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Symmetry
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Asymmetry in Biological Homochirality
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Asymmetry in Biological Homochirality

A special issue of Symmetry (ISSN 2073-8994). This special issue belongs to the section "Chemistry: Symmetry/Asymmetry".

Deadline for manuscript submissions: closed (15 November 2020) | Viewed by 15019

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Dr. David Hochberg

E-Mail Website
Guest Editor
Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain
Interests: symmetries in physics and chemistry; symmetry breaking; chirality; origin of life

Special Issue Information

Dear Colleagues,

The formulation of physical (and chemical) theories is greatly influenced by our perception of the space we live in and within which we observe the phenomena to be explained on a scientific basis. The certainty of these perceptions is universally taken for granted, and they may lead to the notion that some features of the description of physical (and chemical) systems are matters of convention rather than substance. However, what appears to be a matter of convention sometimes turns out to be a substantive physical assumption. As a result, the “convention” may have important physical (and chemical and biological) consequences.

As case in point: the chemistry of life on Earth is based on a basic asymmetry: it uses only one of the two molecules whose three dimensional geometrical structure cannot be superimposed on its mirror image, or reflection though a mirror.  We say that parity P, or space inversion, a fundamental discrete spatial symmetry transformation of physics, is broken at the molecular level. Such molecules are said to possess chirality or handedness. The mirror images structures of a chiral molecule are called enantiomers. Homochirality is ubiquitous in biological chemistry from its very start. Amino acids, the building blocks of proteins, and the sugar backbones present in DNA and RNA are chiral molecules. Thus, the question arises: What are the reasons for molecular systems to break their mirror symmetry? Further, under which conditions? How may a tiny excess of one enantiomer lead to chiral amplification? What is the origin of homochirality on earth? Progress in this problem can only make great strides from the participation of researchers working on chiral symmetry, and coming from diverse backgrounds: Theory, experiment, non-equilibrium thermodynamics, crystallography, catalysis, nucleation, chemical engineering, liquid crystals, surface science, spectroscopy, organic synthesis, and quantum chemistry.

The aim of this Special Issue is to highlight all aspects of chiral symmetry breaking at the molecular level as a problem in biological homochirality. Comprehensive reviews on a particular subject and accounts of research work describing one or several scientific fields in connection with symmetry in biological homochirality are most welcome. In addition, full research papers, communications, short overviews or comments will also be taken into consideration.

Dr. David Hochberg
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Symmetry is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biomolecular homochirality
  • Mirror symmetry breaking
  • Non-equilibrium thermodynamics
  • Weak interaction parity violation
  • Chirality
  • Asymmetric autocatalysis
  • Amplification of chirality
  • Deracemization
  • Chiral symmetry breaking on surfaces, in crystals, in liquids, and at interfaces
  • Prebiotic chemistry
  • Origin of life

Published Papers (5 papers)

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Research

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14 pages, 1869 KiB  
Article
Chiral Oscillations and Spontaneous Mirror Symmetry Breaking in a Simple Polymerization Model
by William Bock and Enrique Peacock-López
Symmetry 2020, 12(9), 1388; https://doi.org/10.3390/sym12091388 - 20 Aug 2020
Cited by 2 | Viewed by 1814
Abstract
The origin of biological homochirality—defined as the preference of biological systems for only one enantiomer—has widespread implications in the study of chemical evolution and the origin of life. The activation—polymerization—epimerization—depolymerization (APED) model is a theoretical model originally proposed to describe chiral symmetry breaking [...] Read more.
The origin of biological homochirality—defined as the preference of biological systems for only one enantiomer—has widespread implications in the study of chemical evolution and the origin of life. The activation—polymerization—epimerization—depolymerization (APED) model is a theoretical model originally proposed to describe chiral symmetry breaking in a simple dimerization system. It is known that the model produces chiral and chemical oscillations for certain system parameters, in particular, the preferential formation of heterochiral polymers. In order to investigate the effect of higher oligomers, our model adds trimers, tetramers, and pentamers. We report sustained oscillations of all chemical species and the enantiomeric excess for a wide range of parameter sets as well as the periodic chiral amplification of a small initial enantiomeric excess to a nearly homochiral state. Full article
(This article belongs to the Special Issue Asymmetry in Biological Homochirality)
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13 pages, 2801 KiB  
Article
Spontaneous Chiral Symmetry Breaking and Entropy Production in a Closed System
by Dilip Kondepudi and Zachary Mundy
Symmetry 2020, 12(5), 769; https://doi.org/10.3390/sym12050769 - 6 May 2020
Cited by 7 | Viewed by 2084
Abstract
In this short article, we present a study of theoretical model of a photochemically driven, closed chemical system in which spontaneous chiral symmetry breaking occurs. By making all the steps in the reaction elementary reaction steps, we obtained the rate of entropy production [...] Read more.
In this short article, we present a study of theoretical model of a photochemically driven, closed chemical system in which spontaneous chiral symmetry breaking occurs. By making all the steps in the reaction elementary reaction steps, we obtained the rate of entropy production in the system and studied its behavior below and above the transition point. Our results show that the transition is similar to a second-order phase transition with rate of entropy production taking the place of entropy and the radiation intensity taking the place of the critical parameter: the steady-state entropy production, when plotted against the incident radiation intensity, has a change in its slope at the critical point. Above the critical intensity, the slope decreases, showing that asymmetric states have lower entropy than the symmetric state. Full article
(This article belongs to the Special Issue Asymmetry in Biological Homochirality)
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10 pages, 421 KiB  
Article
Chiral Interface of Amyloid Beta (Aβ): Relevance to Protein Aging, Aggregation and Neurodegeneration
by Victor V. Dyakin, Thomas M. Wisniewski and Abel Lajtha
Symmetry 2020, 12(4), 585; https://doi.org/10.3390/sym12040585 - 7 Apr 2020
Cited by 7 | Viewed by 3293
Abstract
Biochirality is the subject of distinct branches of science, including biophysics, biochemistry, the stereochemistry of protein folding, neuroscience, brain functional laterality and bioinformatics. At the protein level, biochirality is closely associated with various post-translational modifications (PTMs) accompanied by the non-equilibrium phase transitions (PhTs [...] Read more.
Biochirality is the subject of distinct branches of science, including biophysics, biochemistry, the stereochemistry of protein folding, neuroscience, brain functional laterality and bioinformatics. At the protein level, biochirality is closely associated with various post-translational modifications (PTMs) accompanied by the non-equilibrium phase transitions (PhTs NE). PTMs NE support the dynamic balance of the prevalent chirality of enzymes and their substrates. The stereoselective nature of most biochemical reactions is evident in the enzymatic (Enz) and spontaneous (Sp) PTMs (PTMs Enz and PTMs Sp) of proteins. Protein chirality, which embraces biophysics and biochemistry, is a subject of this review. In this broad field, we focus attention to the amyloid-beta (Aβ) peptide, known for its essential cellular functions and associations with neuropathology. The widely discussed amyloid cascade hypothesis (ACH) of Alzheimer’s disease (AD) states that disease pathogenesis is initiated by the oligomerization and subsequent aggregation of the Aβ peptide into plaques. The racemization-induced aggregation of protein and RNA have been extensively studied in the search for the contribution of spontaneous stochastic stereo-specific mechanisms that are common for both kinds of biomolecules. The failure of numerous Aβ drug-targeting therapies requires the reconsolidation of the ACH with the concept of PTMs Sp. The progress in methods of chiral discrimination can help overcome previous limitations in the understanding of AD pathogenesis. The primary target of attention becomes the network of stereospecific PTMs that affect the aggregation of many pathogenic agents, including Aβ. Extensive recent experimental results describe the truncated, isomerized and racemized forms of Aβ and the interplay between enzymatic and PTMs Sp. Currently, accumulated data suggest that non-enzymatic PTMs Sp occur in parallel to an existing metabolic network of enzymatic pathways, meaning that the presence and activity of enzymes does not prevent non-enzymatic reactions from occurring. PTMs Sp impact the functions of many proteins and peptides, including Aβ. This is in logical agreement with the silently accepted racemization hypothesis of protein aggregation (RHPA). Therefore, the ACH of AD should be complemented by the concept of PTMs Sp and RHPA. Full article
(This article belongs to the Special Issue Asymmetry in Biological Homochirality)
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Other

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22 pages, 2175 KiB  
Essay
Chirality: The Backbone of Chemistry as a Natural Science
by Josep M. Ribó
Symmetry 2020, 12(12), 1982; https://doi.org/10.3390/sym12121982 - 30 Nov 2020
Cited by 13 | Viewed by 3363
Abstract
Chemistry as a natural science occupies the length and temporal scales ranging between the formation of atoms and molecules as quasi-classical objects, and the formation of proto-life systems showing catalytic synthesis, replication, and the capacity for Darwinian evolution. The role of chiral dissymmetry [...] Read more.
Chemistry as a natural science occupies the length and temporal scales ranging between the formation of atoms and molecules as quasi-classical objects, and the formation of proto-life systems showing catalytic synthesis, replication, and the capacity for Darwinian evolution. The role of chiral dissymmetry in the chemical evolution toward life is manifested in how the increase of chemical complexity, from atoms and molecules to complex open systems, accompanies the emergence of biological homochirality toward life. Chemistry should express chirality not only as molecular structural dissymmetry that at the present is described in chemical curricula by quite effective pedagogical arguments, but also as a cosmological phenomenon. This relates to a necessarily better understanding of the boundaries of chemistry with physics and biology. Full article
(This article belongs to the Special Issue Asymmetry in Biological Homochirality)
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30 pages, 12909 KiB  
Concept Paper
Mirror Symmetry Breaking in Liquids and Their Impact on the Development of Homochirality in Abiogenesis: Emerging Proto-RNA as Source of Biochirality?
by Carsten Tschierske and Christian Dressel
Symmetry 2020, 12(7), 1098; https://doi.org/10.3390/sym12071098 - 2 Jul 2020
Cited by 20 | Viewed by 3779
Abstract
Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry [...] Read more.
Recent progress in mirror symmetry breaking and chirality amplification in isotropic liquids and liquid crystalline cubic phases of achiral molecule is reviewed and discussed with respect to its implications for the hypothesis of emergence of biological chirality. It is shown that mirror symmetry breaking takes place in fluid systems where homochiral interactions are preferred over heterochiral and a dynamic network structure leads to chirality synchronization if the enantiomerization barrier is sufficiently low, i.e., that racemization drives the development of uniform chirality. Local mirror symmetry breaking leads to conglomerate formation. Total mirror symmetry breaking requires either a proper phase transitions kinetics or minor chiral fields, leading to stochastic and deterministic homochirality, respectively, associated with an extreme chirality amplification power close to the bifurcation point. These mirror symmetry broken liquids are thermodynamically stable states and considered as possible systems in which uniform biochirality could have emerged. A model is hypothesized, which assumes the emergence of uniform chirality by chirality synchronization in dynamic “helical network fluids” followed by polymerization, fixing the chirality and leading to proto-RNA formation in a single process. Full article
(This article belongs to the Special Issue Asymmetry in Biological Homochirality)
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