Chemical Ecology and Biomolecular Evolution

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.     

Biomimetic nanosystems and novel composite nanobiomaterials

Biophysicochemical approaches to the solution of nanotechnology problems associated with the design of functional biomimetic nanosystems, hybrid and composite nanobiomaterials and study of their structure-function relationships. The results of studies concerned with physicochemical mechanisms of the formation of organized biomimetic nanostructures and bioinorganic nanomaterials in systems involving a bulky liquid phase and the interface (gas-liquid, solid-liquid, liquid-liquid)during the synthesis and structure formation with the participation of the components of colloid systems, inorganic nanoparticles of various composition and clusters of metals, surfactants, polyelectrolytes and their complexes are discussed. In the development of the methods for the formation of composite bioinorganic nanosystems containing inorganic nanocomponents, two major approaches were used: adsorption and incorporation into the biomolecular matrix or colloid system of presynthesized inorganic nanoparticles, as well as the synthesis of the inorganic nanophase immediately in the biomolecular system. The methods of obtaining biomaterials and nanosystems are based on the principles of biomimetics, biomineralization, self-assembly and self-organization, combination and integration of a number of synthetic and physicochemical methods (physical and chemical adsorption, Langmuir technique, the formation of polycomplexes, chemical linking, competitive interactions, and substitution of ligands in supramolecular and coordination complexes) and nanocomponents of different nature. In particular, a novel approach to the preparation of highly organized nanofilm materials was developed, which is based on the effect of self-assembly and self-organization of colloid nanoparticles during the formation of their complexes with polyfunctional biogenic ligands in the volume of the liquid phase in the absence of any surfaces and interfaces. The physical and chemical factors responsible for the formation of structurally ordered biomolecular and composite nanosystems including nano-sized components of different nature and the possibilities to control the composition, structure, and properties of resulting nanomaterials and nanosystems are discussed. The experimental methods and approaches developed may be useful in studies of structure-property relationships and basic mechanisms of structural organization and transformation at the nanoscales level in biological, artificial, and hybrid nanosystems. The problems of practical application of the synthetic methods and the corresponding nanomaterials are discussed.     

Chemically engineered extracts: Bioactivity alteration through sulfonylation

The chemical composition and the biomolecular properties of a series of crude plant extracts were altered without previous knowledge of their detailed chemical composition.     

Three perspectives on the prediction of chemical effects in ecosystems

The increasing production, use and emission of synthetic chemicals into the environment represents a major driver of global change. The large number of synthetic chemicals, limited knowledge on exposure patterns and effects in organisms and their interaction with other global change drivers hamper the prediction of effects in ecosystems. However, recent advances in biomolecular and computational methods are promising to improve our capacity for prediction. We delineate three idealised perspectives for the prediction of chemical effects: the suborganismal, organismal and ecological perspective, which are currently largely separated. Each of the outlined perspectives includes essential and complementary theories and tools for prediction but captures only part of the phenomenon of chemical effects. Links between the perspectives may foster predictive modelling of chemical effects in ecosystems and extrapolation between species. A major challenge for the linkage is the lack of data sets simultaneously covering different levels of biological organisation (here referred to as biological levels) as well as varying temporal and spatial scales. Synthesising the three perspectives, some central aspects and associated types of data seem particularly necessary to improve prediction. First, suborganism- and organism-level responses to chemicals need to be recorded and tested for relationships with chemical groups and organism traits. Second, metrics that are measurable at many biological levels, such as energy, need to be scrutinised for their potential to integrate across levels. Third, experimental data on the simultaneous response over multiple biological levels and spatiotemporal scales are required. These could be collected in nested and interconnected micro- and mesocosm experiments. Lastly, prioritisation of processes involved in the prediction framework needs to find a balance between simplification and capturing the essential complexity of a system. For example, in some cases, eco-evolutionary dynamics and interactions may need stronger consideration. Prediction needs to move from a static to a real-world eco-evolutionary view.     

Towards the preparative and large-scale precision manufacture of virus-like particles

Virus-like particles (VLPs) are of interest in vaccination, gene therapy and drug delivery, but their potential has yet to be fully realized. This is because existing laboratory processes, when scaled, do not easily give a compositionally and architecturally consistent product. Research suggests that new process routes might ultimately be based on chemical processing by self-assembly, involving the precision manufacture of precursor capsomeres followed by in vitro VLP self-assembly and scale-up to required levels. A synergistic interaction of biomolecular design and bioprocess engineering (i.e. biomolecular engineering) is required if these alternative process routes and, thus, the promise of new VLP products, are to be realized.     

Biofuel production improvement with genome-scale models: The role of cell composition

Genome-scale models have developed into a vital tool for rational metabolic engineering. These models balance cofactors and energetic requirements and determine biosynthetic precursor availability in response to environmental and genetic perturbations. In particular, allocation of additional reducing power is an important strategy for engineering potential biofuel production from microbes. Many potential biofuel solvents induce biomolecular changes on the host organism that are not yet captured by genome-scale models. Here, methods of construction for several biomass constituting equations are reviewed along with potential changes to cellular composition with potential biofuels exposure. The biomass constituting equations of potential host organisms with existing genome-scale models are compared side-by-side to explore their evolution over the years and to explore differences that arise when these equations are compiled by different research groups. Genome-scale model simulation results attempt to address and provide guidance for further research into: (i) whether inconsistencies in the biomass constituting equations are relevant to predictions of solvent production, (ii) what level of detail is necessary to accurately describe cellular composition, and (iii) future developments that may enable more accurate characterizations of biomolecular composition.     

Underwater Adhesive of Marine Organisms as the Vital Link Between Biological Science and Material Science

Marine sessile organisms naturally attach themselves to diverse materials in water by a technique that has so far remained unreproducible. Recent studies on the holdfast of marine sessile organisms have revealed natural concepts that are currently beyond our understanding with respect to the molecular design and macroscopic range. The combination of valuable and practical natural design of biotic adhesives as biomolecular materials, together with continuing efforts towards mimetic design, hold the promise of revolution for future materials. This review focuses on recent advances in the study of barnacle underwater cement, a protein complex whose constituents and the properties of individual components are being uncovered. A comparison is made with the model systems used by the mussel and tubeworm.     

d-Amino acids in molecular evolution in space – Absolute asymmetric photolysis and synthesis of amino acids by circularly polarized light

Living organisms on the Earth almost exclusively use l-amino acids for the molecular architecture of proteins. The biological occurrence of d-amino acids is rare, although their functions in various organisms are being gradually understood. A possible explanation for the origin of biomolecular homochirality is the delivery of enantioenriched molecules via extraterrestrial bodies, such as asteroids and comets on early Earth. For the asymmetric formation of amino acids and their precursor molecules in interstellar environments, the interaction with circularly polarized photons is considered to have played a potential role in causing chiral asymmetry. In this review, we summarize recent progress in the investigation of chirality transfer from chiral photons to amino acids involving the two major processes of asymmetric photolysis and asymmetric synthesis. We will discuss analytical data on cometary and meteoritic amino acids and their potential impact delivery to the early Earth. The ongoing and future ambitious space missions, Hayabusa2, OSIRIS-REx, ExoMars 2020, and MMX, are scheduled to provide new insights into the chirality of extraterrestrial organic molecules and their potential relation to the terrestrial homochirality. This article is part of a Special Issue entitled: d-Amino acids: biology in the mirror, edited by Dr. Loredano Pollegioni, Dr. Jean-Pierre Mothet and Dr. Molla Gianluca.     

Molecular probes of DNA bulges: functional assay and spectroscopic analysis

Bulged structures in DNA and RNA have been linked to biomolecular processes involved in numerous diseases, thus probes with affinity for these nucleic acid targets would be of considerable utility to chemical biologists. Herein, we report guided chemical synthesis of small molecules capable of binding to DNA bulges by virtue of their unique (spirocyclic) geometry. The agents, modeled on a natural product congener, show pronounced selectivity for specific bulged motifs and are able to enhance slipped DNA synthesis, a hallmark functional assay of bulge binding. Significantly, bulge-agent complexes demonstrate characteristic fluorescent signatures depending on bulge and flanking sequence in the oligo. It is anticipated that these signature patterns can be harnessed as molecular probes of bulged hotspots in DNA and RNA.     

原核微生物铁超氧化物歧化酶的分子进化

超氧化物歧化酶（superoxide dismutase,SOD）在维持生物体内超氧阴离子自由基产生与消除的动态平衡中起着重要的作用。铁超氧化物歧化酶（ge—SOD）是原核生物和真核生物细胞器中专一的SOD酶,通过GenBank中搜集的原核生物Fe—SOD进行比对分析发现,Fe-SOD是相对保守的蛋白质,其中包含2个保守区域和1个可变区域,金属结合位点固定,Fe．SOD序列的比对可以反映物种间的进化关系,是研究原核生物分子进化的理想素材。     

Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry

Background

Cycles of covalent modification are ubiquitous motifs in cellular signalling. Although such signalling cycles are implemented via a highly concise set of chemical reactions, they have been shown to be capable of producing multiple distinct input-output mapping behaviours – ultrasensitive, hyperbolic, signal-transducing and threshold-hyperbolic.

Results

In this paper, we show how the set of chemical reactions underlying covalent modification cycles can be exploited for the design of synthetic analog biomolecular circuitry. We show that biomolecular circuits based on the dynamics of covalent modification cycles allow (a) the computation of nonlinear operators using far fewer chemical reactions than purely abstract designs based on chemical reaction network theory, and (b) the design of nonlinear feedback controllers with strong performance and robustness properties.

Conclusions

Our designs provide a more efficient route for translation of complex circuits and systems from chemical reactions to DNA strand displacement-based chemistry, thus facilitating their experimental implementation in future Synthetic Biology applications.

     

An introduction to peptide nucleic acid

Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful biomolecular tools, antisense and antigene agents, molecular probes and biosensors.     

Evolution of oxygenic photosynthesis: genome-wide analysis of the OEC extrinsic proteins

The appearance of oxygenic photosynthesis was a key event in the evolution of our green biosphere. Oxygen in the atmosphere is generally believed to come from the biomolecular water-splitting reaction that occurs in oxyphotosynthetic organisms catalysed by the oxygen evolving centre (OEC) of Photosystem II. Using knowledge from complete genomes and current databases, we have investigated the nature and composition of the extrinsic proteins forming the OECs of different organisms, with particular focus on the manganese stabilizing protein that is present in all known oxyphototrophs. This analysis traces the evolution of the extrinsic proteins from ancient cyanobacteria to higher plants and gives hints about the ancestral form of the OEC.     

Transabiotic factors in an aqueous environment (a review)

Excretion of metabolites is a characteristic feature of any alive organism. A big group of these products--second metabolites--because of their variability, quantity and physico-biological activity have a special importance in aquatic environment. Exometabolites of some organisms become an important part of environment for the others. The authors discussed the origin and evolution of exometabolites from simple waste products to biologically active substances. Quantitative and qualitative aspects of metabolic excretion by organisms in water conditions are analysed. The data on composition, origin and biological function of some second metabolites of different groups of aquatic organisms are presented. The authors propose a classification of second metabolites according to their functional significance. The role of metabolites and decay products in the development of chemical information streams in hydrobiocoenosis is analysed. Metabolites (soluble organic substances) form a field of chemical information for biotic community. The most important functions of this field are communication and conditioning. The authors emphasize the importance of investigations of chemical bioinformation field in aquatic ecosystems.     

Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer

Although Chemical Exchange Saturation Transfer (CEST) type NMR experiments have been used to study chemical exchange processes in molecules since the early 1960s, there has been renewed interest in the past several years in using this approach to study biomolecular conformational dynamics. The methodology is particularly powerful for the study of sparsely populated, transiently formed conformers that are recalcitrant to investigation using traditional biophysical tools, and it is complementary to relaxation dispersion and magnetization transfer experiments that have traditionally been used to study chemical exchange processes. Here we discuss the concepts behind the CEST experiment, focusing on practical aspects as well, we review some of the pulse sequences that have been developed to characterize protein and RNA conformational dynamics, and we discuss a number of examples where the CEST methodology has provided important insights into the role of dynamics in biomolecular function.     

分子动力学模拟与分子生物力学

生物大分子的微观结构动力学决定其生物学功能,其力学-化学耦合规律是分子生物力学的重点关注方向。分子动力学模拟是耦合生物大分子力学-化学性质微观结构动力学基础的有效手段,其结果可用于预测结构-功能关系、指导实验设计和诠释实验结果。本文简要介绍了分子动力学模拟的方法学特点、基本工作原理及其在分子生物力学中的应用,并展望了未来可能的发展方向和应用前景。     

NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω₂). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω₂. The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω₁ but these signals were absent in ω₂, indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.     

Recombinant entomopathogenic agents: a review of biotechnological approaches to pest insect control

Although the use of chemical pesticides has decreased in recent years, it is still a common method of pest control. However, chemical use leads to challenging problems. The harm caused by these chemicals and the length of time that they will remain in the environment is of great concern to the future and safety of humans. Therefore, developing new pest control agents that are safer and environmentally compatible, as well as assuring their widespread use is important. Entomopathogenic agents are microorganisms that play an important role in the biological control of pest insects and are eco-friendly alternatives to chemical control. They consist of viruses (non-cellular organisms), bacteria (prokaryotic organisms), fungi and protists (eukaryotic organisms), and nematodes (multicellular organisms). Genetic modification (recombinant technology) provides potential new methods for developing entomopathogens to manage pests. In this review, we focus on the important roles of recombinant entomopathogens in terms of pest insect control, placing them into perspective with other views to discuss, examine and evaluate the use of entomopathogenic agents in biological control.