Mirror symmetry breaking in biochemical evolution.

The problem of origination of molecular asymmetry in biochemical evolution is discussed. The theoretical analysis shows that chiral purity of biomolecules has the biological significance for self-reproduction of organisms. The models of spontaneous symmetry-breaking in molecular systems are given. The aspects of various stages of biochemical evolution associated with the development of chiral polarization are analysed.     

Spontaneous breaking of the L,D symmetry in photolytic production and degradation of amino acids

The radiolysis experiments of amino acids have revealed the presence of bimolecular interaction between like enantiomers which suppress their photodegradation and between opposite enantiomers that enhance the photodegradation. Based on a mathematical model, it is suggested that this phenomenon could have given rise to chiral stereoselection in biochemical evolution.Sumanasekara Chair in Natural science.     

海因酶的研究进展

海因酶在生产手性药物中间体上具有广泛的应用价值,本文综述了海因酶的研究历史、分类与进化、酶学性质、工业应用及发展方向。     

Imaging polarimetry for high throughput chiral screening

Imaging polarimetry was demonstrated as a highly parallel method of determining optical rotation of biochemical samples. The imaging polarimeter utilized a bright, uniform light source wavelength-filtered to near the sodium D line, a sample array flanked by inlet and analyzing polarizers, and a CCD camera fitted with an equal-perspective telecentric lens. The prototype apparatus was demonstrated to have an optical resolution better than 0.08 degrees. The potential for high throughput screening was demonstrated by imaging chiral solutions in 1536-well microtiter plates and by real-time monitoring of 30 simultaneous chiral enzymatic reactions. Improvements in polarizer and CCD technology may broadly expand the technique's applicability to fields such as directed evolution and combinatorial chemistry, where screening throughput is currently limiting for chiral applications.     

Chiral safety of the biosphere as a biophysical problem

The biosphere with its inherent chiral asymmetry fixed in the process of biological evolution at the level of L-amino acids and D-hydrocarbons and some other biologically active compounds of biogenic origin is under strong pressure of chiral substances produced by chemical, pharmaceutical, and other branches of industry and agriculture. Effective use of enantiomers is accompanied by toxic and even mutagenic effects of their mirror-image enantiomorphs. Only small amounts of products are tested for chiral purity; there is no system of global biosphere monitoring as well as no common standards of permissible concenrations. The investigation of the molecular basis of chiral stereospecificity of enzymes and cell receptors is of great interest from the point of view of fundamental biophysics. On the other hand, the development of chiral-selective sensors for environmental monitoring is important from the viewpoint of applied biophysics.     

Probability rule for chiral recognition

Molecular Chirality is of central interest in biological studies because enantiomeric compounds, while indistinguishable by most inanimate systems, show profoundly different properties in biochemical environments. Enantioselective separation methods, based on the differential recognition of two optical isomers by a chiral selector, have been amply documented. Also, great effort has been directed towards a theoretical understanding of the fundamental mechanisms underlying the chiral recognition process. Here we report a comprehensive data examination of enantio separation measurements for over 72000 chiral selector-select and pairs from the chiral selection compendium CHIRBASE. The distribution of alpha = k'(D)/k'(L) values was found to follow a power law, equivalent to an exponential decay for chiral differential free energies. This observation is experimentally relevant in terms of the number of different individual or combinatorial selectors that need to be screened in order to observe alpha values higher than a preset minimum. A string model for enantiorecognition (SMED) formalism is proposed to account for this observation on the basis of an extended Ogston three-point interaction model. Partially overlapping molecular interaction domains are analyzed in terms of a string complementarity model for ligand-receptor complementarity. The results suggest that chiral selection statistics may be interpreted in terms of more general concepts related to biomolecular recognition.     

Chiral purity of nucleotides as a necessary condition of complementarity

This work discusses the question about the role of chiral purity (homochirality) of nucleotides in the formation of complementary replicas. A qualitative answer to this question can be obtained from molecular models constructed to simulate the chiral defect in the polynucleotidic chain. It shows the necessity of homochirality of nucleotides for the complementarity preservation. The necessity of the strong mirror-symmetry breaking in the abiogenic formation of the self-replicating oligonucleotide structures is discussed in the context of prebiological evolution.     

Spontaneous chiral symmetry breaking in early molecular networks

Background  

An important facet of early biological evolution is the selection of chiral enantiomers for molecules such as amino acids and sugars. The origin of this symmetry breaking is a long-standing question in molecular evolution. Previous models addressing this question include particular kinetic properties such as autocatalysis or negative cross catalysis.     

植物抗旱过程中ABA生理作用的研究进展

植物在长期进化中,对干旱等胁迫从生理、生化和分子水平上产生了适应性变化,从而增加逆境存活机会,在这些响应过程中,ABA起着极其重要的作用。本文介绍了近年来研究ABA在植物抗旱中生理作用方面所取得的进展。     

植物抗旱过程中ABA生理作用的研究进展

植物在长期进化中,对干旱等胁迫从生理,生化和分子水平上产生了适应性变化,从而增加逆境存活机会,在这些响过程中,ABA起着极其重要的作用,本文介绍了近年来研究ABA的植物抗旱中生理作用方面所取得的进展。     

Putting the ‘bio’ into bioinformatics

Bioinformatic analyses have grown rapidly in sophistication and efficiency to accommodate the vast increase in available data. One of the major challenges has been to incorporate the growing appreciation of the complexity of molecular evolution into new analytical methods. As the reliance on molecular data in biology and medicine increases, we need to be confident that these methods adequately reflect the underlying processes of genome change. This special issue focuses on the way that patterns and processes of molecular evolution are influenced by features of populations of whole organisms, such as selection pressure, population size and life history. The advantage of this approach to molecular evolution is that it views genomic change not simply as a biochemical or stochastic process, but as the result of a complex series of interactions that shape the kinds of genomic changes that can and do happen.     

Speciation and gene flow between snails of opposite chirality

Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent “single-gene speciation” or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be necessary to investigate populations in which both chiral morphs coexist.     

Mitochondrial gene rearrangements: new paradigm in the evolutionary biology and systematics

Mitochondrial (mt) genomic study may reveal significant insight into the molecular evolution and several other aspects of genome evolution such as gene rearrangements evolution, gene regulation, and replication mechanisms. Other questions such as patterns of gene expression mechanism evolution, genomic variation and its correlation with physiology, and other molecular and biochemical mechanisms can be addressed by the mt genomics. Rare genomic changes have attracted evolutionary biology community for providing homoplasy free evidence of phylogenetic relationships. Gene rearrangements are considered to be rare evolutionary events and are being used to reconstruct the phylogeny of diverse group of organisms. Mt gene rearrangements have been established as a hotspot for the phylogenetic and evolutionary analysis of closely as well as distantly related organisms.     

Semiempirical configuration interaction calculations in biochemical environments: parametrization and application to γD-crystallin, an eye-lens protein

We approach the problem of optical excitations in molecular aggregates in complex biochemical environments from a computational, all-atom perspective. The system is divided into a π orbital part described by a Pariser-Parr-Pople model with configuration interaction using singly excited Slater determinants (PPP-CIS). It is coupled to the protein and water charges of a classical force field. Strategies for a high-accuracy reparameterization and an efficient computational solution are presented. For γD-crystallin, a band edge consisting of charge-transfer states emerges for a coupled molecular aggregate compared to the uncoupled residues. The energies of some charge-transfer states strongly depend on the dielectric properties of the model, giving a first insight into the potential temporal evolution of these excitations. Possible biochemical implications are discussed.     

Catalytically Increased Prebiotic Peptide Formation: Ditryptophan,Dilysine, and Diserine

“Mutual” amino acid catalysis of glycine on the formation of ditryptophan, dilysine, and diserine in the prebiotically relevant Salt-Induced Peptide Formation (SIPF) Reaction was investigated varying the starting concentration and chirality of the educt amino acid, and analyzing the increase of yield resulting from this catalytic effect. Our results show the possibility of an amplified diverse pool of peptides being available for chemical evolution of larger peptides and proteins using also these more complicated amino acids for the evolution of more complex functions in future biochemical cycles and thus for the emergence of life. Catalytic effects are especially high in the case of serine, the most basic amino acid of the three, but are also significant for the other two examples investigated in the present work. Besides that, especially for serine, but also in the case of tryptophan, differences in catalytic yield increase according to the chiral form of the amino acid used could be observed.     

Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization

Oxidoreductases catalyze a large variety of regio-, stereo-, and chemoselective hydrocarbon oxyfunctionalizations, reactions, which are important in industrial organic synthesis but difficult to achieve by chemical means. This review summarizes process implementation aspects for the in vivo application of the especially versatile enzyme class of oxygenases, capable of specifically introducing oxygen from molecular oxygen into a large range of organic molecules. Critical issues such as reaching high enzyme activity and specificity, product degradation, cofactor recycling, reactant toxicity, and substrate and oxygen mass transfer can be overcome by biochemical process engineering and biocatalyst engineering. Both strategies provide a growing toolset to facilitate process implementation, optimization, and scale-up. Major advances were achieved via heterologous overexpression of oxygenase genes, directed evolution, metabolic engineering, and in situ product removal. Process examples from industry and academia show that the combined use of different concepts enables efficient oxygenase-based whole-cell catalysis of various commercially interesting reactions such as the biosynthesis of chiral compounds, the specific oxyfunctionalization of complex molecules, and also the synthesis of medium-priced chemicals. Better understanding of the cell metabolism and future developments in both biocatalyst and bioprocess engineering are expected to promote the implementation of many and various industrial biooxidation processes.     

From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses

Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are identified as major determinants of these rates. Furthermore, a quantitative analysis reveals that, as expected, evolution rates increase linearly with mutation rates for slowly mutating viruses. However, this relationship plateaus for fast mutating viruses. A model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature. The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies.     

雌雄异株植物性别鉴定的研究进展

雌雄异株植物为研究植物的性别决定和进化提供了一个模式体系,由于不同性别的植物具有不同的经济价值,所以其性别鉴定的研究不仅具有重要的理论意义,而且具有极为重要的实践价值。从外部形态、生理生化指标、染色体组型、同工酶、特异蛋白质分子、分子标记等方面,对近15年来国内外有关雌雄异株植物性别鉴定研究的进展作了总结,并对各种鉴定方法的优缺点进行了评价,同时对其研究发展趋势作了展望。     

Emerging subject for chiral separation science: cluster boron compounds

The structural chirality is an inherent feature of fully synthetic boron cluster compounds that sometimes exhibit unique biochemical effects. HPLC studies with zwitter-ionic cluster boron compounds and electrophoretic studies with boron cluster anions reveal that the chiral separability of these species is remarkably dissimilar to that of organic species, if uncharged cyclodextrins are used as chiral selectors. Furthermore, marked differences were found between the analytical characteristics of the chiral separations of the boron cluster species and those of the organic species with uncharged cyclodextrins. The present-day experimental database indicates that the rules valid for the chiral separations of the organic species cannot be applied to the chiral separations of the boron cluster species without experimental verification. The current extent of research work devoted to the investigation of chirality and chiral separations of boron cluster species is negligibly small in comparison with that devoted to the investigation of chirality and chiral separations of organic species. This makes difficult a reliable explanation of both the particularities observed in chiral separations of boron cluster species with cyclodextrins as chiral selectors and the strange effects related to these separations at the moment.     

Evolution of mirror images by sexually asymmetric mating behavior in hermaphroditic snails

Abstract Directionally asymmetric animals generally exhibit no variation in handedness of whole-body architecture. In contrast, reversed chirality in both coil and entire anatomy has frequently evolved in snails. We demonstrate a nonrandom pattern and deterministic process of chiral evolution, as predicted by the following hypothesis. Bimodal shell shapes are associated with discrete mating behaviors in hermaphroditic pulmonates. Flat-shelled species mate reciprocally, face-to-face. This sexual symmetry prevents interchiral mating because genitalia exposed by a sinistral on its left side cannot be joined with those exposed by a dextral on its right. Thus, selection against the chiral minority, resulting from mating disadvantage, stabilizes chiral monomorphism. Tall-shelled species mate nonreciprocally: the 'male' copulates by mounting the 'female's' shell, mutually aligned in the same direction. This sexual asymmetry permits interchiral copulation with small behavioral adjustments. Therefore, the positive frequency-dependent selection is relaxed, and reversal alleles persist longer in populations of tall-shelled species. We verified both the assumption and the prediction of this hypothesis: significantly lower interchiral mating success in a low-spired species and higher chiral evolution rate in high-spired taxa. Sexual asymmetry is the key to understanding the accelerated chiral evolution in high-spired pulmonates.