Abstract
A method has been developed to calculate and represent the geometry of α-helices of membrane proteins. Geometrical parameters are computed from coordinate files in the protein data bank. The axis of the helix is determined from the local centroids of tetrapeptide units of the helix. The method provides lower and upper cutoff values of the distance between backbone atoms C i (carbonyl carbon) and Ni+4 for allocation of a hinge in a helix. The method calculates other geometrical parameters like the length of helix, twist per residue, height per residue, kink and swivel angles. Packing of bundles of α-helices is represented by relative angles of inclination and distance vectors. The parameters are useful in quantitative descriptions of structural features of membrane proteins.
Figure Representation of the organization of the helix bundle in 1rwt by helix axis Θ1(i)- Θ n (i), helix center Θ0(i) of ith helix and centroid (C) of centers the three helices. Arrow-head indicates C-terminal end of a helix.
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Acknowledgements
Permission to use the programs developed by Prof. C. Ramakrishnan, IISc, Bangalore, and a preview version of MODELYN by Dr. C. N. Mandal, IICB, Kolkata, India is gratefully acknowledged.
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Mohapatra, P.K., Khamari, A. & Raval, M.K. A method for structural analysis of α-helices of membrane proteins. J Mol Model 10, 393–398 (2004). https://doi.org/10.1007/s00894-004-0212-y
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DOI: https://doi.org/10.1007/s00894-004-0212-y