Structural bioenergetics and energy transduction mechanisms.

Life depends on transduction processes that couple cellular metabolism to environmental energy sources such as light or reduced compounds. These primary energy sources must be efficiently converted into forms that can be utilized by cells for biosynthesis, motility, transport, regulation, and other metabolic functions. In recent years, there has been an explosive increase in the determination of structures for proteins mediating energy transduction processes. These developments provide the opportunity to evaluate the structural basis for the efficient coupling of two energetic processes, which defines the area of structural bioenergetics. Here, we present some general features of energy transduction processes, including arguments that effective coupling of two processes by a transduction protein occurs by way of conformational states that are common to the catalysis of each process. This is illustrated by examples from the nucleotide switch family of proteins, with emphasis on the nitrogenase system where ATP hydrolysis is coupled to an electron transfer reaction.     

A new numerical approach to mechanically analyse biological structures

In this work, an advanced discretization meshless technique is used to study the structural response of a human brain due to an impact load. The 2D and 3D brain geometrical models, and surrounding structures, were obtained through the processing of medical images, allowing to achieve a realistic geometry for the virtual model and to define the distribution of the mechanical properties accordingly with the medical images colour scale. Additionally, a set of essential and natural boundary conditions were assumed in order to reproduce a sudden impact force applied to the cranium. Then, a structural numerical analysis was performed using the Natural Neighbour Radial Point Interpolation Method (NNRPIM). The obtained results were compared with the finite element method (FEM) and a solution available in the literature. This work shows that the NNRPIM is a robust and accurate numerical technique, capable to produce results very close to other numerical approaches. In addition, the variable fields obtained with the meshless method are much smoother than the FEM corresponding solution.     

Rod structures of bound water: a possible role in self-organization of biological systems and nondissipative energy transmission

Cluster–rod structure were designed, which are comprised of tetrahedral atoms with a typical torsion angle of ~38° at interatomic bonds. These structures correspond to a muscle tissue and clathrin lattice by their metrics and topology and can be formed by bound water in these systems. It is shown that the considered rod structures, which are fragments of bound water structures, can also be involved in nondissipative energy transmission as elastic energy storing structures. The estimated length of the bound water rod structure required to absorb the energy of decomposition of an ATP molecule into ADP and a phosphate group is comparable with myosin head sizes and its step along an actin filament. A mechanism of cooperative transition of the rod structure to a fragment of the ice Ih structure was demonstrated. This transition is accompanied by nondissipative release of stored energy.     

Robust,universal biomarker assay to detect senescent cells in biological specimens

Cellular senescence contributes to organismal development, aging, and diverse pathologies, yet available assays to detect senescent cells remain unsatisfactory. Here, we designed and synthesized a lipophilic, biotin‐linked Sudan Black B (SBB) analogue suitable for sensitive and specific, antibody‐enhanced detection of lipofuscin‐containing senescent cells in any biological material. This new hybrid histo‐/immunochemical method is easy to perform, reliable, and universally applicable to assess senescence in biomedicine, from cancer research to gerontology.     

Information content of chemical structures and some possible biological applications

The purpose of this paper is to calculate the amount of information contained in a chemical or biological structure, and to estimate the energy needed for obtaining an organization unit. The first problem is solved by applying H. J. Morowitz's reasoning (Bull. Math. Biophysics,17, 81–86, 1955) and, for the second one, calculations based upon bond formation heat are carried out.Information content theoretical physical entropy, real physical entropy, informational entropy or negentropy entropic information or neginformation, heat amount, as well as relationships between these system parameters, are defined and used. The investigation covers 63 chemical substances (inorganic and organic compounds). The numerical results should show that common organized systems happen to be between two extreme kinds of systems: highly disordered systems and ideally organized systems. Some speculative numerical applications are carried out regarding chlorophyllian photosynthesis and information amount accumulated through biological growth. It seems that Information Theory may predict some biocalorimetric results.     

A systematic approach to infer biological relevance and biases of gene network structures

The development of high-throughput technologies has generated the need for bioinformatics approaches to assess the biological relevance of gene networks. Although several tools have been proposed for analysing the enrichment of functional categories in a set of genes, none of them is suitable for evaluating the biological relevance of the gene network. We propose a procedure and develop a web-based resource (BIOREL) to estimate the functional bias (biological relevance) of any given genetic network by integrating different sources of biological information. The weights of the edges in the network may be either binary or continuous. These essential features make our web tool unique among many similar services. BIOREL provides standardized estimations of the network biases extracted from independent data. By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology.     

Disulfide bond structures of IgG molecules: Structural variations,chemical modifications and possible impacts to stability and biological function

The disulfide bond structures established decades ago for immunoglobulins have been challenged by findings from extensive characterization of recombinant and human monoclonal IgG antibodies. Non-classical disulfide bond structure was first identified in IgG₄ and later in IgG₂ antibodies. Although, cysteine residues should be in the disulfide bonded states, free sulfhydryls have been detected in all subclasses of IgG antibodies. In addition, disulfide bonds are susceptible to chemical modifications, which can further generate structural variants such as IgG antibodies with trisulfide bond or thioether linkages. Trisulfide bond formation has also been observed for IgG of all subclasses. Degradation of disulfide bond through β-elimination generates free sulfhydryls disulfide and dehydroalanine. Further reaction between free sulfhydryl and dehydroalanine leads to the formation of a non-reducible cross-linked species. Hydrolysis of the dehydroalanine residue contributes substantially to antibody hinge region fragmentation. The effect of these disulfide bond variations on antibody structure, stability and biological function are discussed in this review.Key words: recombinant monoclonal antibody, disulfide bond, trisulfide bond, free sulfhydryl, dehydroalanine, thioether, aggregation     

A possible biological function of carbohydrate structures which are typical of erythrocytes

Carbohydrates of erythrocyte glycoconjugates seem to be specifically designed so that they do not appreciably interact with other types of cells or ligands. This applies to glycosphingolipids (GSLs) and glycoproteins (GPs). An important distinction between the two types of glycoconjugates seems to be that GPs, apart from carrying carbohydrates, have some biological function which is most likely associated with their protein moieties. GSLs of erythrocytes, including the ABH, PP1 and Pk blood group substances, are viewed as energetically cheap membrane-packing substances filling in the membrane areas not covered by functional GPs. Their sole function should be the formation of inert carbohydrate protective layer at the membrane. The role of the inert carbohydrate structures in the development, tumorigenesis and evolution of blood group polymorphism is discussed.     

In situ amplification using universal energy transfer-labeled primers.

We developed an amplification detection system in which a universal energy transfer-labeled primer (UniPrimer) is used in combination with any target-specific primer pair. The target specific primers each have a 5' tail sequence, which is homologous to the 3' end of the UniPrimer which, in turn, has a hairpin structure on the 5' end. The hairpin structure brings the fluorophore and quencher into close proximity when the primer is free in solution, providing efficient quenching. When the primer is incorporated into the PCR product, the hairpin structure is unfolded and a fluorescent signal can be detected. Using hepatitis C and human papillomavirus as model systems, this study demonstrates several advantages in the hot-start in situ PCR technique with the UniPrimer system, including target specific detection of one DNA copy per cell without a separate in situ hybridization step and detection of an RNA target by RT in situ PCR without overnight DNase digestion. The UniPrimer-based in situ PCR allows rapid and simple detection of any DNA or RNA target without concern for the background from DNA repair invariably evident in paraffin-embedded tissue when a labeled nucleotide is used.     

A universal thermodynamic approach to analyze biomolecular binding experiments

Binding processes of any kind can be characterized as an association of a given ligand with some binding factor. This includes macromolecules as well as supramolecular aggregates such as micelles or membranes. The underlying molecular binding mechanism may be more or less complicated due to various intermediate steps (involving for instance conformational changes, aggregation, cooperativity, etc.). A sensible discussion of possible binding models naturally calls for a model-independent access to basic thermodynamic properties. The present contribution will demonstrate how this can quite generally be accomplished by a pertinent processing of properly selected experimental data. The method requires a series of titration measurements comprising the use of variable amounts of both the ligand and the binding factor. It leads to a linear mass conservation plot (i.e. amount of the ligand vs. a matching amount of the binding factor) whose slope and ordinate intercept are equal to the binding ratio (i.e. bound ligand per binding factor) and the free ligand concentration, respectively. This establishes the specific binding isotherm. The approach also reveals latent structurally determined features of the applied physical measuring signal. A number of examples including specific binding, unspecific adsorption and insertion in two-dimensional molecular films will illustrate the methodology.     

Tightly bound to DNA proteins: possible universal substrates for intranuclear processes

Tightly bound to DNA proteins (TBPs) are a protein group that remains attached to DNA after its deproteinization by phenol, chloroform or salting-out. TBP are bound to DNA with covalent phosphotriester or non-covalent ion and hydrogen bonds. They appear to be a vast protein group involved in numerous intranuclear processes. The TBPs fraction co-purified with DNA deproteinized by mild procedures is extremely heterogeneous, tissue and species-specific. The protein fraction co-purified with DNA after harsh deproteinization procedures appears to be formed from few polypeptides common to different species and tissues. Interaction sites between DNA and TBPs depend on the physiological status of the cell. The binding sites of TBPs to DNA do not co-localize with the nuclear matrix attachment regions. We hypothesize that TBPs form a universal substrate for intranuclear processes.     

Parametric approach to genomic imprinting analysis with applications to Angelman's syndrome

Genomic imprinting is a mechanism by which only one copy of a gene pair is expressed, and this expression is determined by the parental origin of the copy. The deregulation of imprinted genes has been implicated in a number of human diseases. The Imprinted Gene Catalogue now has more than 200 genes listed, and estimates based on mouse models suggest many more may exist in humans. Therefore, the development of methods to identify such genes is important. In this communication, we present a parametric model-based approach to analyzing arbitrary-sized pedigree data for genomic imprinting. We have modified widely used LINKAGE program to incorporate our proposed approach. In addition, our approach allows for the use of sex-specific recombinations in the analysis, which is of particular importance in a genome-wide analysis for imprinted genes. We compared our imprinting analysis approach to that implemented in the GENEHUNTER-IMPRINT program using simulation studies as well as by analyzing causal genes in Angelman's syndrome families, which are known to be imprinted. These analyses showed that the proposed approach is very powerful for detecting imprinted genes in large pedigrees.     

A realist approach to biological events

In this paper, I aim to show that the multiple realisability and the causal efficacy of biological events can best be explained by construing biological events as determinables of more determinate physical events. The determination relation itself is spelled out in terms of inclusive essence. In order to secure actual causation for biological events (in contrast to causal influence), two conditions are introduced such that for some events, biological events qualify as their cause. Finally, certain consequences of the presented theory are discussed, such as the question of how the biological token event can retain its identity across modal modifications of its realiser, and such as how the presented solution bears on the classical problem of biological causation.     

Synaptosomal bioenergetics. The role of glycolysis, pyruvate oxidation and responses to hypoglycaemia

The bioenergetic interaction between glycolysis and oxidative phosphorylation in isolated nerve terminals (synaptosomes) from guinea-pig cerebral cortex is characterized. Essentially all synaptosomes contain functioning mitochondria. There is a tight coupling between glycolytic rate and respiration: uncoupler causes a tenfold increase in glycolysis and a sixfold increase in respiration. Synaptosomes contain little endogenous glycolytic substrate and glycolysis is dependent on external glucose. In glucose-free media, or following addition of iodoacetate, synaptosomes continue to respire and to maintain high ATP/ADP ratios. In contrast to glucose, the endogenous substrate can neither maintain high respiration in the presence of uncoupler nor generate ATP in the presence of cyanide. Pyruvate, but not succinate, is an excellent substrate for intact synaptosomes. The in-situ mitochondrial membrane potential (delta psi m) is highly dependent upon the availability of glycolytic or exogenous pyruvate; glucose deprivation causes a 20-mV depolarization, while added pyruvate causes a 6-mV hyperpolarization even in the presence of glucose. Inhibition of pyruvate dehydrogenase by arsenite or pyruvate transport by alpha-cyano-4-hydroxycinnamate has little effect on ATP/ADP ratios; however respiratory capacity is severely restricted. It is concluded that synaptosomes are valuable models for studying the control of mitochondrial substrate supply in situ.