Chiral Dualism as an Instrument of Hierarchical Structure Formation in Molecular Biology

The origin of chiral asymmetry in biology has attracted the attention of the research community throughout the years. In this paper we discuss the role of chirality and chirality sign alternation (L–D–L–D in proteins and D–L–D–L in DNA) in promoting self-organization in biology, starting at the level of single molecules and continuing to the level of supramolecular assemblies. In addition, we also discuss chiral assemblies in solutions of homochiral organic molecules. Sign-alternating chiral hierarchies created by proteins and nucleic acids are suggested to create the structural basis for the existence of selected mechanical degrees of freedom required for conformational dynamics in enzymes and macromolecular machines.

[1]  Anaís Dorta-Urra,et al.  Homochirality: A Perspective from Fundamental Physics , 2019, Symmetry.

[2]  Michel Petitjean,et al.  Chirality and Symmetry Measures: A Transdisciplinary Review , 2003, Entropy.

[3]  H. Ågren,et al.  Hierarchical chiral expression from the nano- to mesoscale in synthetic supramolecular helical fibers of a nonamphiphilic C3-symmetrical π-functional molecule. , 2011, Journal of the American Chemical Society.

[4]  N. C. Price,et al.  How to study proteins by circular dichroism. , 2005, Biochimica et biophysica acta.

[5]  Minghua Liu,et al.  Symmetry Breaking in Self-Assembled Nanoassemblies , 2019, Symmetry.

[6]  E. Yashima,et al.  Helical polymers: synthesis, structures, and functions. , 2009, Chemical reviews.

[7]  V. Bystrov,et al.  Molecular modeling and computational study of the chiral-dependent structures and properties of self-assembling diphenylalanine peptide nanotubes , 2019, Journal of Molecular Modeling.

[8]  G. Wächtershäuser,et al.  From pre‐cells to Eukarya – a tale of two lipids , 2002, Molecular microbiology.

[9]  D. Amabilino.  Chirality at the Nanoscale , 2009 .

[10]  Liuyang Sun,et al.  Chirality detection of enantiomers using twisted optical metamaterials , 2017, Nature Communications.

[11]  Riina Aav,et al.  The Breaking of Symmetry Leads to Chirality in Cucurbituril-Type Hosts , 2018, Symmetry.

[12]  V. Letokhov.  On difference of energy levels of left and right molecules due to weak interactions , 1975 .

[13]  G. Gottarelli,et al.  The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: an overview. , 2008, Chirality.

[14]  M. Mayor,et al.  Chirality in curved polyaromatic systems. , 2017, Chemical Society reviews.

[15]  Qiangbin Wang,et al.  Origin of the Plasmonic Chirality of Gold Nanorod Trimers Templated by DNA Origami. , 2018, ACS applied materials & interfaces.

[16]  A. Schwartz.  Origin of Life: The origin of macromolecular chirality , 1994, Current Biology.

[17]  R. Nolte,et al.  Mastering molecular matter. Supramolecular architectures by hierarchical self-assembly , 2003 .

[18]  Jie Chen,et al.  Hierarchical Self-Assembly of a Porphyrin into Chiral Macroscopic Flowers with Superhydrophobic and Enantioselective Property. , 2017, ACS nano.

[19]  Gregory S. Tschumper,et al.  Electroweak Quantum Chemistry for Possible Precursor Molecules in the Evolution of Biomolecular Homochirality , 2000 .

[20]  David Avnir,et al.  Quantitative symmetry and chirality—A fast computational algorithm for large structures: Proteins, macromolecules, nanotubes, and unit cells , 2011, J. Comput. Chem..

[21]  Min Lu,et al.  A seven-helix coiled coil , 2006, Proceedings of the National Academy of Sciences.

[22]  Cyrus Chothia,et al.  Conformation of twisted β-pleated sheets in proteins , 1973 .

[23]  V. Tverdislov,et al.  Physical aspects of the emergence of living cell precursors: the ion and chiral asymmetries as two fundamental asymmetry types , 2008 .

[24]  M. Mikhaleva,et al.  Self assembly of supramolecular homochiral structures in solutions of chiral biomimetics , 2015 .

[25]  D. Blackmond,et al.  On the origin of single chirality of amino acids and sugars in biogenesis. , 2012, Accounts of chemical research.

[26]  Milan Randic,et al.  Molecular Shapes and Chirality , 1996, J. Chem. Inf. Comput. Sci..

[27]  V. Tverdislov.  Chirality as a primary switch of hierarchical levels in molecular biological systems , 2013, Biofizika.

[28]  D. Vollhardt,et al.  Effect of molecular chirality on the morphology of biomimetic langmuir monolayers. , 2003, Chemical reviews.

[29]  O. Mayans,et al.  Molecular insights into the self‐assembly mechanism of dystrophia myotonica kinase , 2006, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[30]  J. Podlech.  Origin of organic molecules and biomolecular homochirality , 2001, Cellular and Molecular Life Sciences CMLS.

[31]  R. Nolte,et al.  Helical superstructures from charged Poly(styrene)-Poly(isocyanodipeptide) block copolymers , 1998, Science.

[32]  Sung-Hou Kim,et al.  Four-helical-bundle structure of the cytoplasmic domain of a serine chemotaxis receptor , 1999, Nature.

[33]  Y Yamagata,et al.  A hypothesis for the asymmetric appearance of biomolecules on earth. , 1966, Journal of theoretical biology.

[34]  Nozomu Suzuki,et al.  Possible Roles of Amphiphilic Molecules in the Origin of Biological Homochirality , 2019, Symmetry.

[35]  Biserka Kojic-Prodic,et al.  Symmetry versus Asymmetry in the Molecules of Life: Homomeric Protein Assemblies , 2010, Symmetry.

[36]  Takashi Onaka,et al.  Astrophysical Sites that Can Produce Enantiomeric Amino Acids , 2018, Symmetry.

[37]  E. Malyshko,et al.  On regularities in the spontaneous formation of structural hierarchies in chiral systems of nonliving and living matter , 2018, Physics-Uspekhi.

[38]  M. Steinmetz,et al.  The coiled-coil trigger site of the rod domain of cortexillin I unveils a distinct network of interhelical and intrahelical salt bridges. , 2000, Structure.

[39]  Kensei Kobayashi,et al.  Origin of Terrestrial Bioorganic Homochirality and Symmetry Breaking in the Universe , 2019, Symmetry.

[40]  Yoshito Tobe,et al.  The Asymmetry is Derived from Mechanical Interlocking of Achiral Axle and Achiral Ring Components -Syntheses and Properties of Optically Pure [2]Rotaxanes- , 2018, Symmetry.

[41]  Circular dichroism and its use in protein-folding studies. , 2011, Methods in molecular biology.

[42]  P. Burk,et al.  Supramolecular chirogenesis in zinc porphyrins by enantiopure hemicucurbit[n]urils (n = 6, 8). , 2019, Chemical communications.

[43]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[44]  M. P. Neal,et al.  The Hausdorff chirality measure and a proposed Hausdorff structure measure , 2009 .

[45]  E. Mandelkow,et al.  On the surface lattice of microtubules: helix starts, protofilament number, seam, and handedness , 1986, The Journal of cell biology.

[46]  E. Malyshko,et al.  A periodic system of chiral structures in molecular biology , 2017 .

[47]  Roberto Dominguez,et al.  Actin structure and function. , 2011, Annual review of biophysics.

[48]  K. Matsuno,et al.  Cell chirality: its origin and roles in left–right asymmetric development , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.