Problems of biochemical organization]

Biological organization has been defined as a unity of structure, function and regulation. Biological organization of hierarchical multilevel biological systems is represented by a hierarchy of functioning controllable structures. The hierarchy of levels of material organization predetermines the existence of a hierarchy of regulatory mechanisms. Biochemical organization involves the levels of material organization corresponding to biomacromolecules, supramolecular complexes and cellular organelles. The levels of biomacromolecules and supramolecular structures effectuating elementary functions and controlled by basic regulatory mechanisms occupy key positions in biological systems. These levels play the role of standard functional blocks; their combination leads to hierarchically higher structural levels (cell, tissue, organ, systems of organs, organism) performing more complex functions and controlled by hierarchically more important regulatory mechanisms. The peculiarities of regulation of biological systems that are due to the existence of a hierarchy of regulatory mechanisms are discussed.     

对应关系形成的一般分子机制

对应关系形成的分子机制的阐明对于在理论上深入了解对应关系本质和生命系统运行机制,在应用方面帮助人工利用、干预或构建对应关系具有重要意义．分子生物学的快速发展为对应关系的分子机制进行更深入和全面的认识提供了条件．本文在综合比较各种生物大分子基础上,提出系统性的多单体生物大分子模型理论,试图揭示对应关系形成的一般分子机制．该模型理论认为多单体生物大分子具有种类的高多样性,对应关系对多单体生物大分子高效完成各种生物学功能具有必要性,同时,多单体生物大分子的结构和性质也为对应关系的形成提供了可能性．对应关系的形成过程是一个相对独立的可分为3个阶段的复杂过程．在多单体生物大分子结构和性质基础上,从与配体间的识别机制、作用机制及亲和性三方面揭示了对应关系的形成机制．对多单体生物大分子产生对应关系的必然性、形成的分子机制的复杂性及在理论和应用方面的重要价值也进行了讨论．     

Problems and perspectives in studying the biological role of carnosine

In describing carnosine among the constituents of muscle tissue in 1900, V. Gulevitsch opened the question of its real biological role. Investigation of carnosine-related phenomena occurred simultaneously with the study of its metabolic transformation within the cell. It has now been demonstrated that carnosine has the ability to protect cells against oxidative stress as well as to increase their resistance toward functional exhaustion and accumulation of senile features. Mechanisms of such protection are explained in terms of proton buffering, heavy metal chelating, as well as free radical and active sugar molecule scavenging, preventing modification of biomacromolecules and keeping their native functional activity under oxidative stress. Several carnosine derivatives are characterized by different rates of splitting by tissue carnosinase and by different biological efficiencies, thus the biological significance of enzymatic modification of carnosine during its tissue metabolism may be increased resistance of cells operating under unfavorable conditions.     

From Water and Ions to Crowded Biomacromolecules: In Vivo Structuring of a Prokaryotic Cell

Summary: The interactions and processes which structure prokaryotic cytoplasm (water, ions, metabolites, and biomacromolecules) and ensure the fidelity of the cell cycle are reviewed from a physicochemical perspective. Recent spectroscopic and biological evidence shows that water has no active structuring role in the cytoplasm, an unnecessary notion still entertained in the literature; water acts only as a normal solvent and biochemical reactant. Subcellular structuring arises from localizations and interactions of biomacromolecules and from the growth and modifications of their surfaces by catalytic reactions. Biomacromolecular crowding is a fundamental physicochemical characteristic of cells in vivo. Though some biochemical and physiological effects of crowding (excluded volume effect) have been documented, crowding assays with polyglycols, dextrans, etc., do not properly mimic the compositional variety of biomacromolecules in vivo. In vitro crowding assays are now being designed with proteins, which better reflect biomacromolecular environments in vivo, allowing for hydrophobic bonding and screened electrostatic interactions. I elaborate further the concept of complex vectorial biochemistry, where crowded biomacromolecules structure the cytosol into electrolyte pathways and nanopools that electrochemically “wire” the cell. Noncovalent attractions between biomacromolecules transiently supercrowd biomacromolecules into vectorial, semiconducting multiplexes with a high (35 to 95%)-volume fraction of biomacromolecules; consequently, reservoirs of less crowded cytosol appear in order to maintain the experimental average crowding of ∼25% volume fraction. This nonuniform crowding model allows for fast diffusion of biomacromolecules in the uncrowded cytosolic reservoirs, while the supercrowded vectorial multiplexes conserve the remarkable repeatability of the cell cycle by preventing confusing cross talk of concurrent biochemical reactions.

Are the smallest particles of living matter which still exhibit all its functions of the order of magnitude of molecules and atoms, or are they of different order? The first step toward an answer to this question was accomplished by Moritz Nussbaum, who found that if an Infusorian be divided into two pieces, one with and one without a nucleus, only the [former] will continue to live and perform all the functions of self-preservation and development which are characteristic of living organisms. This shows that not only more than two definite substances, but two different structural elements, are needed for life.—Jacques Loeb, 1906 (122)

     

Physicochemical principles of tissue material interactions

Biocompatibility of a material has to be adapted to the specific properties of the locus of application that are the type of tissue and the composition of extracellular fluid or the blood being in contact with the surface. The biocompatibility is beyond that greatly influenced by the design of the medical device which has to be planned close to the material's properties and the function within the body. Physical chemical reactions at and physical properties of the surface which influence the adsorption behavior for biomacromolecules. Conformational or functional changes of f.i. proteins due to physical forces originating from the surface could be the communication messages to the immunological system. The immersion of a material into an aqueous electrolyte leads generally to a space charge layer on both sides of the interface forming the electrical double layer, physically described by the isoelectric point of the materials surface. A numerical example hints on the importance of the double layer structure for the 'communication' between an implant and the surrounding extracellular fluid including beside ions complex structured proteins as biomacromolecules. Biocompatibility depends on the physical structure of the material and physicochemical properties of the interface to the biosystem. The conductivity of the surface film control reactions across the interface with biomacromolecules of the biological environment. Conformational unchanged macromolecules are the prior condition for biocompatibility and controls the attachment and probably also the degree of attachment via adhesion proteins. Later on, when the cells develop tension through the cytoskeleton on these attachment sites, the strength of the integrin adhesion protein-matrix protein interaction might probably prove decisive in differentiation state of the cell. It has been proved by molecular biological methods that an undestroyed oxide layer of anatase on titanium through passivation leaves for instance albumin conformational unchanged.     

Sequential and parallel dual labeling of nanoparticles using click chemistry

Bioorthogonal ‘click’ reactions have recently emerged as promising tools for chemistry and biological applications. By using a combination of two different ‘click’ reactions, ‘double-click’ strategies have been developed to attach multiple labels onto biomacromolecules. These strategies require multi-step modifications of the biomacromolecules that can lead to heterogeneity in the final conjugates. Herein, we report the synthesis and characterization of a set of three trifunctional linkers. The linkers having alkyne and cyclooctyne moieties that are capable of participating in sequential copper(I)-catalyzed and copper-free cycloaddition reactions with azides. We have also prepared a linker comprised of an alkyne and a 1,2,4,5-terazine moiety that allows for simultaneous cycloaddition reactions with azides and trans-cyclooctenes, respectively. These linkers can be attached to synthetic or biological macromolecules to create a platform capable of sequential or parallel ‘double-click’ labeling in biological systems. We show this potential using a generation 5 (G5) polyamidoamine (PAMAM) dendrimer in combination with the clickable linkers. The dendrimers were successfully modified with these linkers and we demonstrate both sequential and parallel ‘double-click’ labeling with fluorescent reporters. We anticipate that these linkers will have a variety of application including molecular imaging and monitoring of macromolecule interactions in biological systems.     

Biomacromolecular localization in bacterial cells by the diffusion and capture mechanism

Subcellular localization of biomacromolecules (nucleotides and proteins) is the base for their proper function in bacterial cells. One model to explain the localization of biomacromolecules, particularly proteins, is “diffusion and capture”. In this model, proteins are localized by diffusion through the cytoplasm or the membrane until binding to another protein or proteins that were already previously sequestered in cells. The use of fusions with fluorescent proteins to follow the fate of biomacromolecules has given new insight into the molecular localization mechanisms in living cells. Here, several proteins following a diffusion and capture mechanism to reach their proper location in the cells are presented. Some RNAs also seem to localize by this mechanism. It is an intrinsic feature that the information for molecular localization should exist in the sequences of protein itself. However, very little information has been available in this field to date.     

Homochirality and long-range transfer in biological systems.

It has been shown that the chiral purity of biomacromolecules has important biological significance not only from the standpoint of lock-and-key stereocomplementarity, but also as a basis for long-range communication in biosystems. An explicit demonstration is given for the case of proton transfer along the hydrogen-bonded chain that is formed by amino acids containing OH groups. It is found that the replacement of the L-amino acid residue by the D-isomer in a peptide chain suppresses proton transport through the hydrogen bond network.     

A calorimetric and infrared spectroscopic study of the stabilizing solute proline.

We have studied the calorimetric and infrared spectroscopic properties of the amino acid proline which has been implicated in the stabilization of biomacromolecules during reduced water states. It has been suggested that the ability of this molecule to protect biomacromolecules during these stress states may be related to the formation of polymeric aggregates of proline monomers in solution. The structure of this aggregate is thought to be an alternates stack, forming a hydrophilic colloid-like polymer which is thought to interact with hydrophobic moieties of biomacromolecules, reducing the exposed hydrophobic area during reduced water conditions. Calorimetric data presented in this work show that in increasing concentration of proline in solution the enthalpy associated with the melting of bulk water is greatly reduced, indicating strong hydrogen bonding character of proline in aqueous solution. Proline shows two eutectic phase separations at moderate concentrations and one of these eutectics may be the proposed intermolecular state. A partial phase diagram for proline is presented. Fourier-transform infrared spectroscopic data indicate that the COO- asymmetric stretch of proline shows marked splitting with increasing proline concentration. This suggests that the carboxylate is in different environments, with the high energy vibrations representing COO- groups which are participating in the hydrogen bonding pattern associated with the formation of the intermolecular stack. Changes in the CH2 asymmetric and symmetric stretches of the pyrrolidine rings of proline are consistent with the proposed stack structure. We also suggest a possible mechanism by which these intermolecular associations may be important in the protection of biomacromolecules during reduced water states.     

Luminescent polypeptides

Polypeptides, as biomacromolecules, hold immense potential in various biological applications such as tissue engineering, immunomodulating agents, and target binding. Among these applications, the attention towards luminescent polypeptides has grown significantly, due to their ability to visualize biological processes effectively. In this perspective, we have compiled information on three distinct types of luminescent polypeptides: natural fluorescent proteins, luminophores-bioconjugated polypeptides, and synthesized polypeptides with clusteroluminescence. Last, we shed light on the significance and prospects of clusteroluminescent polypeptides, which are expected to emerge as crucial new-generation bioluminophores, offering high emission efficiency and tunable emission wavelengths.     

Detection, synthesis, structure, and function of oligo(3-hydroxyalkanoates): contributions by synthetic organic chemists.

Two types of the biological macromolecules poly(R-3-hydroxyalkanoates) have been identified: the high-molecular-weight microbial storage material (sPHA) and a short-chain variety, consisting of butyrate and valerate residues, complexed with other biomacromolecules such as calcium polyphosphate or proteins (cPHB/PHV). While sPHA has attracted, and still enjoys, a lot of attention from numerous scientists around the world, research on cPHB and the structurally and functionally related polymalate (PMA) is still in its infancy. In this article, we present a review on the chemical synthesis, structure, function and interactions of monodisperse cPHAs, the oligo(3-hydroxyalkanoates), with emphasis on the butyrates (OHB); we report hitherto unpublished results on the enzymatic degradation of cPHB and PMA, on a new analytical method for HB/HV detection in biological samples, and on OHB-mediated Ca2+ transport through phospholipid bilayers of artificial vesicles; finally, we discuss possible mechanisms of ion transport through cell membranes, as caused by cPHB. The speculative--and provocative--question is asked whether the structurally simple PHAs may have evolved as storage materials and amphiphilic macromolecules before poly-peptides, -saccharides, and -nucleic acids, in the history of life, or under prebiotic conditions.     

Proteoglycan sequence

Proteoglycans (PGs) are among the most structurally complex biomacromolecules in nature. They are present in all animal cells and frequently exert their critical biological functions through interactions with protein ligands and receptors. PGs are comprised of a core protein to which one or multiple, heterogeneous, and polydisperse glycosaminoglycan (GAG) chains are attached. Proteins, including the protein core of PGs, are now routinely sequenced either directly using proteomics or indirectly using molecular biology through their encoding DNA. The sequencing of the GAG component of PGs poses a considerably more difficult challenge because of the relatively underdeveloped state of glycomics and because the control of their biosynthesis in the endoplasmic reticulum and the Golgi is poorly understood and not believed to be template driven. Recently, the GAG chain of the simplest PG has been suggested to have a defined sequence based on its top-down Fourier transform mass spectral sequencing. This review examines the advances made over the past decade in the sequencing of GAG chains and the challenges the field face in sequencing complex PGs having critical biological functions in developmental biology and pathogenesis.     

Quantitative structure-retention relationships in affinity high-performance liquid chromatography

In this report the affinity high-performance liquid chromatography data, which were determined on silica-based human serum albumin, alpha1-acid glycoprotein, keratin, collagen, melanin, amylose tris(3,5-dimethylphenylcarbamate), and basic fatty acid binding protein columns, are discussed. Using a quantitative structure-retention relationship (QSRR) approach the affinity data were interpreted in terms of structural requirements of specific binding sites on biomacromolecules. The unique chromatographic properties of immobilized artificial membrane and cholesterol stationary phases were also analyzed from the point of view of mimicking biological processes. It has been demonstrated that chemometric processing of appropriately designed sets of chromatographic data derived in systems comprising biomolecules provides information of relevance for molecular pharmacology and rational drug design.     

Resistant macromolecules of extant and fossil microalgae

The occurrence and composition of macromolecular resistant walls of microalgae and their fossil macromolecular counterparts are reviewed. To date, several algal groups have been identified to produce fossilizable biomacromolecules. Only two biosynthetic pathways seem to be responsible for this, of which the acetate/malate pathway used by Chlorophyta, Eustigmatophyta and Dinophyta is considered to lead to a series of closely related resistant biomacromolecules, called algaenans. Algaenans consist of a network of predominantly linear carbon chains. A different, as yet unidentified, pathway is used by the Dinophyta to produce the aromatic walls of their cysts. The poly‐ketide or acetogenic pathway may have been responsible for resorcinol‐based algae or bacteria‐derived microfossils of the acritarch Gloeocapsamorpha prisca, either through synthesis of the biomacromolecule or through a third pathway, the post‐mortem polymerization of its resorcinol lipids. The postmortem polymerization of lipids also appears to be responsible for the formation of fatty acid‐based macromolecules in Eocene dinoflagellate‐shaped remains from Pakistan. Finally, there is a clear need for elucidating the chemical differences between the biomacromolecules produced by the algae and their fossil analogs in the sediments. This notably applies to the release and condensation of aliphatic and aromatic moieties both at normal and at elevated temperature and pressure conditions.     

Analytical ultracentrifugation in structural biology

Researchers in the field of structural biology, especially X-ray crystallography and protein nuclear magnetic resonance, are interested in knowing as much as possible about the state of their target protein in solution. Not only is this knowledge relevant to studies of biological function, it also facilitates determination of a protein structure using homogeneous monodisperse protein samples. A researcher faced with a new protein to study will have many questions even after that protein has been purified. Analytical ultracentrifugation (AUC) can provide all of this information readily from a small sample in a non-destructive way, without the need for labeling, enabling structure determination experiments without any wasting time and material on uncharacterized samples. In this article, I use examples to illustrate how AUC can contribute to protein structural analysis. Integrating information from a variety of biophysical experimental methods, such as X-ray crystallography, small angle X-ray scattering, electrospray ionization-mass spectrometry, AUC allows a more complete understanding of the structure and function of biomacromolecules.     

Biomolecular imaging using atomic force microscopy

Atomic force microscopy (AFM) has become a well-established technique for imaging single biomacromolecules under physiological conditions. The exceptionally high spatial resolution and signal-to-noise ratio of the AFM enables the substructure of individual molecules to be observed. In contrast to other methods, specimens prepared for AFM remain in a plastic state, which enables direct observation of the dynamic molecular response, creating unique opportunities for studying the structure–function relationships of proteins and their functionally relevant assemblies. This review presents recent advances in methods and applications of AFM to imaging biological samples. It is clear that AFM will become an increasingly important tool for probing both the structural and kinetic properties of biological macromolecules.     

Radiofrequency and microwave interactions between biomolecular systems

The knowledge of mechanisms underlying interactions between biological systems, be they biomacromolecules or living cells, is crucial for understanding physiology, as well as for possible prevention, diagnostics and therapy of pathological states. Apart from known chemical and direct contact electrical signaling pathways, electromagnetic phenomena were proposed by some authors to mediate non-chemical interactions on both intracellular and intercellular levels. Here, we discuss perspectives in the research of nanoscale electromagnetic interactions between biosystems on radiofrequency and microwave wavelengths. Based on our analysis, the main perspectives are in (i) the micro and nanoscale characterization of both passive and active radiofrequency properties of biomacromolecules and cells, (ii) experimental determination of viscous damping of biomacromolecule structural vibrations and (iii) detailed analysis of energetic circumstances of electromagnetic interactions between oscillating polar biomacromolecules. Current cutting-edge nanotechnology and computational techniques start to enable such studies so we can expect new interesting insights into electromagnetic aspects of molecular biophysics of cell signaling.     

Advances in PSMA theranostics

The validation of prostate specific membrane antigen (PSMA) as a molecular target in metastatic castration-resistant prostate cancer has stimulated the development of multiple classes of theranostic ligands that specifically target PSMA. Theranostic ligands are used to image disease or selectively deliver cytotoxic radioactivity to cells expressing PSMA according to the radioisotope conjugated to the ligand. PSMA theranostics is a rapidly advancing field that is now integrating into clinical management of prostate cancer patients. In this review we summarize published research describing the biological role(s) and activity of PSMA, highlight the most clinically advanced PSMA targeting molecules and biomacromolecules, and identify next generation PSMA ligands that aim to further improve treatment efficacy. The goal of this review is to provide a comprehensive assessment of the current state-of-play and a roadmap to achieving further advances in PSMA theranostics.     

Pulmonary gene delivery using polymeric nonviral vectors

Pulmonary delivery provides an easy and well tolerated means of access for the administration of biomacromolecules to the pulmonary epithelium and could therefore be an attractive approach for local and systemic therapies. A growing number of reports, which are summarized in this review, mirror the viability of pulmonary gene delivery. Special attention has been paid to the biological barriers in the lung that must be overcome for successful delivery, and which can be divided into anatomic, physical, immunologic, and metabolic barriers. In light of these barriers, successful nonviral polymer-based formulations of therapeutic genes are presented depending on the chemical nature of the polymer. In addition to polyethyleneimine-based nonviral vectors, which have been most intensively studied for pulmonary gene delivery in the past, other polymeric, dendritic, and targeted materials are also described here, including novel and biodegradable polymers. As new materials need in vitro or ex vivo testing before in vivo application, sophisticated models for all three approaches have been illustrated. Although pulmonary siRNA delivery enjoys popularity in clinical trials, pulmonary gene delivery has so far not been translated into clinical applications. With this review, potential hurdles are demonstrated, but novel approaches that may lead to optimized systems are described as well.