Russian Journal of Biological Physics and Chemisrty Russian Journal of Biological Physics and Chemisrty АКТУАЛЬНЫЕ ВОПРОСЫ БИОЛОГИЧЕСКОЙ ФИЗИКИ И ХИМИИ 2499-9962 54668 Моделирование в биофизике Modelling in biophycis Моделирование в биофизике Method for determining the chirality of protein helical structures Методика оценки хиральности спиральных структур белков Шпигун Д К Shpigun D K denish.den@mail.ru Луценко А О Lutsenko A O aleksluchrus@yandex.ru Сидорова А Э Sidorova A E sky314bone@mail.ru Московский государственный университет имени М.В. Ломоносова ru Lomonosov Moscow State University ru Московский государственный университет имени М.В. Ломоносова ru Lomonosov Moscow State University ru Московский государственный университет имени М.В. Ломоносова ru Lomonosov Moscow State University ru 25 09 2021 25 09 2021 6 3 418 423 20 09 2021 20 09 2021 https://rusjbpc.ru/en/nauka/article/54668/view

В данной работе рассмотрены различные подходы к количественной оценке молекулярной хиральности - одной из актуальных проблем биохимической физики. Предложен новый, относительно простой, метод оценки хиральности спиральных структур белковых молекул. Метод основан на нахождении опорных точек - атомов альфа-углерода в полипептидной цепи и последующем расчете смешанных произведений векторов, соединяющих эти точки. Специальное внимание уделено нормировке хиральности спиральных белковых структур. Проанализировано 983 белков из 12 классов, (данные базы PDB). Показано, что, наряду с энергетически более выгодными правыми α- и 310-спиралями, среди исследованных белков имеются элементы вторичной структуры в левой конформации. На основании разработанного метода получена карта хиральности спиральных структур исследованных белков. Данный метод можно рассматривать как шаг к распространению понятия хиральности на иерархически вышестоящие категории объектов - белковые глобулы и надмолекулярные структуры.

In the present study, various approaches to the quantitation of the molecular chirality, one of the pressing problems of biochemical physics, are considered. A new relatively simple method for estimating chirality in protein secondary structures is proposed. The method is based on defining the reference (control) points - alpha-carbon atoms in the polypeptide chain followed by calculating the mixed products of bond vectors associated with relative position of these points. Special attention was given to the normalization of chirality in protein helical structures. We analyzed 983 proteins of 12 classes taken from the PDB database. Along with energetically favorable right-handed α- and 310-helixes, the secondary structure motifs in the left-handed conformation were found. Based on the developed method a chirality map of protein helical structures was obtained. This method can be considered as a step towards extending the concept of chirality to hierarchically higher categories of objects - protein globules and supramolecular structures.

 белки хиральность альфа-углерод α-спираль 310-спираль карта хиральности proteins chirality alpha-carbon α-helix 310-helix chirality map

Cintas P. Chirality of living systems: a helping hand from crystals and oligopeptides. Angew. Chem.Int. Ed. Engl., 2002, vol. 41, pp. 1139-1145. Cintas P. Chirality of living systems: a helping hand from crystals and oligopeptides. Angew. Chem.Int. Ed. Engl., 2002, vol. 41, pp. 1139-1145. Barron L.D. From Cosmic Chirality to Protein Structure: Lord Kelvin’s Legacy. Chirality, 2012. doi: 10.1002/chir.22017 Barron L.D. From Cosmic Chirality to Protein Structure: Lord Kelvin’s Legacy. Chirality, 2012. doi: 10.1002/chir.22017 Tverdislov V.A., Malyshko E.V. On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter. Physics Uspekhi, 2019, vol. 62, no. 4, pp. 354-363. Tverdislov V.A., Malyshko E.V. On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter. Physics Uspekhi, 2019, vol. 62, no. 4, pp. 354-363. Tverdislov V.A. Chirality as a primary switch of hierarchical levels in molecular biological systems. Biophysics, 2013, vol. 58, no. 1, pp. 159-164. Tverdislov V.A. Chirality as a primary switch of hierarchical levels in molecular biological systems. Biophysics, 2013, vol. 58, no. 1, pp. 159-164. Crick F.H.C. The packing of α-helices: simple coiled-coils. Acta Cryst., 1953, vol. 6, pp. 689-692. Crick F.H.C. The packing of α-helices: simple coiled-coils. Acta Cryst., 1953, vol. 6, pp. 689-692. Barlow D.J., Thornton J.M. Helix geometry in proteins. J. Mol. Biol, 1988, vol. 201, pp. 601-619. Barlow D.J., Thornton J.M. Helix geometry in proteins. J. Mol. Biol, 1988, vol. 201, pp. 601-619. Efimov A.V. Chirality and Handedness of Protein Structures. Biochemistry, 2018, vol. 83, no 1, pp. 103-110. Efimov A.V. Chirality and Handedness of Protein Structures. Biochemistry, 2018, vol. 83, no 1, pp. 103-110. Novotny Kleywegt G.J. A Survey of left-handed helices in protein structures. Mol. Biol, 2005, vol. 347, no. 2, pp. 231-241. Novotny Kleywegt G.J. A Survey of left-handed helices in protein structures. Mol. Biol, 2005, vol. 347, no. 2, pp. 231-241. Cao Ch., Wang G., Liu A., Xu Sh., Wang L., Zou Sh. A new secondary structure assignment algorithm using Cα backbone fragments.Int. J. Mol. Sci, 2016, vol. 17, pp. 333-349. Cao Ch., Wang G., Liu A., Xu Sh., Wang L., Zou Sh. A new secondary structure assignment algorithm using Cα backbone fragments.Int. J. Mol. Sci, 2016, vol. 17, pp. 333-349. Ramachandran G.N., Ramakrishnan C., Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol, 1963, vol. 7, no. 1, pp. 95-99. Ramachandran G.N., Ramakrishnan C., Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol, 1963, vol. 7, no. 1, pp. 95-99. Harris A.B., Kamien R.D., Lubensky T.C. Molecular chirality and chiral parameters. Rev. Mod. Phys, 1999, vol. 71, pp. 1745-1757. Harris A.B., Kamien R.D., Lubensky T.C. Molecular chirality and chiral parameters. Rev. Mod. Phys, 1999, vol. 71, pp. 1745-1757. Guye P.A. Influence de la constitution chimique des dеrivеs du carbone sur le sens et les variations de leur pouvoir rotatoire.Compt. Rendus, 1890, vol. 110, p. 714. Guye P.A. Influence de la constitution chimique des derives du carbone sur le sens et les variations de leur pouvoir rotatoire.Compt. Rendus, 1890, vol. 110, p. 714. Ruch E., Schönhofer A. Naherungsformeln fur spiegelungsantimetrische Molekuleigenschaften. Theor. Chim. acta, 1968, vol. 10, no. 2, pp. 91-110. Ruch E., Schönhofer A. Naherungsformeln fur spiegelungsantimetrische Molekuleigenschaften. Theor. Chim. acta, 1968, vol. 10, no. 2, pp. 91-110. Randic M., Razinger M. Molecular shapes and chirality. J. Chem. Inform.Comp. Sci., 1996, vol. 36, no. 3, pp. 429-441. Randic M., Razinger M. Molecular shapes and chirality. J. Chem. Inform.Comp. Sci., 1996, vol. 36, no. 3, pp. 429-441. Peng X-L., Fang K-T, Hu Q-N, Liang Yi-Z. Impersonality of the connectivity index and recomposition of topological indices according to different properties. Molecules, 2004, vol. 9, no. 12, pp. 1089-1099. Peng X-L., Fang K-T, Hu Q-N, Liang Yi-Z. Impersonality of the connectivity index and recomposition of topological indices according to different properties. Molecules, 2004, vol. 9, no. 12, pp. 1089-1099. Zhao T., Zhang O., Long H., Xu L. Graph theoretical representation of atomic asymmetry and molecular chirality of benzenoids in two-dimensional space. PLOS ONE, 2014, vol. 9, no. 7, p. e102043. Zhao T., Zhang O., Long H., Xu L. Graph theoretical representation of atomic asymmetry and molecular chirality of benzenoids in two-dimensional space. PLOS ONE, 2014, vol. 9, no. 7, p. e102043. Buda A.В., Mislow K.A. A Hausdorff chirality measure. J. Amer. Chem. Soc., 1992, vol. 114, no. 15, pp. 6006-6012. Buda A.V., Mislow K.A. A Hausdorff chirality measure. J. Amer. Chem. Soc., 1992, vol. 114, no. 15, pp. 6006-6012. Petitjean M. Chiral mixtures. J. Math. Physics, 2002, vol. 43, no. 8, pp. 4147-4157. Petitjean M. Chiral mixtures. J. Math. Physics, 2002, vol. 43, no. 8, pp. 4147-4157. Avnir D., Meyer A.V. Quantifying the degree of molecular shape. A chirality measure. J. Molec. Struct. (Theochem.), 1991, vol. 226, pp. 211-222. Avnir D., Meyer A.V. Quantifying the degree of molecular shape. A chirality measure. J. Molec. Struct. (Theochem.), 1991, vol. 226, pp. 211-222. Zabrodsky H., Avnir D. Continuous Symmetry Measures, IV: Chirality. J. Amer. Chem. Soc., 1995, vol. 117, pp. 462-473. Zabrodsky H., Avnir D. Continuous Symmetry Measures, IV: Chirality. J. Amer. Chem. Soc., 1995, vol. 117, pp. 462-473. Wang H., Avnir D., Tuvi-Arad I. Chiral Ramachandran plots II: general trends and protein chirality spectra. Biochemistry, 2018, vol. 57, no. 45, pp. 6395-6403. Wang H., Avnir D., Tuvi-Arad I. Chiral Ramachandran plots II: general trends and protein chirality spectra. Biochemistry, 2018, vol. 57, no. 45, pp. 6395-6403. Зоркий П.М., Афонина Н.Н. Симметрия молекул и кристаллов. М.: Изд-во Моск. Унта, 1979, 176 с. @@Zorky P.M., Afonina N.N. Symmetry of molecules and crystals. Moscow: Unta, 1979, 176 p. (In Russ.) Zorkiy P.M., Afonina N.N. Simmetriya molekul i kristallov. M.: Izd-vo Mosk. Unta, 1979, 176 s. @@Zorky P.M., Afonina N.N. Symmetry of molecules and crystals. Moscow: Unta, 1979, 176 p. (In Russ.) Alikhanidi S.E., Kuz’min V.E. Quantitative Evaluation of Molecular Chirality on Base of an Optimized Approach to Original and Reflected Structures Comparison. Reports of NAS of Ukraine, 1999, vol. 3, pp. 138-141. Alikhanidi S.E., Kuz’min V.E. Quantitative Evaluation of Molecular Chirality on Base of an Optimized Approach to Original and Reflected Structures Comparison. Reports of NAS of Ukraine, 1999, vol. 3, pp. 138-141. Mezey P.G. Generalized chirality and symmetry deficiency. J. Math. Chem., 1998, vol. 23, pp. 65-84. Mezey P.G. Generalized chirality and symmetry deficiency. J. Math. Chem., 1998, vol. 23, pp. 65-84. Luzanov A.V. Positive chirality measures from chiroptical pseudoscalars: applications to carbon-containing molecular systems. Functional materials, 2015, vol. 22, no. 3, pp. 355-364. Luzanov A.V. Positive chirality measures from chiroptical pseudoscalars: applications to carbon-containing molecular systems. Functional materials, 2015, vol. 22, no. 3, pp. 355-364. Sidorova A.E., Malyshko E.V., Kotov A.R., Tverdislov V.A., Ustinin M.N. Quantitative criteria of chirality in hierarchical protein structures. Biophysics, 2019, vol. 64, no. 2, pp. 155-166. Sidorova A.E., Malyshko E.V., Kotov A.R., Tverdislov V.A., Ustinin M.N. Quantitative criteria of chirality in hierarchical protein structures. Biophysics, 2019, vol. 64, no. 2, pp. 155-166. The Protein Data Bank. URL: http://www.rcsb.org/ The Protein Data Bank. URL: http://www.rcsb.org/ Сидорова А.Э., Луценко А.О., Шпигун Д.К., Малышко Е.В., Твердислов В.А. Методы определения знака хиральности спиральных и суперспиральных структур белков. Биофизика, 2021, т. 66, № 3, с. 421-428. @@Sidorova A.E., Lutsenko A.O., Shpigun D.K., Malyshko E.V., Tverdislov V.A. Methods to determine the chirality sign for helical and superhelical protein structures. Biophysics, 2021, vol. 66, no. 3, pp. 421-428. (In Russ.) Sidorova A.E., Lucenko A.O., Shpigun D.K., Malyshko E.V., Tverdislov V.A. Metody opredeleniya znaka hiral'nosti spiral'nyh i superspiral'nyh struktur belkov. Biofizika, 2021, t. 66, № 3, s. 421-428. @@Sidorova A.E., Lutsenko A.O., Shpigun D.K., Malyshko E.V., Tverdislov V.A. Methods to determine the chirality sign for helical and superhelical protein structures. Biophysics, 2021, vol. 66, no. 3, pp. 421-428. (In Russ.) Sidorova A.E., Malyshko E.V., Lutsenko A.O., Shpigun D.K., Bagrova O.E. Protein helical structures: defining handedness and localization features. Symmetry, 2021, vol. 13, no 5, p. 879. Sidorova A.E., Malyshko E.V., Lutsenko A.O., Shpigun D.K., Bagrova O.E. Protein helical structures: defining handedness and localization features. Symmetry, 2021, vol. 13, no 5, p. 879.