Special Issue "Symmetry of Life and Homochirality"

Guest Editor
Prof. Dr. David Cline
Physics & Astronomy Department, College of Letters & Sciences, UCLA, 3-166 Knudsen Hall, Box 951547, Los Angeles, CA 90095-1547, USA
Website: http://personnel.physics.ucla.edu/directory/faculty/cline.htm
E-Mail:
Interests: astroparticle physics; solar neutrino puzzle and nucleon decay; unique detection of primordial black holes; gamma-ray astronomy

Dear Colleagues,

In 1848 L. Pasteur carried out one of the most important experiments in Life Sciences when he transmitted polarized light through a medium with crystal found near a wine producing facility. These crystals were large enough that the individual symmetry (or resolution) of the crystal could be determined. He discovered that these biological materials caused polarized light to have its plane rotated (or optical activity). Two key results come from this experiment:
(a)-Biological materials are built out of 3-dimensional molecules (stereo
(b)-Most of the key molecules in life are either left-handed or D (right-handed)
We now know that 19 of the 20 Amino Acids that make proteins in life are left-handed. This is sometimes called Chiral Symmetry breaking or Homochirality.
In the physical world the concepts of Symmetry and Symmetry breaking are of key importance, while Symmetry principles are key to important physical theories (i.e. Lorentz Invariance and the Theory of Relativity). Asymmetry comes into the nature of the weak force (that drives the energy production in the sun). This depends on a symmetry breaking that leads to a massive particle the Z° with the same properties as the photon of liquid but is 90 proton masses heaver.*
Some Biologists believe that the very existence of life depends on the chiral symmetry breaking or Homochirality; therefore, understanding the origin of this aspect of life could be related to the understanding of the origin of life to some.

*The author was part of the team that in 1983 discovered the Z° particles at Geneva, Switzerland.

Prof. Dr. David Cline
Guest Editor

Please visit the Instructions for Authors page before submitting a manuscript. For the first couple of issues, to be published in 2010, the Article Processing Charges (APC) will be waived for well-prepared manuscripts. English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.

Type of Paper: Review
Title: Origin of Homochirality of Amino Acids in the Biosphere
Author: Shosuke Kojo
Affiliation: Department of Food Science & Nutrition, Nara Women’s University, Nara 630-8506 Japan; E-mail: kojo@cc.nara-wu.ac.jp
Abstract: to be added

Type of Paper: Review
Title: "Mirror Symmetry Breaking" and Amplification of Homochirality with Crystalline Architectures
Authors: Meir Lahav and Isabelle Weissbuch; E-Mail: meir.lahav@weizmann.ac.il
Abstract: to be added

Type of Paper: Article
Title: Experimental Evidence Suggesting that Homochirality Emerged With The Genetic Code
Author: Robert Root-Bernstein, Professor of Physiology, Michigan State University, East Lansing, MI 48824 USA; rootbern@msu.edu
Abstract: The origin of homochirality remains one of the profound mysteries of life’s evolution. Why do all living things on Earth utilize L-amino acids and D-sugars? Hypotheses on this subject date back to the discovery of homochirality by Pasteur and can be divided into those that propound the existence of an asymmetric force which selects for preferred chirality and those that propose it arose through a “frozen accident”. Despite lack of evidence for any of these hypotheses, all theories of the origin of the genetic code assume that homochirality emerged before the code itself. What if all of this is wrong? Last year I proposed a radically different hypothesis: the reason that homochirality and an essentially universal genetic code both characterize living organisms is that they arose as a function of each other (Bioessays,….). This co-evolution hypothesis assumes that the genetic code arose through amino acid-codon (or anticodon) pairing, and then makes a number of unique, testable predictions. First, prior to the evolution of transcription apparatus, the code had no preferred chirality and no preferred directionality. Second, it follows that every codon had at least two different amino acid assignments (one read 5’>3’ and the other, 3’>5’). Third, these codon assignments could have involved L-amino acids with L-codons, D-amino acids with D-codons, L-amino acids with D-codons, and D-amino acids with L-codons, so that multiple, redundant codes evolved. Fourth, selection for an unambiguous set of codon assignments was determined by a combination of binding affinity, amino acid prevalence, and codon prevalence, which resulted in a clear preference for L- amino acids pairing with D-codons. The present research experimentally tests the first three of these predictions. Noxxon Pharma AG (Berlin) provided two D-aptamers (D-CGUA and D-AUGC) and two L-aptamers or Spiegelmers® (L-CGUA and L-AUGC). UV spectroscopy was used to determine the binding constants of these four aptamers with twelve pairs of L- and D-amino acids: Arg, Cys, Met, Val, Leu, Ileu, Phe, Glu, Ser, Thr, Pro, Gly. The resulting binding constants demonstrate, as predicted, that: 1) there is little or no preference for directionality; 2) every codon binds multiple amino acids with different affinities; 3) there is a 2-3-fold preference of D-amino acids for L-codons and L-amino acids for D-codons; and 4) given what is known of amino acid prevalences from prebiotic chemistries and current amino acid usage, the resulting redundant encodings favor an L-amino-acid-D-codon genetic code.

Type of Paper: Review
Author: Gábor Lente
Affiliation: Department of Inorganic and Analytical Chemistry, University of Debrecen ,P.O.B. 21, Debrecen, H-4010 Hungary. Fax: + 36 52 489667; Tel: + 36 52 512900/22373; E-mail: lenteg@delfin.unideb.hu
Title: The Role of Stochastic Models in Interpreting the Origins of Biological Chirality
Abstract: This review summarizes recent stochastic modeling efforts in the theoretical research aimed at interpreting the origins of biological chirality. Stochastic kinetic models, especially those based on the continuous time discrete state approach, have great potential in modeling absolute asymmetric reactions, experimental examples of which have been reported in the past decade. An overview of the relevant mathematical background is given and several examples are presented to show how the significant numerical problems characteristic of the use of stochastic models can be overcome by creative elementary algebra. In these stochastic models, a particulate view of matter is used rather than the concentration-based view of traditional chemical kinetics using continuous functions to describe the properties system. This has the advantage of giving adequate description of single-molecule events, which were probably important in the origin of biological chirality. The presented models can interpret and predict the random distribution of enantiomeric excess among repetitive experiments, which is the most striking feature of absolute asymmetric reactions. It is argued that the use of the stochastic kinetic approach should be much more widespread in the relevant literature.

Type of Paper: Article
Title: Mirror Symmetry Breaking at Helical Polymer Level: Preference between Left and Right by Chemical and Physical Origins
Author: Michiya Fujiki
Affiliation: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0036, Japan; Tel: + 81 743 72 6040; Fax: + 81 743 72 6049; E-mail: fujikim@ms.naist.jp
Abstract: From elemental particles to human beings, matter and living worlds in our universe are dissymmetric with respect to mirror symmetry. In 1860, Pasteur conjectured that biomolecular handedness on the blue planet homochirality may originate from certain inherent dissymmetric force existing in the universe. Kipping, a pioneer of organosilicon chemistry, had much interest in the handedness of organic and inorganic substances, including sodium chlorate, sodium ammonium tartarate, and organosilicon compounds from 1898 to 1909 in his early research life. Since Kipping first synthesized several Si-Si bonded oligomers bearing phenyl groups, nowadays Si-Si bonded highpolymers that carry various organic groups organopolysilanes become possible to prepare by sodium-mediated reduction of the corresponding diorganodichlorosilanes in excellent yields. Among these organopolysilanes, optically active helical organopolysilanes with enantiomeric pairs of organic groups, as a bridge between animate and inanimate chiral polymers, may be suited to test the mirror symmetry breaking hypothesis by weak neutral current (WNC) origin in the realm of chemistry and material science. Several theoritical studies predicted that a tiny WNC existing chiral molecules with stereogenic and/or stereogenic bondings paermit us to distinguish between mirror-image molecules. Theoretists based on several amplification mechanisms claimed that, if appropriate mirror image molecules are employed, some differences, though still being very subtle, are detectable by precission spectroscopic measuremensts.
In a previous communication, the author preliminary reported a possibility of detecting subtle differences in chiroptical and achiral 29Si-NMR and viscometric data of helical organopolysilanes with (S)- and (R)-3,7-dimethyloctyl substituents with 96% ee. The present paper demonstrated further results of mirror symmetry breaking at helical organopolysilane level by testing equality in chiroptical, 29Si-NMR, and viscometric data of six different enantiomeric organopolysilanes carrying the chiral and achiral pendants.

Type of Paper: Review
Title: Photochirogenesis: Photochemical Models on the Origin of Life’s Handedness
Authors: Cornelia Meinert 1, Laurent Nahon 2, Jean-Jacques Filippi 1, Soeren V. Hoffmann 3, Jan Hendrik Bredehöft 4, Wolfram H.-P. Thiemann 4, Louis d’Hendecourt 5, Pierre de Marcellus 5 and Uwe J. Meierhenrich 1,*
Affiliation: 1 University of Nice-Sophia Antipolis, UMR 6001 CNRS, LCMBA, Faculté des Sciences, 28 Avenue Valrose, 06108 Nice, France; E-mail: Cornelia.Meinert@unice.fr; Jean-Jacques.Filippi@unice.fr; Uwe.Meierhenrich@unice.fr
2 Synchrotron SOLEIL, l’Orme des Merisiers, Saint Aubin BP 48, 91192 Gif-sur-Yvette, France; E-mail: laurent.nahon@synchrotron-soleil.fr
3 University of Aarhus, Institute for Storage Ring Facilities (ISA), Ny Munkegade 120, 8000 Aarhus C, Denmark; E-mail: vronning@phys.au.dk
4 University of Bremen, Institute for Applied and Physical Chemistry, Leobener Str. NW2, 28359 Bremen, Germany; E-mail: thoralf@uni-bremen.de; thiemann@uni-bremen.de
5 Institut d’Astrophysique Spatiale (IAS), Bât. 121, Université Paris-Sud, 91405 Orsay Cedex, France; E-mail: Louis.DHendecourt@ias.u-psud.fr; pierre.demarcellus@ias.u-psud.fr
* Author to whom correspondence should be addressed.
Abstract: Our research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids had been identified in both chondritic meteorites and simulated interstellar ices. Current research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’, i.e. associated with circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from C1 and N1 units by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

Type of Paper: Article
Title: Chiroptical Properties of Amino and Diamino Acids: a Density Functional Theory Study
Authors: Martine Adrian-Scotto 1, Serge Antonczak 1, Jan Hendrik Bredehöft 2 and Uwe J. Meierhenrich 1,*
Affiliation: 1 University of Nice-Sophia Antipolis, UMR 6001 CNRS, LCMBA, Faculté des Sciences, 28 Avenue Valrose, 06108 Nice, France; E-mail: Martine.Adrian-Scotto@unice.fr; antoncza@unice.fr; Uwe.Meierhenrich@unice.fr
2 University of Bremen, Institute for Applied and Physical Chemistry, Leobener Str. NW2, 28359 Bremen, Germany; E-mail: thoralf@uni-bremen.de
* Author to whom correspondence should be addressed.
Abstract: Amino acids and diamino acids are involved in many scenarios elucidating possible origins of life on Earth. Amino acids were parts of early proteins (enzymes), in which their exact order of recruitment has actually been estimated. Diamino acids might have served as molecular building blocks of an early genetic material such as peptide nucleic acid (PNA). One of the well-known challenges when discussing biopolymers such as enzymes and oligonucleotides in living organisms is the phenomenon that these polymers implement monomers of exclusively one handedness, a feature called homochirality. Many attempts have been made to understand this process of racemic symmetry breaking. Assuming an extraterrestrial origin of the molecular building blocks amino acids and diamino acids, their susceptibility to asymmetric photolysis by the absorption of circularly polarized electromagnetic radiation in interstellar space was proposed. In order to investigate the electronic and chiroptical properties of amino and diamino acids more precisely, we called upon a quantum molecular modelling approach based on Density Functional Theory. We have studied various molecules with the help of B3LYP computations using the basis functions 6-31G(d,p). In particular, the experimentally measured circular dichroic behaviour of amino and diamino acids is discussed versus their computed computed chiroptical properties.

Type of Paper: Article
Title: Mirror Symmetry Breaking Driven by Localized Source of Energy in Turbulent Environment
Authors: Raphaël Plasson and Axel Brandenburg; E-mail: rplasson@nordita.org; brandenb@nordita.org
Abstract: Starting from a racemic -- or symmetric -- system, it is possible to evolve spontaneously towards a non-racemic state by a bifurcation mechanism, based on autocatalytic processes. Such mirror symmetry breaking system have now been successfully developed, both theoretically and experimentally. A strong requirement for these systems is the need for a source of energy, able to be consumed by the system, and directed toward the autocatalytic cycles. In a prebiotic environment, such sources of energy would likely be inhomogeneously distributed. On the basis of numerical simulations of simple mirror symmetry breaking systems, we'll describe the role and influence of diffusion and advection processes in inhomogeneous systems. We'll address the possibility of transport of energy and of propagation of the asymmetric state.

Type of Paper: Article
Title: Homomeric Protein Assemblies in View of Symmetry versus Asymmetry
Authors: Biserka Kojić-Prodić and Zoran Štefanić
Affiliation: Rudjer Bošković Institute, POB 180, 10002-Zagreb, Croatia; E-mail: kojic@irb.hr
Abstract: The protein assemblies are of a great importance in functions of a cell. Therefore, they have attracted researches to examine them from different points of view. Protein interactions, however, are the most important for understanding their functions. The three-dimensional structures of proteins provided by X-ray structure analysis (stored in Protein Data Bank, PDB) offer an abundance of detailed information revealing the nature of protein homomeric and heteromeric complexes. The classification of protein assemblies provided by Levy, Pereira-Leal, Chothia, and Teichmann at http://www.3Dcomplex.org enables an overview of protein oligomers whereas their structural symmetry and functions were discussed in the review by Goodsell and Olson (Ann. Rev. Biophys. Biomol. Struct. 2000, 29, 105-153). Among proteins of known three-dimensional structures about 50-80% of them exist as homomeric protein complexes. Protein monomers lack any intrinsic, underlying symmetry, i.e. enantiomorphic protein molecules involve left-handed amino acids. However, the asymmetry imposed by the limitation of L-amino acids does not appear to extend to the level of quaternary structures (homomeric complexes) as observed by Chothia. In protein assembling stable states are more likely symmetric than asymmetrical although there are some exceptions.
Homochirality is a characteristic hallmark of life. Thus, it is a consequence of life but it is also pre-condition for life. Polymerization of peptides into proteins would not go efficiently from racemic solutions. In crystals, proteins involving left-handed amino acids can crystallize in enantiomorphic space groups, only. Among 230 existing space groups 65 are enantiomorphic containing limited symmetry elements that are rotation and screw-rotation axes. Any axis of rotation symmetry of a crystal lattice must be two-fold, three-fold, four-fold, or six-fold. Five-fold, seven-fold, and higher-fold rotation symmetry axes are incompatible with the symmetry under spatial displacement of the three-dimensional crystal lattice. We would like to pay attention to the very special cases of homomers revealing non-crystallographic symmetry in crystals and to discuss them in view of symmetry–asymmetry relationship. After all, it is not simple to see how symmetry and dynamics merge to generate both chaos and structure at the same time.

Type of Paper: Review
Title: Biochirality and the Origin of Life
Authors: Marcelo Gleiser and Sara Walker
Affiliation: Department of Physics and Astronomy, Dartmouth College, Hanover, NH 03755, USA. E-mail: mgleiser@dartmouth.edu; sara.walker@dartmouth.edu
Abstract: The biomolecules that make up all terrestrial living creatures display a clear spatial asymmetry: protein amino acids are “left-handed” (levorotatory) and the sugars of RNA and DNA are “right-handed” (dextrorotatory). One of the fundamental open questions of modern science is how to explain this spatial selectivity, or biochirality. In this review, we will explore the relationship between chirality and the origin of life. In particular, we will investigate what possible roles chirality may have played as life was emerging in prebiotic Earth. To this end, we will examine some of the models for the emergence of chirality that have been proposed in the recent literature, as well as discuss the possible sources of chiral asymmetry, such as weak neutral currents, circularly-polarized light, clay surface templating, and others. Our goal is to help elucidate the intricate relationship between chirality and the origin of life, and to define directives for further searches of extraterrestrial chiral signatures.