This paper is at advancement of a method recently developed at the Department of Biophysics of the Faculty of Physics of Moscow State University for evaluating the chirality sign of superhelical protein structures. The method was originally developed for superhelices of "coiled-coil" type, as the most common superhelical protein structures, but it is applicable also to other types of superhelices. The method is based on the concept that states that the direction of the angle between the axis of the superhelix and the axes of the constituent helices allows to determine the sign of chirality of the entire structure. To perform calculations it is necessary to know which amino acid residues of the polypeptide chain are involved in the formation of the superhelix, as well as to have information about the mutual spatial arrangement of the alpha-carbons of the amino acids of the helices that make up the superhelix; this information can be obtained from the CC+ Database and the PDB file for a specific superhelix. The use of a small amount of initial data and the simplicity of calculations make the method convenient and fast to use, the reliability of the results of this study is confirmed by a validation carried out on the protein structures presented in the PDB database. This method can be considered as a step towards determining not only the sign of chirality of superhelical protein structures, but also the degree of their chirality, which, in its turn, can lead to the extension of the concept of chirality to hierarchically higher categories of objects - protein globules and supramolecular structures.
proteins, chirality, helix, superhelix, coiled-coil
1. Sidorova A.E., Tverdislov V.A. Samoorganizaciya v ierarhii aktivnyh sred kak dvizhuschaya sila evolyucii biosfery. Vestn. Mosk. un-ta. Ser. 3. Fiz. Astron., 2012, № 2, 65 s. @@Sidorova A.E., Tverdislov V.A. Self-organization as the driving force for the evolution of the biosphere. Moscow University Physics Bulletin, 2012, vol. 67, no. 2, 213 p. (In Russ.)
2. Brandrn C.-I., Tooze J.Introduction to Protein Structure. New York: Garland Publishing, 1999, 35 p.
3. Pauling L., Corey R.B., Branson H.R. The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. PNAS, 1951, vol. 37, 205 p. doi: 10.1073/pnas.37.4.205
4. Branden C.-I., Tooze J.Introduction to Protein Structure. New York: Garland Publishing, 1999, 16 p.
5. Pauling L., Corey R.B.Compound Helical Configurations of Polypeptide Chains: Structure of Proteins of the α-Keratin Type. Nature, 1953, vol. 171, 59 p. DOI: 10.1038/171059a0
6. Crick F.H.S. The Fourier Transform of a Coiled-Coil. Acta Cryst., 1953, vol. 6, 685 p. doi: 10.1107/S0365110X53001952
7. Crick F.H.S. The Packing of α-Helices: Simple Coiled-Coils. Acta Cryst., 1953, vol. 6, 689 p. doi: 10.1107/S0365110X53001964
8. Yu Y.B. Coiled-coils: stability, specificity, and drug delivery potential. Advanced Drug Delivery Reviews, 2002, vol. 54, 1113 p. doi: 10.1016/S0169-409X(02)00058-3
9. Finkel'shteyn A.V., Pticyn O.B. Fizika belka: kurs lekciy s cvetnymi i stereoskopicheskimi illyustraciyami i zadachami. Moskva: KDU, 2012, 142 s. @@Finkelstein A.V., Ptitsyn O.B. Physics of protein: course of lectures with colored and stereoscopis illustrations and tasks. Moscow: KDU, 2012, 142 p. (In Russ.)
10. Lupas A.N., Gruber M. The structure of α-helical coiled coils. Advances in Protein Chemistry, 2005, vol. 70, 37 p. doi: 10.1016/S0065-3233(05)70003-6
11. Fraser R.D.B., MacRae T.P. Conformation in Fibrous Proteins and Related Synthetic Polypeptides. London: Academic Press, 1973, 456-465 pp.
12. Phillips G.N. What Is the Pitch of the α-Helical Coiled Coil? PROTEINS: Structure, Function, and Genetics, 1992, vol. 14, 425 p. doi: 10.1002/prot.340140403
13. Neukirch S., Goriely A., Hausrath A.C. Chirality of Coiled Coils: Elasticity Matters. Physical review letters, 2007, vol. 100, 038105 p. doi: 10.1103/PhysRevLett.100.038105
14. RCSB PDB: Protein 1A36. URL: https://www.rcsb.org/structure/1a36 (accessed: 12.07.2021).
15. CC+, a relational database of coiled-coil structures. URL: http://coiledcoils.chm.bris.ac.uk/ccplus/search/ (accessed: 12.07.2021).
