BSU bulletin. Chemistry. Physics
Bibliographic description:
, HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS // BSU bulletin. Chemistry. Physics. - 2016. №2-3. . - С. 10-17.
Title:
HELICAL PARAMETERS OF REGULAR π-HELICES IN PROTEINS
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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 percentages depend on resolution of solved structures and method for assignment of secondary structures. Culled 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.
HELFIT program determines the helical parameters-pitch, residues per turn, radius, and handedness and p = rmsd/(N-1)1/2 for π-helices, where RMSD is the root mean squares deviation from the best fit helix and N is helix length. p-value, estimates helical regularity and all regular π-helices with p 0.10Å were identified. Helical parameters of π-helices are compared with the helical parameters of canonical π-helices and other types of protein helices.
HELFIT program determines the helical parameters-pitch, residues per turn, radius, and handedness and p = rmsd/(N-1)1/2 for π-helices, where RMSD is the root mean squares deviation from the best fit helix and N is helix length. p-value, estimates helical regularity and all regular π-helices with p 0.10Å were identified. Helical parameters of π-helices are compared with the helical parameters of canonical π-helices and other types of protein helices.
Keywords:
310-helix, α-helix, π-helix, helical parameters, regular helix, protein structures, protein chains.
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9. Hobohm U., Scharf M., Schneider R., Sander C. Selection representative set of protein structures // Protein Sci. - 1992. - V. 1. - P. 409–417.
10. IUPAC-IUB, Commission on Biochemical Nomenclature // J. Mol. Biol. - 1970. - V. 52. - P. 1–17.
11. Kabsch W., Sander C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features // Biopolymers. - 1983. - V. 22. - P. 2577–2637.
12. Kovacs H., Mark A. E., Johansson J. and van Gunsteren W. F. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water // J. Mol. Biol. - 1995. - V. 247. - P. 808-822.
13. Lee K. H., Benson D. R. and Kuczera K. Transitions from α to π helix observed in molecular dynamics simulations of synthetic peptides // Biochemistry. - 2000. - V. 39. - P. 13737-13747.
14. Low B. W., Baybutt R. B. The pi-helix - a hydrogen bonded configuration of the polypeptide chain // J. Am. Chem. Soc. - 1952. - V. 74. - P. 5806-5814.
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17. Ramachandram G. N and Sasisekharan V. Conformation of polypeptides and proteins // Adv. Protein Chem. - 1968. - V. 23. - P. 283-437.
18. Rohl C. A and Doing A. J. Models for the 3(10)-helix/coil, pi-helix/coil, and alpha-helix/3(10)-helix/coil transitions in isolated peptides // Protein Sci. - 1996. - V. 5. - P. 1687-1696.
19. Weaver T. M. The pi-helix translates structure into function // Protein Sci. - 2000. - V. 9. - P. 201–206.
20. Manoj Tyagi, Aure lie Bornot, Bernard Offmann and Alexandre G. de Brevern. Analysis of loop boundaries using different local structure assignment methods // Protein science. - 2009. - V. 18. - P. 1869-1881.
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