Abstract
A review of materials within the concept of chirality as a symmetric basis of self-organization in biomacromolecules is presented. The following topics are considered: methods for determining the chirality of regular and irregular protein structures, the distribution of helical and superhelical structures in polypeptide chains, a model for the formation of a three-dimensional structure of the right-handed α-helix from a chain of L-amino acid residues, and a model for the formation of the right-handed α-helix based on a two-particle model of movement in the Lennard-Jones potential. The applied aspects of the concept of chirality in pharmacology and bioengineering, the chirality of drugs with bioactive enantiomers and the mechanisms of self-assembly of helical structures of phenylalanine and diphenylalanine nanotubes of different chirality are discussed. The basic concepts of molecular machines as chiral hierarchical structures are presented.
Similar content being viewed by others
REFERENCES
V.A. Tverdislov, Biophysics 58 (1), 159 (2013).
V. A. Tverdislov and E. Malyshko, Phys.– Usp. 62 (4), 354 (2019).
E. V. Malyshko, O. E. Bagrova, and V. A. Tverdislov, Biofizika 65 (3), 439 (2020).
P. A. Guye, C. R. 116, 1451 (1893).
E. Ruch and A. Schonhofer, Theor. Chim. Acta 10 (2), 91 (1968).
M. Randic, Chemometr. Intell. Lab. Syst. 10, 213 (1991).
X. L. Peng, et al., Molecules 9 (12), 1089 (2004).
Y. Du, et al., J. Chem. Inf. Comput. Sci. 42 (5), 993 (2002).
D. Yaffe and Y. J. Cohen, Chem. Inf. Comput. Sci. 41 (2), 463 (2001).
E. S. Goll and P. C. Jurs, J. Chem. Inf. Comput. Sci. 39 (6), 1081 (1999).
H. E. McClelland and P. C. Jurs, J. Chem. Inf. Comput. Sci. 40 (4), 967 (2000).
A. R. Katritzky, S. Sild, and M. J. Karelson, Chem. Inf. Comput. Sci. 38 (5), 840 (1998).
T. Zhao, Q. Zhang, H. Long, and L. Xu, PLoS One 9 (7), (2014).
M. Randic, J. Chem. Inf. Comput. Sci. 41 (3), 639 (2001).
A. B. Buda, T. A. der Heyde, and K. Mislow, Angew. Chem. 31 (8), 989 (1992).
P. G. Mezey, J. Mol. Struct.: THEOCHEM 455 (2–3), 183 (1998).
G. Gilat and L. S. Schulman, Chem. Phys. Lett. 121 (1–2), 13 (1985).
H. Zabrodsky, S. Peleg, and D. Avnir, J. Am. Chem. Soc. 114 (20), 7843 (1992).
M. Pinsky, C. Dryzun, D. Casanova, et al., J. Comput. Chem. 29 (16), 2712 (2008).
V. E. Kuz’min, I. B. Stel’mach, M. B. Bekker, and D. V. Pozigun, J. Phys. Org. Chem. 5 (6), 295 (1992).
P.W. Fowler, Symmetry: Cult. Sci. 16 (4), 321 (2005).
A. V. Luzanov and D. J. Nerukh, Math. Chem. 41 (4), 417 (2007).
G. Raos, Macromol. Theory Simul. 11 (7), 739 (2002).
G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, J. Mol. Biol. 7 (1), 95 (1963).
M. Petitjean, Entropy 5, 271 (2003).
R. D. B. Fraser and T. P. MacRae, Conformation in Fibrous Proteins and Related Synthetic Polypeptides (Acad. Press, New York).
G. N. Phillips, Proteins 14, 425 (1992).
S. Neukirch, A. Goriely, A.C. Hausrath, Phys. Rev. Lett. 100, 038105 (2008).
S. W. Robinson, A. M. Afzal, and D. P. Leader, in Handbook of Pharmacogenomics and Stratified Medicine, Ed. by S. Padmanabhan (Acad. Press, New York, 2014), pp. 259–287.
J. S. Richardson, Adv. Prot. Chem. 34, 167 (1981).
P. N. Lewis, F. A. Momany, and H. A. Scheraga, Isr. J. Chem. 11, 121 (1973).
C. Wilmot and J. Thornton, J. Mol. Biol. 203, 221 (1988).
A. G. de Brevern, Sci. Rep. 6, 33191 (2016).
E. G. Hutchinson and J. Thornton, Prot. Sci. 3, 2207 (1994).
D. Ting, G. Wang, M. Shapovalov, et al., PLoS Comput. Biol. 6, e1000763 (2010).
M. Shapovalov, V. Slobodan, R. L. Dunbrack, PLoS Comput. Biol. 15, e1006844 (2019).
C. Fang, Y. Shang, and N. Xu, Sci. Rep. 8, 15741 (2018).
M. U. Johansson, V. Zoete, O. Michielin, and N. Guex, BMC Bioinf. 13, 173 (2012).
W. J. Duddy, J. W. M. Nissink, F. H. Allen, and E. J. Milner-White, Prot. Sci. 13, 3051 (2008).
N. Eswar and C. Ramakrishnan, Protein Eng., Des. Sel. 12, 447 (1999).
A. E. Sidorova, E. V. Malyshko, A. R. Kotov, et al., Bull. Russ. Acad. Sci.: Phys. 83 (1), 85 (2019).
A. E. Sidorova, A. O. Lutsenko, D. K. Shpigun, et al., Biophysics 66, 357 (2021).
A. Sidorova, E. Malyshko, A. Lutsenko, et al., Symmetry 13, 879 (2021).
A. Sidorova, V. Bystrov, A. Lutsenko, et al., Nanomaterials 11 (12), (2021).
V. Bystrov, A. Sidorova, A. Lutsenko, et al., Nanomaterials 11, 2415 (2021).
https://www.rcsb.org/structure/2ACT
M. Fodje and S. Al-Karadaghi, Protein Eng., Des. Sel. 15, 353 (2002).
D. V. Nataraj, N. Srinivasan, R. Sowdhamini, and C. Ramakrishnan, Curr. Sci. 69, 434 (1995).
M. Shapovalov, V. Slobodan, and R. L. Dunbrack, PLoS Comput. Biol. 15, e1006844 (2019).
RCSB PDB. Available online: https://www.rcsb.org
J. F. Leszczynski and G. D. Rose, Science 234, 849 (1986).
https://www.rcsb.org/structure/1BB1
A. E. Sidorova, E. V. Malyshko, A. O. Lutsenko, et al., Symmetry 13 (5) (2021).
CC+ Database. http://coiledcoils.chm.bris.ac.uk/ccplus/search/. Cited January 15, 2022.
E. V. Malyshko, O. E. Bagrova, and V. A. Tverdislov, Biofizika 65 (3), 439 (2020).
A. S. Ivanov, Biomed. Khim. 57 (1), 31 (2011).
A. E. Sidorova, N. T. Levashova, E. V. Malyshko, and V. A. Tverdislov, Moscow Univ. Phys. Bull. 74 (3), 213 (2019).
Y. B. Zeldovich and D. A. Frank-Kamenetsky, Acta Physicochim. 9, 341 (1938).
A. Zaikin and A. Zhabotinsky, Nature 225, 535 (1970).
V. A. Vasil’ev, Yu. M. Romanovskii, and V. G. Yakhno, Autowave Processes (Nauka, Moscow, 1987) [in Russian].
R. A. FitzHugh, Biophys. J. 445 (1961).
R. R. Aliev and A. V. Panfilov, Chaos, Solitons Fractals 3, 293 (1996).
Yu. E. Elkin, V. N. Biktashev, and A. V. Holden, Chaos, Solitons Fractals 9 (9), 1597 (1998).
Y. Kuramoto and T. Tsuzuki, Theor. Phys. 54, 687 (1975).
J. M. Davidenko, A. V. Pertsov, R. Salomonsz, et al., Nature 355, 349 (1992).
A. L. Hodgkin and A. F. Huxley, J. Physiol. 117, 500 (1952).
D. Marquardt, SIAM J. Appl. Math. 11 (2), 431 (1963).
A. M. Zhabotinsky and A. N. Zaikin, J. Theor. Biol. 40, 45 (1973).
G. R. Ivanitskii, V. I. Krinskii, and E. E. Sel’kov, Mathematical Biophysics of the Cell (Nauka, Moscow, 1978) [in Russian].
Dzh. Marri, Nonlinear Differential Equation in Biology (Mir, Moscow, 1983) [in Russian].
V. I. Krinskii and A. V. Kholopov, Biofizika 12, 524 (1967).
O. A. Mornev, I. M. Tsyganov, O. V. Aslanidi, and M. A. Tsyganov, Pis’ma Zh. Eksp. Teor. Fis. 77 (6), 319 (2003).
L. Pauling and R. B. Corey, Proc. Natl. Acad. Sci. U. S. A. 37, 235 (1951).
A. V. Finkel’shtein and O. B. Ptitsyn, Protein Physics: A Course of Lectures with Color and Stereoscopic Illustrations and Tasks (Knizhnyi dom “Universitet”, Moscow, 2012) [in Russian].
A. E. Sidorova, E. V. Malyshko, A. R. Kotov, et al., Bull. Russ. Acad. Sci.: Phys. 83 (1), 85 (2019).
A. E. Sidorova, E. V. Malyshko, A. R. Kotov, et al., Biophysics 64 (2), 155 (2019).
H. M. Berman, et al., Nucleic Acids Res. 28, 235 (2000).
Yu. A. Ovchinnikov, Bioorganic Chemistry (Prosveshchenie, Moscow, 1987) [in Russian].
K. A. Zuev, N. T. Levashova, E. V. Malyshko, et al., Moscow Univ. Phys. Bull. 76 (4), 226 (2021).
K. A. Zuev, N. T. Levashova, E. V. Malyshko, et al., Moscow Univ. Phys. Bull. 76 (4), 226 (2021).
D. Nel’son and M. Koks, Lehninger Principles of Biochemistry, (WH Freeman, 2005).
R. Young and H. Bremer, Biochem. J. 160, 185 (1976).
K. A. Zuev, N. T. Levashova, E. V. Malyshko, et al., Moscow Univ. Phys. Bull. 76 (4), 226 (2021).
L. A. Nguyen, H. He, and C. Pham-Huy, Int. J. Biomed. Sci. 2 (2), 85 (2006).
E. V. Semenova, E. V. Malyshko, and V. A. Tverdislov, Aktual. Vopr. Biol. Fiz. Khim. 6 (1), 142 (2021).
E. V. Malyshko, E. V. Semenova, O. E. Bagrova, et al., Biophysica 1 (1), 22 (2021).
R. Vardanyan and V. Hruby, Synthesis of Best-Seller Drugs (Acad. Press, 2016).
R. Pool, Fat: Fighting the Obesity Epidemic (Oxford Univ. Press, Oxford, 2001).
Y. Horikiri, T. Suzuki, and M. Mizobe, J. Pharm. Sci. 87 (3), 289 (1998).
H. Alkadi and R. Jbeily, Infect. Disord.: Drug Targets 18 (2), 88 (2018).
A. M. Evans, Clin. Rheumatol. 20 (Suppl. 1), S9 (2001).
H. Beng, H. Zhang, R. Jayachandra, et al., Chirality 30, 759 (2018).
G. A. Jacobson, S. Raidal, K. Robson, et al., Br. J. Clin. Pharmacol. 83, 1436 (2017).
M. Singh, P. Malik, and R. Bhushan, J. Chromatogr. Sci. 54 (5), 842 (2016).
E. Szoko, H. Kalasz, and K. Magyar, Eur. J. Drug Metab. Pharmacokinet. 24 (4), 315 (1999).
S. A. Anttila and E. V. Leinonen, CNS Drug Rev. 7 (3), 249 (2001).
Q. Zhou, T. W. Yao, and S. Zeng, World J. Gastroenterol. 7 (6), 830 (2001).
H. K. Kroemer, C. Funck-Brentano, D. J. Silberstein, et al., Circulation 79 (5), 1068 (1989).
C. H. Gorbitz, Acta Cryst. 74, 311 (2018).
M. Calvin, Chemical Evolution. Molecular Evolution, Towards the Origin of Living System on the Earth and Elsewhere (Claredon Press, Oxford, 1969).
A. L. Lehninger, Biochemistry. The Molecular Basis of Cell Structure and Function (Worth Publishers, New York, 1972).
V. Bystrov, Computer Simulation Nanostructures: Bioferroelectric Amino Acids. Bioferroelectricity: Peptide Nanotubes and Thymine Nucleobase (LAMBERT, 2020).
V. S. Bystrov, I. K. Bdikin, and B. Singh, Nanomaterials Sci. Eng. 2 (1), 11 (2020)
V. S. Bystrov and S. V. Filippov, “Computer modeling and numerical studies of peptide nanotubes based on diphenylalanine,” Preprint IPM, No. 78 (2021).
V. S. Bystrov, P. S. Zelenovskiy, A. S. Nuraeva, et al., Math. Biol. Bioinf. 14 (1), 94 (2019).
V. S. Bystrov, P. S. Zelenovskiy, A. S. Nuraeva, et al., J. Mol. Model. 25 (199), 18 (2019).
P. S. Zelenovskiy, A. S. Nuraeva, S. Kopyl, et al., Cryst. Growth Des. 19, 6414 (2019).
V. Bystrov, J. Coutinho, P. Zelenovskiy, et al., Nanomaterials 10 (10), 1999 (2020).
V. S. Bystrov, P. S. Zelenovskiy, A. S. Nuraeva, et al., Math. Biol. Bioinf. 14 (1), 94 (2019).
I. V. Likhachev and V. S. Bystrov, Math. Biol. Bioinf. 16 (2), 244 (2021).
V. A. Tverdislov, E. V. Malyshko, and S. A. Il’chenko, Izv. Ross. Akad. Nauk: Ser. Fiz. 79 (12), 1728 (2015).
Funding
The research was carried out with the financial support of the Foundation for the Development of Theoretical Physics and Mathematics “BASIS” within projects no. 21-2-9-42-1 (to E.V. Semenova) and no. 21-2-1-14-1 (to O.E. Bagrova), as well as the Interdisciplinary Scientific and Educational School of Lomonosov Moscow State University “Fundamental and Applied Space Research”.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
CONFLICT OF INTEREST
The authors declare that they have no conflicts of interest.
COMPLIANCE WITH ETHICAL STANDARDS
This article does not contain any studies involving humans or animals as research objects.
Additional information
Translated by E. Puchkov
Abbreviations: PDB, Protein Data Bank; PNT, peptide nanotube.
Rights and permissions
About this article
Cite this article
Tverdislov, V.A., Sidorova, A.E., Bagrova, O.E. et al. Chirality As a Symmetric Basis of Self-Organization of Biomacromolecules. BIOPHYSICS 67, 673–691 (2022). https://doi.org/10.1134/S0006350922050190
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S0006350922050190