Computational studies of the domain movement and the catalytic mechanism of thymidine phosphorylase

Thymidine phosphorylase (TP) is a dual substrate enzyme with two domains. Each domain binds a substrate. In the crystal structure of Escherichia coli TP, the two domains are arranged so that the two substrate binding sites are too far away for the two substrates to directly react. Molecular dynamics simulations reveal a different structure of the enzyme in which the two domains have moved to place the two substrates in close contact. This structure has a root-mean-square deviation from the crystal structure of 4.1 A. Quantum mechanical calculations using this structure find that the reaction can proceed by a direct nucleophilic attack with a low barrier. This mechanism is not feasible in the crystal structure environment and is consistent with the mechanism observed for other N-glycosidic enzymes. Important catalytic roles are found for the three highly conserved residues His 85, Arg 171, and Lys 190.     

The molecular organizational characteristics of the cell nucleus components at different phases of the mitotic cycle and in the resting state]

Data about the changes of the cell nucleus structure at different levels of its organization are summarized in the review. The data about the change of the DNA break number during the cycle and in resting state are presented and the role of the changes of the repair efficiency in this process is discussed. The changes of the chromatin protein spectrum, the chromatin structure at nucleosomal and supranucleosomal levels, the DNA superhelicity, topoisomerase activity, nuclear matrix composition and structure are discussed as well. The nucleus structure during the S-phase and mitosis and the cycle-related changes of the chromatin structure in lower eukaryotes are reviewed separately.     

染色体三维结构重建方法研究

染色体三维结构重构问题是近年生物领域中基因组学的热点研究问题,是以二维交互频率数据为基础来预测其三维空间结构。最新相关实验表明染色质的三维空间结构对于基因表达、调控等方面都具有重要意义。而Hi-c数据能利用染色质交互信息形成二维接触矩阵重构出染色体三维结构。本综述以染色体三维结构重建方法为研究对象,通过对染色体三维结构重建方法进行比较分析,综述了目前基于Hi-c数据在染色体三维结构重建中的经典方法,系统介绍了染色体三维结构重建技术的发展脉络,以促进染色体三维结构重建的进一步研究。     

Comparison of fragments comprising the first two helices of the human y4 and the yeast ste2p g-protein-coupled receptors

Solution NMR techniques are used to determine the structure and the topology of micelle integration of a large fragment of the Y4 receptor, a human G-protein-coupled receptor, that contains the entire N-terminal domain plus the first two transmembrane (TM) segments. The structure calculations reveal that the putative TM helices are indeed helical to a large extent, but that interruptions of secondary structure occur close to internal polar or charged residues. This view is supported by ¹⁵N relaxation data, amide-water exchange rates, and attenuations from micelle-integrating spin labels. No contacts between different helices are observed. This is in contrast to a similar TM1-TM2 fragment from the yeast Ste2p receptor for which locations of the secondary and the tertiary structure agreed well with the predictions from a homology model. The difference in structure is discussed in terms of principal biophysical properties of residues within central regions of the putative TM helices. Overall, using the biophysical scale of Wimley and White the TM regions of Ste2p display much more favorable free energies for membrane integration. Accordingly, the full secondary structure and the tertiary structure in TM1-TM2 of the Y4 receptor is likely to be formed only when tertiary contacts with other TM segments are created during folding of the receptor.     

Review of the molecular characteristics of gene mutations of the germline and somatic cells of the human

Molecular analyses of the limited number of de novo germinal mutations identified in humans indicate that an array of alterations in gene structure can be generated. Similar conclusions are derived from the large data set obtained from molecular analyses of alleles that segregate in the human population and cause genetic diseases. The molecular alterations include nucleotide substitutions as well as insertions, deletions and other rearrangements of the DNA. The lesions may be located in the coding or the noncoding regions of genes or may involve the flanking sequences. The insertions and deletions involve fragments ranging from single nucleotides to many kilobases, and involve both unique sequences and repetitive elements. The nature of the lesions observed to date as either de novo mutations or segregating variants suggests there are locus-specific characteristics of the alterations in DNA structure that are recovered as genetic diseases. Differences in mutation spectra among genetic loci appear to reflect both the structure of the target sequences and the relationship between gene structure and gene function. No induced germinal mutations have been identified, thus no data are available that reveal the relationships between mutagenic exposures and the molecular fingerprints of the lesion induced in the human germ cell and transmitted to the subsequent generations. In contrast, the prospects for analyzing the roles of genetic target, exposure history and individual responsiveness to exposure in creating particular molecular lesions in somatic cells are excellent, both for alterations of single nucleotides and for major alterations of gene structure.(ABSTRACT TRUNCATED AT 400 WORDS)     

The micropylar plate of the eggs of Phasmida, with a survey of the range of plate form within the order

Eggs of Phasmida are characterized by the presence of a micropylar plate system. The nature of this plate is discussed and the relevance of differences in plate structure to the taxonomy of the order is considered. A survey is made of the range of plate structure throughout the order, covering the external plate structure of 384 species and the internal plate structure of 179 species in forty of the forty-four subgroups of the order.     

Three-dimensional structure of goose-type lysozyme from the egg white of the Australian black swan, Cygnus atratus

The egg white of C. atratus contains two forms of lysozyme, a 'chick-type' which is similar to that found in the egg white of the domestic hen, and a 'goose-type' similar to that found in the egg white of the Embden goose. The molecular structure of the goose-type lysozyme has been determined at a resolution of a 2.8 A by X-ray crystallographic analysis. The structure consists of two domains linked by a long stretch of alpha-helix. In all, there are seven helical segments in the structure. While there is no amino acid sequence homology with either hen egg-white or bacteriophage T4 lysozymes, there are portions of the structure where the folding of the main chain is similar to that found in portions of either hen egg-white lysozyme or T4 lysozyme or both. In particular, there is a consistency of structure in the arrangement of acid groups in the catalytic site. G-o plots calculated for this structure and for the bacteriophage T4 lysozyme structure show that both have similar 'modules' of structure with boundaries occurring at structurally equivalent positions. Three of the common boundaries are equivalent structurally to three of the four module boundaries observed in G-o plots of hen egg-white lysozyme. The variation in the position of the remaining boundary may be related to differences in substrate binding.     

Structure of the mRNA of eukaryotic cells]

A review is given of the principal achievements in studying the structure of mRNA in eukaryotic cells. The data are provided on the size and life time, complexity and distribution of different kinds of mRNA by the frequency of repetitions; composition and structure of mRNP. The structures of individual mRNA's and general pattern of the structure of eukaryotic mRNA and mRNP are considered.     

On the algorithms for determining the primary structure of biopolymers

The algorithm for determining the primary structure of biopolymers from complete and partial digests are analyzed. The problem of determining the primary structure is formulated in the form of the problem of word reconstruction in the limits of which the corresponding algorithms are analyzed. Difficulties arising in constructing the algorithms for determining the primary structure of nucleic acids from a partial digest are discussed. They seem to be due to the extensive testing of variants. When there is a certain scheme of the initial data from a partial digest we propose an economical testing (searching) algorithm. The scheme of an effective algorithm for reconstruction of the primary structure fromN complete digests is given.     

An extensively associated dimer in the structure of the C713S mutant of the TIR domain of human TLR2

The Toll/interleukin-1 receptor (TIR) domains are conserved modules in the intracellular regions of the Toll-like receptors (TLRs) and interleukin-1 receptors (IL-1Rs). The domains are crucial for the signal transduction by these receptors, through homotypic interactions among the receptor and the downstream adapter TIR domains. Previous studies showed that the BB loop in the structure of the TIR domain forms a prominent conserved feature on the surface and is important for receptor signaling. Here we report the crystal structure of the C713S mutant of the TIR domain of human TLR2. An extensively associated dimer is observed in the crystal structure and mutations of several residues in this dimer interface abolished the function of the receptor. Moreover, the structure shows that the BB loop can adopt different conformations, which are required for the formation of this dimer. This asymmetric dimer might represent the TLR2:TLRx heterodimer in the function of this receptor.     

Local interactions drive the formation of nonnative structure in the denatured state of human alpha-lactalbumin: a high resolution structural characterization of a peptide model in aqueous solution.

There are a small number of peptides derived from proteins that have a propensity to adopt structure in aqueous solution which is similar to the structure they possess in the parent protein. There are far fewer examples of protein fragments which adopt stable nonnative structures in isolation. Understanding how nonnative interactions are involved in protein folding is crucial to our understanding of the topic. Here we show that a small, 11 amino acid peptide corresponding to residues 101-111 of the protein alpha-lactalbumin is remarkably structured in isolation in aqueous solution. The peptide has been characterized by 1H NMR, and 170 ROE-derived constraints were used to calculate a structure. The calculations yielded a single, high-resolution structure for residues 101-107 that is nonnative in both the backbone and side-chain conformations. In the pH 6.5 crystal structure, residues 101-105 are in an irregular turn-like conformation and residues 106-111 form an alpha-helix. In the pH 4.2 crystal structure, residues 101-105 form an alpha-helix, and residues 106-111 form a loopike structure. Both of these structures are significantly different from the conformation adopted by our peptide. The structure in the peptide model is primarily the result of local side-chain interactions that force the backbone to adopt a nonnative 310/turn-like structure in residues 103-106. The structure in aqueous solution was compared to the structure in 30% trifluoroethanol (TFE), and clear differences were observed. In particular, one of the side-chain interactions, a hydrophobic cluster involving residues 101-105, is different in the two solvents and residues 107-111 are considerably more ordered in 30% TFE. The implications of the nonnative structure for the folding of alpha-lactalbumin is discussed.     

An analysis of the structure of the bilaminar lamellae of the hamster egg

The unfertilized hamster egg contains a ubiquitous distribution of lamellate structures. Normally the lamellae are bilaminar, although occasionally both single sheets and multiple sheets are seen. Detailed analysis of the structure of a single bilaminar lamella shows that each sheet of the two-sheet structure is identical and made up of repeating rhombohedral units whose principal axes are in the ratio of 2:1. Each sheet lies at 90 degrees to the other. Using this information, a single bilaminar lamella has been reconstructed. This reconstruction accounts for its major ultrastructural features.     

Asymmetric stability among the transmembrane helices of lactose permease

Combining structure determinations from nuclear magnetic resonance (NMR) data and molecular dynamics simulations (MD) under the same environmental conditions revealed a startling asymmetry in the intrinsic conformational stability of secondary structure in the transmembrane domain of lactose permease (LacY). Eleven fragments, corresponding to transmembrane segments (TMs) of LacY, were synthesized, and their secondary structure in solution was determined by NMR. Eight of the TMs contained significant regions of helical structure. MD simulations, both in DMSO and in a DMPC bilayer, showed sites of local stability of helical structure in these TMs, punctuated by regions of conformational instability, in substantial agreement with the NMR data. Mapping the stable regions onto the crystal structure of LacY reveals a marked asymmetry, contrasting with the pseudosymmetry in the static structure: the secondary structure in the C-terminal half is more stable than in the N-terminal half. The relative stability of secondary structure is likely exploited in the transport mechanism of LacY. Residues supporting proton conduction are in more stable regions of secondary structure, while residues key to substrate binding are found in considerably unstable regions of secondary structure.     

Ultrastructure of the stria vascularis of the auricular labyrinth of the rabbit]

In the composition of the stria vascularis of the rabbit cochlea there are three types of cells: edging, medial and basal cells. The structure of these cells, their disposition and interrelationships within the stria vascularis are described. The nodes of the basal membrane whose ramification covers long mitichondria concentrating at the basement of edging cells are found in the structure of capillaries of the cochlea stria vascularis. It may be supposed that this powerful mitochondrial apparatus refers to the capillary system of the stria vascularis and represents a hypertrophic mitochondrial apparatus of pericytes. The capillaries of the stria vascularis are distributed mainly in longitudinal direction while the capillaries disposed transversely which are likely to be anastomoses were also found.     

The characteristics of the action of gamma irradiation on the secondary structure of ribonuclease in vitro and the effect of oxygen on this process]

The change in the secondary structure of ribonuclease after 60Co gamma irradiation with a dose of 1,000 Gy in 0.2% aqueous solution was estimated using the circular dichroism method. The beta structures were significantly changed, while other types of the secondary structure (alpha-helix and beta-turns) changed insignificantly. The secondary structure injury was also affected by oxygen. The data are attributed to characteristics of the secondary structure of this enzyme.     

New mechanism for the formation of discrete stripes in the solar radio spectrum

Dispersion relations are derived for the eigenfrequency spectrum of a spatially periodic nonlinear plasma resonators created in the solar atmosphere due to the development of thermal instability. The eigenfrequency spectra of such resonators are calculated, and it is shown that they are capable of generating tens of discrete stripes (a so-called zebra structure) the number of which is independent of the ratio of the plasma frequency to the gyrofrequency in the source. This may help to overcome all difficulties in explaining the large number of stripes in the zebra structure, as well as the small magnitude of the magnetic field. The spatially periodic plasma resonators under consideration act as a filter with numerous transparency windows separated from one another by opaque regions. The number of stripes and their frequencies in the zebra structure depend on the spatial period of plasma nonuniformity, which is equal to meters or decameters for conditions typical of the solar atmosphere. The high brightness temperature of radio emission in the zebra structure is attributed to coherent emission from a large number of identical small-scale plasma sources. Some regular properties of the observed zebra structure are explained.     

A transformational-grammar approach to the study of the regulation of gene expression

An important problem in biology is the lack of a set of common principles unifying biological knowledge. We propose generative grammar for constructing an integrative paradigm for the understanding of genome organization and the regulation of gene expression. Linguistic terms in molecular biology are defined. A genetic syntactic structure is defined as being equivalent to a sentence. The hypotheses for the grammar of genome structure are: (i) the "grammaticality" of the linguistic approach studies the "regulability" of genome structures; (ii) the "regulability" of genetic structures is independent from their specific biochemical meaning and (iii) the dynamics of regulation is implicit in the genome structure. A general structure is presented for the grammar; the application of phase-structure rules is justified by the existence of lexical categories. Transformational rules are utilized to represent loops of regulation. Negative inducible, positive repressible, positive inducible and negative repressible alternative mechanisms of regulation are represented, by four transformational rules, and the application of these rules is established by two principles. Finally, this approach is compared to other linguistic applications in molecular biology.     

Comparison of the fine-scale genetic structure of three dipterocarp species

We investigated the fine-scale genetic structure of three tropical-rainforest trees, Hopea dryobalanoides, Shorea parvifolia and S. acuminata (Dipterocarpaceae), in Peninsular Malaysia, all of which cooccurred within a 6-ha plot in Pasoh Forest Reserve. A significant genetic structure was found in H. dryobalanoides, weaker (but still significant) genetic structure in S. parvifolia and nonsignificant structure in S. acuminata. Seeds of all three species are wind dispersed, and their flowers are thought to be insect pollinated. The most obvious difference among these species is their height: S. parvifolia and S. acuminata are canopy species, whereas H. dryobalanoides is a subcanopy species. Clear differences were also found among these species in their range of seed dispersal, which depends on the height of the release point; so taller trees disperse their seed more extensively. The estimates of seed dispersal area were consistent with the degree of genetic structure found in the three species. Therefore, tree height probably had a strong influence on the fine-scale genetic structure of the three species.     

Comparative modeling methods: application to the family of the mammalian serine proteases

Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structures and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequences for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.     

Structure of the centriolar complex in the hepatocytes of intact and regenerating mouse live

The structure of the cellular center in polyploid hepatocytes of intact and regenerating liver of adult mice has been studied. It was shown that the structure of the centriolar complex depends on stages of the cellular cycle. No pericentriolar structures (such as satellites, appendages and others) and cytoplasmic microtubules were found in the centriolar complex within G0-period. The satellites and appendages are formed in the half of the centrioles within G1-period. The microtubules can branch off some satellites; the daughter centrioles begin to form within S-period; there are diplosomes in the cells within G2-period, some mother centrioles are surrounded with the fine fibrillar halo. It is concluded that the structure of the centriolar complex within G0-period is distinguished by that within G1-period. The structure of the centriolar complex in polyploid hepatocytes has the same feature of reorganization in certain interphase periods of the cell cycle as in diploid cells of some cultured cells and the thyroid epithelium.