-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Columbic interactions. J. Mol. Biol. 248:1995b;361-373.
25. Mishra A. K., Ahluwalia J. C. Apparent molal volumes of amino acids, N-acetylamino acids and peptides in aqueous solutions. J. Phys. Chem. 88:1984;86-92.
26. Murzin A. G., Brenner S. E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;537-540.
27. Nadassy K., Wodak S. J., Janin J. Structural features of protein-nucleic acid recognition sites. Biochemistry. 38:1999;1999-2017.
28. Peters K. P., Fauck J., Frommel C. The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol. 256:1996;201-213.
29. Pontius J., Richelle J., Wodak S. J. Deviations from standard atomic volumes as a quality measure of protein crystal structures. J. Mol. Biol. 264:1996;121-136.
30. Richards F. M. The interpretation of protein structures: total volume, group volume distributions and packing density. J. Mol. Biol. 82:1974;1-14.
31. Richards F. M. Packing defects, cavities, volume fluctuations, and access to the interior of proteins. including some general comments on surface area and protein structure. Carlsberg. Res. Commun. 44:1979;47-63.
32. Richards F. M. Calculation of molecular volumes and areas for structures of known geometry. Methods Enzymol. 115:1985;440-464.
33. Rowland R. S., Taylor R. Intermolecular nonbonded contact distances in organic crystal structures: comparison with distances expec ted from VDW radii. J. Phys. Chem. 100:1996;7384-7391.
34. Shoichet B. K., Kuntz I. D. Protein dock ing and complementarity. J. Mol. Biol. 221:1991;327-346.
35. Squire P. G., Himmel M. E. Hydrodynamics and protein hydration. Arch. Biochem. Biophys. 196:1979;165-177.
36. Voronoi G. F. Nouvelles applications des paramétres continus á la théorie de formes quadratiques. J. Reine Agnew. Math. 134:1908;198-287.