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At least 19 recordsLinked to original sources

Cell-water transfer and stability of biological structures (resonance of biological structures).

A model is proposed according to which life is the totality of resonant thermodynamically open systems. The Earth's physical fields are the necessary condition of these systems existence and their dynamic stability. The size of the cell is a function of the magnetic field intensity according to the proposed equation. Thermodynamic equations are also proposed for the computation of the optimal oxidation stage and membrane potential, and for the water dielectric permeability. All equations result in values which correspond to experimental data without fitting coefficients. The proposed theory explains the structure of the biological system as result of the dynamic stability and least action principle. This theory also includes the explanation of the influence of Earth magnetic field and analysis of associated water properties.

Biological Transport↗

Perspectives in inorganic structural biology: solution structures of metalloproteins.

The achievements in the structural characterization in solution, through NMR spectroscopy, of proteins containing metal ions are reviewed and discussed. We call this branch "inorganic structural biology". The results of this approach are presented here for cytochrome b5, used in this paper as a case system. These results are discussed particularly in the light of their relevance for understanding the biological function of the proteins. Furthermore, the extension of the characterization to the internal motions and to the folding/unfolding processes, as well as the development of tools for structure prediction, are critically presented. The message is that the complete characterization of a biological molecule cannot be limited to a static description of the structure but it should go beyond, analyzing the internal motions occurring at various time scales as well as the behavior in different conditions, such as in the presence of denaturing agents.

Animals↗

Recent progress in the biology, chemistry and structural biology of DNA glycosylases.

Since the discovery in 1974 of uracil DNA glycosylase (UDG), the first member of the family of enzymes involved in base excision repair (BER), considerable progress has been made in the understanding of DNA glycosylases, the polypeptides that remove damaged or mispaired DNA bases from DNA. We also know the enzymes that act downstream of the glycosylases, in the processing of abasic sites, in gap filling and in DNA ligation. This article covers the most recent developments in our understanding of BER, with particular emphasis on the mechanistic aspects of this process, which have been made possible by the elucidation of the crystal structures of several glycosylases in complex with their respective substrates, substrate analogues and products. The biological importance of individual BER pathways is also being appreciated through the inactivation of key BER genes in knockout mouse models.

Amino Acid Sequence↗

Towards single atom analysis of biological structures.

Mapping single atoms in biological structures is now becoming within the reach of analytical electron microscopy. Electron energy-loss spectroscopy (EELS) in the field-emission scanning transmission electron microscope (STEM) provides a particularly high sensitivity for detecting the biologically important element, phosphorus. Imaging can be performed at low dose with dark-field STEM prior to analysis at high dose, so that structures of macromolecular assemblies can be correlated with the numbers of specific atoms that they contain. Measurements confirm theoretical predictions that single atom detection requires a nanometer-sized probe. Although phosphorus atoms may have moved several nanometers from their original positions by beam-induced structural degradation at the high required dose of approximately 10(9) e/nm2, damaged molecules are nevertheless stable enough to be analyzed at 1 or 2 nm resolution. Such analyses can only be achieved by means of spectrum-imaging with correction for specimen drift. Optimal strategies for mapping small numbers of phosphorus atoms have been investigated using well-characterized specimens of DNA plasmids and tobacco mosaic virus.

Carbon↗

Anthropometry and the biological structure of the Hvar population.

Biological structure of the population of the island of Hvar was investigated by using the data on anthropometric variation among nine village populations; 24 body and 14 head dimensions were analysed from 487 male and 437 female adult subjects. Univariate and multivariate analyses revealed heterogeneity among the populations, which says much for the strength of the isolating factors on the island. Using correlations of anthropometric and geographic distance, the observed patterns of variation among villages were closely related to geography, suggesting migration to be an important factor in the formation of the island's population structure. Populations of the examined villages were further grouped to form the population of the eastern part and the population of the western part of the island, which have an ethnodemographic and sociocultural basis. The analyses revealed heterogeneity between the populations and thus provided evidence to support the hypothesis about the existence of the genetically different groups living in the same biotope.

Adult↗

[Classification of organisms and structuralism in biology].

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.

Biological Evolution↗

The structural biology of expression and function of tissue factor.

Analysis of the structural biology of TF provides insights into the both the expression of the gene and the function of this cell surface receptor in the initiation of the coagulation protease cascades. The advance of information may permit inferential hypotheses for the structural biology of other cofactor regulated catalytic steps in blood coagulation.

Amino Acid Sequence↗

The use of a charge-coupled device for quantitative optical microscopy of biological structures.

The properties of a charge-coupled device (CCD) and its application to the high-resolution analysis of biological structures by optical microscopy are described. The CCD, with its high resolution, high sensitivity, wide dynamic range, photometric accuracy, and geometric stability, can provide data of such high quality that quantitative analysis on two- and three-dimensional microscopic images is possible. For example, the three-dimensional imaging properties of an epifluorescence microscope have been quantitatively determined with the CCD. This description of the imaging properties of the microscope, and the high-quality image data provided by the CCD, allow sophisticated computational image processing methods to be used that greatly improve the effective resolution obtainable for biological structures. Image processing techniques revealed fine substructures in Drosophila embryonic diploid chromosomes in two and three dimensions. The same approach can be extended to structures as small as yeast chromosomes or to other problems in structural cell biology.

Animals↗

Challenges at the frontiers of structural biology.

Knowledge of the three-dimensional structures of proteins is the key to unlocking the full potential of genomic information. There are two distinct directions along which cutting-edge research in structural biology is currently moving towards this goal. On the one hand, tightly focused long-term research in individual laboratories is leading to the determination of the structures of macromolecular assemblies of ever-increasing size and complexity. On the other hand, large consortia of structural biologists, inspired by the pace of genome sequencing, are developing strategies to determine new protein structures rapidly, so that it will soon be possible to predict reasonably accurate structures for most protein domains. We anticipate that a small number of complex systems, studied in depth, will provide insights across the field of biology with the aid of genome-based comparative structural analysis.

Animals↗

Structural biology and its applications to the health sciences.

Part of the decipherment of genomic information lies in understanding the structure and function of the protein products of these genes. Protein structure is of further importance because of the molecular basis of many diseases. Structural biology is the field of research focusing on the experimental determination of the structure of biological molecules. We review the field of structural biology and its application to medical research and drug discovery, and describe the structural results recently obtained in our laboratory for the detoxifying enzyme glutathione S-transferase from the Asian mosquito Anopheles dirus species B, an important malaria vector. These enzymes have detoxifying activity toward pesticides and thus contribute to pesticide resistance in insects.

Amino Acid Sequence↗

An account of NMR in structural biology.

With the ability to determine atomic resolution structures of biological macromolecules in semi-physiological conditions, nuclear magnetic resonance spectroscopy (NMR) has become an eminent tool in structural biology. NMR provides a means for studying critical biological phenomena including protein structure, dynamics and folding as well as a practical approach to drug design.

Crystallography, X-Ray↗

[Theoretical aspects of the quantitative study of the chemical structure-biological action relationship].

The study of the interrelationship between the chemical structure of the drug molecule and their biologic activity is one of the most modern aspects of current pharmacology and pharmacochemistry. The information, obtained by these studies, contributes for more precise and detailed understanding of the mechanisms of drug molecule interaction with some biologic structures, and this helps to clarify a series of biologic and physiological phenomena. The authors describe in this paper some methods, which are used, when the dependences between structure and action are search for as well as the basic physiocochemical and quantum -- chemical values, which determine the pharmacological effect of drugs.

Binding Sites↗

Aromatic ring-flipping in supercooled water: implications for NMR-based structural biology of proteins.

We have characterized, for the first time, motional modes of a protein dissolved in supercooled water: the flipping kinetics of phenylalanyl and tyrosinyl rings of the 6 kDa protein BPTI have been investigated by NMR at temperatures between -3 and -16.5 degrees C. At T = -15 degrees C, the ring-flipping rate constants of Tyr 23, Tyr 35, and Phe 45 are smaller than 2 s(-1), i.e., flip-broadening of aromatic NMR lines is reduced beyond detection and averaging of NOEs through ring-flipping is abolished. This allows neat detection of distinct NOE sets for the individual aromatic (1)H spins. In contrast, the rings of Phe 4, Tyr 10, Tyr 21, Phe 22, and Phe 33 are flipping rapidly on the chemical shift time scale with rate constants being in the range from approximately 10(2) to 10(5) s(-1) even at T = -15 degrees C. Line width measurements in 2D [(1)H,(1)H]-NOESY showed that flipping of the Phe 4 and Phe 33 rings is, however, slowed to an extent that the onset of associated line broadening in the fast exchange limit is registered. The reduced ring-flipping rate constant of Phe 45 in supercooled water allowed very precise determination of Eyring activation enthalpy and entropy from cross relaxation suppressed 2D [(1)H,(1)H]-exchange spectroscopy. This yielded DeltaH = 14 +/- 0.5 kcal.mol(-1) and DeltaS = -4 +/- 1 cal.mol(-1).K(-1), i.e., values close to those previously derived by Wagner and Wüthrich for the temperature range from 4 to 72 degrees C (DeltaH = 16 +/- 1 kcal.mol(-1) and DeltaS = 6 +/- 2 cal.mol(-1).K(-1)). The preservation of the so far uniquely low value for DeltaS indicates that the distribution of internal motional modes associated with the ring flip of Phe 45 is hardly affected by lowering T well below 0 degrees C. Hence, if a globular protein does not cold denature, aromatic flipping rates, and thus likely also the rates of other conformational and/or chemical exchange processes occurring in supercooled water, can be expected to be well estimated from activation parameters obtained at ambient T. This is of keen interest to predict the impact of supercooling for future studies of biological macromolecules, and shows that our approach enables one to conduct NMR-based structural biology at below 0 degrees C in an unperturbed aqueous environment. A search of the BioMagResBank indicated that the overwhelming majority of the Phe and Tyr rings (>95%) are flipping rapidly on the chemical shift time scale at ambient T, while our data for BPTI and activation parameters available for ring-flipping in Iso-2-cytochrome c reveal that in these smaller proteins a total of six out of seventeen rings ( approximately 35%) are "frozen in" at T = -15 degrees C. This suggests that a large fraction of Tyr and Phe rings in globular proteins that are flipping rapidly on the chemical shift time scale at ambient T can be effectively slowed in supercooled water. The present investigation demonstrates that supercooling of protein solutions appears to be an effective means to (i) harvest potential benefits of stalled ring-flipping for refining NMR solution structures, (ii) recruit additional aromatic rings for investigating protein dynamics, and (iii) use multiple slowly flipping rings to probe cold denaturation. The implications for NMR-based structural biology in supercooled water are addressed.

Animals↗

Structural biology of zinc.

The biological function of zinc is governed by the composition of its tetrahedral coordination polyhedron in the metalloprotein, and each ligand group that coordinates to the metal ion does so with a well-defined stereochemical preference. Consequently, protein-zinc recognition and discrimination requires proper chemical composition and proper stereochemistry of the metal-ligand environment. However, it should be noted that the entire protein behaves as the "zinc ligand," since residues that are quite distant from the metal affect recognition and function by through-space (either solvent or the protein milieu) or through-hydrogen bond coulombic interactions. Additionally, long-range interactions across hydrogen bonds serve to orient ligands and therefore minimize the entropy loss incurred on metal binding. Since zinc is not subject to ligand field stabilization effects, it is easy for the tetrahedral protein-binding site to discriminate zinc from other first-row transition metal ions: It is only for Zn2+ that the change from an octahedral to a tetrahedral ligand field is not energetically disfavored. Structural considerations such as these must illuminate the engineering of de novo zinc-binding sites in proteins. Zinc serves chemical, structural, and regulatory roles in biological systems. In biological chemistry zinc serves as an electrophilic catalyst; that is, it stabilizes negative charges encountered during an enzyme-catalyzed reaction. The coordination polyhedron of catalytic zinc is usually dominated by histidine side chains. In biological structure zinc is typically sequestered from solvent, and its coordination polyhedron is almost exclusively dominated by cysteine thiolates. Structural or regulatory zinc is found as either a single metal ion or as part of a cluster of two or more metals. In multinuclear clusters cysteine thiolates either bridge two metal ions or serve as terminal ligands to a single metal ion. Even in complex multinuclear clusters, Zn2+ displays tetrahedral coordination. The structural biology of zinc continues to receive attention in catalytic and regulatory systems such as leucine aminopeptidase, alkaline phosphatase, transcription factors, and steroid receptors. For example, zinc-mediated hormone-receptor association has recently been demonstrated in the binding of human growth hormone to the extracellular binding domain of the human prolactin receptor (Cunningham et al., 1990). To be sure, structural studies of zinc in biology will continue to be a fruitful source of bioinorganic advances, as well as surprises, in the future.

Amino Acid Sequence↗

Key biological structures of the human being's informational image.

This article deals with the corporeal and informational images of human beings. These images can be represented by key biological structures, such as biocells, nerve fibers, and acupuncture points. These structures are shown to transmit and process informational signals by means of electromagnetic (field) waves. An experimental setup is designed to study biological structures in the millimeter-wave range.

Acupuncture↗

Quantization of directional properties in biological structures using the Minimal Spanning Tree.

A method that uses the Minimal Spanning Tree graph has previously been developed (Dussert et al., 1987, J. theor. Biol. 125, 317) in order to analyse the degree of order in biological structures. This graph is shown here to be very powerful in bringing out directional properties of biological structures which cannot be revealed by a simple visual examination. The method is illustrated by means of various computer simulations.

Computer Simulation↗

A system for the three-dimensional reconstruction of biological structures.

A system of programs for building three-dimensional models of biological structures was developed. Outlines of features such as cells, tissue edges, and neuron pathways are traced into a computer from tissue sections mounted on a light microscope or projected onto a data tablet. The three-dimensional models are built from a series of the two-dimensional outlines. The cathode ray tube displays of the three-dimensional models can be smoothly rotated for study, and a static display with hidden lines removed can be produced. Volume and surface area calculations for the models can be done. It is possible to obtain further anatomical data by counting and mapping silver grains in autoradiographs of tissue sections. The density of grains reveals pathways and boundaries in the structure. Displays of silver grain maps and counts can be superimposed on displays of the model of the structure.

Animals↗