BSU bulletin. Chemistry. Physics
Bibliographic description:
, , HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS (Part 2) // BSU bulletin. Chemistry. Physics. - 2016. №4. . - С. 17-25.
Title:
HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS (Part 2)
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The α-helix, 310-helix, π-helix and -helix have been observed in protein structures. They account for 32% of residues, 4%, 0.3% and 0.2%, respectively. However, these per- centages depend on resolution of solved structures and method for assignment of secondary structures. May 2016, culled Protein Data Bank (PDB) data set, containing 2901 protein chains with less than 25% sequence identity and 1.6Å resolution (R-value 0.25), was used in this analysis. Secondary structure assignments are performed by DSSP, STRIDE and SECSTR for π-helices. Helical parameters-pitch, residues per turn, radius, handedness and p = rmsd/(N−1)1/2 for π-helices are determined by HELFIT program. p-Value, esti- mates helical regularity and all π-helices with p 0.10Å, were identified as regular. Heli- cal parameters of protein π-helices are compared with those of canonical π-helices and other types of protein helices.
Keywords:
310-helix, α-helix, π-helix, helical parameters, regular helix, protein struc- tures, protein chains.
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2. Pauling L., Corey R. B., Branson H. R. The structure of proteins; two hydrogen- bonded helical configurations of the polypeptide chain // Proc. Natl. Acad. Sci. USA. —1951. — V. 37, № 4. — P. 205-211.
3. Low B. W., Baybutt R. B. The π-helix a hydrogen bonded configuration of the polypeptide chain // J. of the American Chemical Society. — 1952. — V. 74(22). — P.5806-5807.
4. Kabsch W., Sander C. How good are predictions of protein secondary structure? // FEBS Lett. — 1983. — 155(2). — P. 179-82.
5. Frishman D., Argos P. Knowledge-based protein secondary structure assignment // Proteins. — 1995. — 23(4). — P. 566-579.
6. Tyagi M., Bornot A., Offmann B., De Brevernet A. Analysis of loop boundaries using different local structure assignment methods // Protein Science. — 2009. — 18(9). — P. 1869-1881.
7. Fodje M. N., Al-Karadaghi S. Occurrence, conformational features and amino acid propensities for the pi-helix // Protein Eng. — 2002. — 15(5). — P. 353-358.
8. Richardson J. S. The anatomy and taxonomy of protein structure // Adv. Protein Chem. — 1981. — V. 34. — P. 167-339.
9. Weaver T. M. The pi-helix translates structure into function // Protein Sci. — 2000. — 9(1). — P. 201-6.
10. Boobbyer D. N., Goodford P. J., McWhinnie P. M., Wade R. C. New hydrogen- bond potentials for use in determining energetically favorable binding sites on molecules of known structure // J. of medicinal chemistry. — 1989. — 32(5). — P. 1083-1094.
11. Enkhbayar P., Damdinsuren, S., Osaki M., Matsushima N. HELFIT: Helix fitting by a total least squares method // Comput. Biol. Chem. — 2008. — 32(4). — P. 307-10.
12. Baker E. N. and Hubbard R. E. Hydrogen bonding in globular proteins // Prog
Biophys Mol. Biol. — 1984. — 44(2). — Р. 97-179.
13. Barlow D. J. and Thornton J. M. Helix geometry in proteins // J. Mol. Biol. —
1988. — 201(3). — P. 601-19.
14. Ramachandran G. N. and Sasisekharan V. Conformation of polypeptides and proteins // Adv. Protein Chem. — 1968. — 23. — P. 283-438.
15. Perutz M. New X-Ray Evidence on the Configuration of Polypeptide Chains: Polypeptide Chains in Poly-gamma-benzyl-L-glutamate // Keratin and Hemoglobin. Nature. — 1951. — 167. — P. 1053-1054.
16. Lees W. J., Benson T. E., Hogle J. M., Walsh C. T. (E)-enolbutyryl-UDP-N- acetylglucosamine as a mechanistic probe of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) // Biochemistry. — 1996. — 35(5). — P. 1342-51.
17. Cooley R. B., Arp D. J., Karplus P. A. Evolutionary origin of a secondary
structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality // J. of molecular biology. — 2010. — 404(2). — P. 232-246.
18. Duneau J. P., Genest D., Genest M. Detailed description of an alpha helix, pi bulge transition detected by molecular dynamics simulations of the p185c-erbB2 V659G transmembrane domain // J. Biomol. Struct. Dyn. — 1996. — 13(5). — P. 753-69
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