Helix-helix interactions and their impact on protein motifs and assemblies

Journal of Theoretical Biology

Volumn 264, Issue 2, 2010, Pages 585-592

  Kurochkina, Natalya ^a  

^a The School of Theoretical Modeling   (United States)

Author keywords

Helix interactions; Heptad repeat; Protein assembly; Protein conformation; Structural motif

Indexed keywords

COAT PROTEIN; HEMERYTHRIN; LACTATE DEHYDROGENASE; MYOHEMERYTHRIN; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG;

AMINO ACID; CORRELATION; GENE; PROTEIN;

ALPHA HELIX; ARTICLE; CONTACT ANGLE; CONTROLLED STUDY; ENZYME CONFORMATION; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; ROSSMANN FOLD; STRUCTURE ANALYSIS; TIM BARREL; TOBACCO MOSAIC VIRUS;

AMINO ACID MOTIFS; ANIMALS; CAPSID PROTEINS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEINS; TOBACCO MOSAIC VIRUS;

TOBACCO MOSAIC VIRUS;

EID: 77951653016     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.02.026     Document Type: Article

References (50)

1. Alber T., Banner D.W., Bloomer A.C., Petsko G.A., Phillips D., Rivers P.S., Wilson I.A. On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. Philos. Trans. R. Soc. London 1981, 293:159-171.
2. 1) of Escherichia coli-K12. Biochem. Biophys. Res. Commun. 1989, 158:489-496.
3. Banner D.W., Kokkinidis M., Tsernoglou D. Structure of the ColE1 Rop protein at 1.7Å resolution. J. Mol. Biol. 1987, 196:657-675.
4. Bernstein F.C., Koetzle T.F., Williams G.J.B., Meyer E.F., 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, 112:535-542.
5. Bhyravbhatla B., Watowich S.J., Caspar D.L. Refined atomic model of the four-layer aggregate of the tobacco mosaic virus coat protein at 2.4-A resolution. Biophys. J. 1998, 74:604-615.
6. Brinkmann U., Di Carlo A., Vasmatzis G., Kurochkina N., Beers R., Lee B., Pastan I. Stabilization of a recombinant Fv fragment by base loop interconnection and VH-VL permutation. J. Mol. Biol. 1997, 268:107-117.
7. Carlacci L., Chou K.C. Electrostatic interactions between loops and α-helices in four-helix bundle proteins. Protein Eng. 1990, 4:225-227.
8. Carlacci L., Chou K.C. Monte Carlo method applied in the search for low energy conformations of ßaßaß structures. Biopolymers 1990, 30:135-150.
9. Carlacci L., Chou K.C. Energetic approach to the folding of four α-helices connected sequentially. Protein Eng. 1990, 3:509-514.
10. Carlacci L., Chou K.C. New development on energetic approach to the packing in proteins. J. Comput. Chem. 1991, 12:410-415.
11. Carlacci L., Chou K.C., Maggiora G.M. A heuristic approach to predicting the tertiary structure of bovine somatotropin. Biochemistry 1991, 30:4389-4398.
12. Chothia C. Structural invariants in protein folding. Nature 1975, 254:304-308.
13. Chothia C., Levitt M., Richardson D. Helix to helix packing in proteins. J. Mol. Biol. 1981, 145:215-250.
14. Chou K.C. Review: low-frequency collective motion in biomacromolecules and its biological functions. Biophys. Chem. 1988, 30:3-48.
15. Chou K.C., Carlacci L. Energetic approach to the folding of alpha/beta barrels. Proteins 1991, 9:280-293.
16. Chou K.C., Carlacci L., Maggiora G.M., Parodi L.A., Schultz M.W. An energy-based approach to packing the 7-helix bundle of bacteriorhodopsin. Protein Sci. 1992, 1:810-827.
17. Chou K.C., Maggiora G.M., Nemethy G., Scheraga H.A. Energetics of the structure of the four-alpha-helix bundle in proteins. Proc. Natl. Acad. Sci. USA 1988, 85:4295-4299.
18. Chou K.C., Maggiora G.M., Scheraga H.A. The role of loop-helix interactions in stabilizing four-helix bundle proteins. Proc. Natl. Acad. Sci. USA 1992, 89:7315-7319.
19. Chou K.C., Nemethy G., Rumsey S., Tuttle R.W., Scheraga H.A. Interactions between an alpha-helix and a beta-sheet: energetics of alpha/beta packing in proteins. J. Mol. Biol. 1985, 186:591-609.
20. Chou K.C., Nemethy G., Scheraga H.A. Energetic approach to packing of α-helices: 1. Equivalent helices. J. Phys. Chem. 1983, 87:2869-2881.
21. Chou K.C., Nemethy G., Scheraga H.A. Energetic approach to packing of α-helices: 2. General treatment of nonequivalent and nonregular helices. J. Am. Chem. Soc. 1984, 106:3161-3170.
22. Chou K.C., Nemethy G., Scheraga H.A. Review: energetics of interactions of regular structural elements in proteins. Acc. Chem. Res. 1990, 23:134-141.
23. Chou K.C., Nemethy G., Rumsey S., Tuttle R.W., Scheraga H.A. Interactions between two beta-sheets: energetics of beta/beta packing in proteins. J. Mol. Biol. 1986, 188:641-649.
24. Chou K.C., Zhang C.T., Maggiora G.M. Disposition of amphiphilic helices in heteropolar environments. Proteins: Struct. Funct. Genet. 1997, 28:99-108.
25. Chou K.C., Zheng C. Strong electrostatic loop-helix interactions in bundle motif protein structures. Biophys. J. 1992, 63:682-688.
26. Crick F. Acta Crystallogr. 1953, 6:689.
27. Efimov A. Packing of α-helices in globular proteins. Layer structure of globin hydrophobic cores. J. Mol. Biol. 1979, 134:23-40.
28. Frolow F., Kalb (Gilboa) A.J., Yariv J. The structure of a unique two-fold symmetric, haem-binding site. Nat. Struct. Biol. 1994, 1:453-460.
29. Gernert K.M., Surles M.C., Labean T.H., Richardson J.S., Richrdson D.C. The alacoil: a very tight, antiparallel coiled-coil of helices. Protein Sci. 1995, 4:2252-2260.
30. Gerritsen M., Chou K.C., Nemethy G., Scheraga H.A. Energetics of multi-helix interactions in protein folding: application to myoglobin. Biopolymers 1985, 24:1271-1293.
31. Harris N.L., Presnell S.R., Cohen F.E. Four helix bundle diversity in proteins. J. Mol. Biol. 1994, 236:1356-1368.
32. Hendrickson W.A., Klippenstein G.L., Ward K.B. Tertiary structure of myohemerythrin at low resolution. Proc. Natl. Acad. Sci. 1975, 72:2160-2164.
33. Holm L., Sander C. Structural alignment of globins, phycocyanins and colicin A. FEBS Lett. 1993, 315:301-306.
34. Kauzmann W. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 1959, 14:1-63.
35. Kohn W.D., Mant C.T., Hodges R.S. α-helical protein assembly motifs. J. Biol. Chem. 1977, 272:2583-2586.
36. Kurochkina N. Amino acid composition of parallel helix-helix interfaces. J. Theor. Biol. 2007, 247:110-121.
37. Kurochkina N. Specific sequence combinations at parallel and antiparallel helix-helix interfaces. J. Theor. Biol. 2008, 255:188-198.
38. Lee B., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 1971, 55:379-400.
39. Mathews F.S. The structure, function, and evolution of cytochromes. Prog. Biophys. Mol. Biol. 1985, 45:1-56.
40. Namba K., Stubbs G. Structure of tobacco mosaic virus at 3.6 Angstroms resolution. Implications for assembly. Science 1986, 231:1401-1406.
41. Namba K., Pattanayek R., Stubbs G. Visualization of protein-nucleic acid interactions in a virus. Structure of intact tobacco mosaic virus at 2.9 Angstrom resolution by X-ray fiber diffraction. J. Mol. Biol. 1989, 208:307-325.
42. O'Shea E.K., Klemm J.D., Kim P.S., Alber T. Crystal structure of GCN4 leucine zipper, a two-stranded parallel coiled coil. Science 1991, 254:539-544.
43. Paliakasis C.D., Kokkinidis M. The stability of the four-α-helix bundle motif in proteins. Protein Eng. 1991, 4:849-850.
44. Pielak R.M., Jason R., Schnell J.R., Chou J.J. Mechanism of drug inhibition and drug resistance of influenza A M2 channel. Proc. Natl. Acad. Sci. USA 2009, 106:7379-7384.
45. Privalov P.L., Gill S.J. Stability of protein structure and hydrophobic interaction. Adv. Protein Chem. 1988, 39:191-234.
46. Rao S.T., Rossmann M.G. Comparison of super-secondary structure in proteins. J. Mol. Biol. 1973, 76:241-256.
47. Richards F.M. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 1977, 6:151-176.
48. Schnell J.R., Chou J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 2008, 451:591-595.
49. Sheriff S., Hendrickson W.A., Smith J.L. Structure of myohemerythrin in the azidomet state at 1.7/1.3Å resolution. J. Mol. Biol. 1987, 197:273-296.
50. Stoll V.S. Insights into substrate binding by d-2-ketoacid dehydrogenases from the structure of Lactobacillus pentosus d-lactate dehydrogenase. Structure 1996, 4:437-447.