A common sequence-associated physicochemical feature for proteins of beta-trefoil family

Different amino acid sequences can fold into similar tertiary structures but the reasons for it are not very clear. It has been suggested in the literature that these sequences may have some common features associated with them but the exact nature of such shared properties remains largely unknown. We studied a representative sample of proteins from the beta-trefoil family and observed that their amino acid sequences, despite being considerably divergent from each other, can be accounted for by matching to a repetition of three physicochemically similar segments. This observation in turn is consistent with the three-fold pseudo-symmetry in tertiary structures of these proteins.     

A method for discovering transmembrane beta-barrel proteins in Gram-negative bacterial proteomes

Transmembrane beta-barrel (TMB) proteins play pivotal roles in many aspects of bacterial functions. This paper presents a k-nearest neighbor (K-NN) method for discriminating TMB and non-TMB proteins. We start with a method that makes predictions based on a distance computed from residue composition and gradually improve the prediction performance by including homologous sequences and searching for a set of residues and di-peptides for calculating the distance. The final method achieves an accuracy of 97.1%, with 0.876 MCC, 86.4% sensitivity and 98.8% specificity. A web server based on the proposed method is available at http://yanbioinformatics.cs.usu.edu:8080/TMBKNNsubmit.     

Interplay of symmetries of block polymers and confining geometries

The morphologies that block polymers exhibit under various types of confinement are reviewed with emphasis on experimental results and theoretical predictions. Confining geometries in all three dimensions are considered and special attention is paid to cylindrical and spherical boundary conditions. Past experimental techniques and theoretical understanding are discussed and an outlook for future advances due to the possibility for novel, well ordered and aligned morphologies to occur when polymers are confined between surfaces of varying distance, curvature, and surface chemistry is provided. Confinement creates new morphologies which are not present in the bulk, indicating that the confined thermodynamic boundary conditions result in phase behavior that is distinct from the bulk and that there is the possibility for new phases and order-order transitions to be discovered as future researchers impose new types of confinement and explore a greater range of block polymer architecture, composition and molecular weights. The article concludes with a brief introduction of interference lithography, which can be used to form arbitrary and novel boundary conditions, and a perspective on the future outlook of the phase behavior of confined block polymers.     

Comprehensive comparison of two protein family of P-ATPases (13A1 and 13A3) in insects

The P-type ATPases (P-ATPases) are present in all living cells where they mediate ion transport across membranes on the expense of ATP hydrolysis. Different ions which are transported by these pumps are protons like calcium, sodium, potassium, and heavy metals such as manganese, iron, copper, and zinc. Maintenance of the proper gradients for essential ions across cellular membranes makes P-ATPases crucial for cell survival. In this study, characterization of two families of P-ATPases including P-ATPase 13A1 and P-ATPase 13A3 protein was compared in two different insect species from different orders. According to the conserved motifs found with MEME, nine motifs were shared by insects of 13A1 family but eight in 13A3 family. Seven different insect species from 13A1 and five samples from 13A3 family were selected as the representative samples for functional and structural analyses. The structural and functional analyses were performed with ProtParam, SOPMA, SignalP 4.1, TMHMM 2.0, ProtScale and ProDom tools in the ExPASy database. The tertiary structure of Bombus terrestris as a sample of each family of insects were predicted by the Phyre2 and TM-score servers and their similarities were verified by SuperPose server. The tertiary structures were predicted via the “c3b9bA” model (PDB Accession Code: 3B9B) in P-ATPase 13A1 family and “c2zxeA” model (PDB Accession Code: 2ZXE) in P-ATPase 13A3 family. A phylogenetic tree was constructed with MEGA 6.06 software using the Neighbor-joining method. According to the results, there was a high identity of P-ATPase families so that they should be derived from a common ancestor however they belonged to separate groups. In protein–protein interaction analysis by STRING 10.0, six common enriched pathways of KEGG were identified in B. terrestris in both families. The obtained data provide a background for bioinformatic studies of the function and evolution of other insects and organisms.     

Hidden Markov model and Chapman Kolmogrov for protein structures prediction from images

Protein structure prediction and analysis are more significant for living organs to perfect asses the living organ functionalities. Several protein structure prediction methods use neural network (NN). However, the Hidden Markov model is more interpretable and effective for more biological data analysis compared to the NN. It employs statistical data analysis to enhance the prediction accuracy. The current work proposed a protein prediction approach from protein images based on Hidden Markov Model and Chapman Kolmogrov equation. Initially, a preprocessing stage was applied for protein images’ binarization using Otsu technique in order to convert the protein image into binary matrix. Subsequently, two counting algorithms, namely the Flood fill and Warshall are employed to classify the protein structures. Finally, Hidden Markov model and Chapman Kolmogrov equation are applied on the classified structures for predicting the protein structure. The execution time and algorithmic performances are measured to evaluate the primary, secondary and tertiary protein structure prediction.     

人类和黑猩猩的回文序列的对称性分析

首次通过分析人类和黑猩猩的X染色体上的一条回文序列,来寻找这种对称性破缺的规律．分析结果表明,与红毛猩猩相比,尽管在人类回文序列上发生的突变总数比在黑猩猩上的少,但是在各自的序列上,它们的左臂的突变总数与右臂的突变总数都基本上是相同的,这意味着它们的回文序列的进化都是同步的．然而,在每个臂上,A／T→G／C的突变数目却大于G／C→A／T的,这表明回文序列的成分并没有达到平衡,并且GC含量有上升的趋势．此外,通过两臂之间的序列比较发现,发生在人类回文序列上的突变数目多于发生在黑猩猩上的突变数目,并且这种突变更容易发生在具有相似化学结构的碱基之间．因此,黑猩狠回文序列上的对称性看起来要比人类回文序列上的对称性高．     

Concurrent symmetries: the interplay between local and global molecular symmetries

We analyze in this article the degree to which different groups of atoms retain local symmetries when assembled in a molecule. This study is carried out by applying continuous symmetry measures to several families of mixed sandwiches, a variety of piano-stool molecules, and several organic groups. An analysis of the local symmetry of the electron density shows that, sandwiched between two regions of different symmetry that correspond to the ligand sets, its symmetry is cylindrical at the central metal atom.     

Secondary and Tertiary Structure of Polysaccharides in Solutions and Gels

Many polysaccharide chains can adopt ordered helical and ribbon-like secondary structures. It seems however that these chains are often so stiff and extended that the cooperative interactions necessary for stability in the solvent environment can only be achieved when inter-chain as well as intra-chain interactions are favorable. Hence we commonly find two-or more-stranded associations of helices, of ribbons, or of helices with ribbons. These can be regarded as tertiary and higher levels of structure. The ordered secondary structure characteristically requires a regular repeating sequence of sugar residues, and the termination of this sequence by insertion of a residue of different type may also terminate the secondary structure and hence the association in which it is involved. This is the mechanism by which native polysaccharides may link up to form three dimensional networks, or gels, in which state they perform their natural roles in maintaining the hydration and integrity of biological tissues. For several polysaccharides there is evidence that the mechanism of biological control over the fine topology and properties of the gel network is mediated by enzymes which modify sugar residues at the polymer level to change the pattern of “interrupting” sugar residues.     

分子轨道图形理论中对称面定理的扩展

对唐敖庆教授和江元生教授建立的对称面定理做了一定的扩展，引进了原子轨道对称性的概念，扩展后的对称面定理可以应用于包含过渡金属和非相邻相互作用等较为复杂的体系中     

Atomistic Simulation Study of Cu0.327Ni0.673 Alloys: from Solid Solution to Phase Segregation

We present a combined Monte‐Carlo/molecular dynamics study of a Cu_0.327Ni_0.673 alloy system. On the basis of nearest‐neighbor coordination number analyses atomic clustering and phase segregation is explored. Along this line, free energy profiles are calculated and separated into entropic and energetic contributions. The competition of both terms was found in accordance to the experimental phase diagrams (phase separation of the solid solution below about 600 Kelvin). Two independent simulation runs were performed. At 1000 Kelvin the observed configurations correspond to solid solutions exhibiting a weak tendency to cluster atoms of identical species. At room temperature the energetic favoring of atomic separation is clearly dominant and leads to the formation of Ni‐rich and Cu‐rich domains. The latter are separated by interfacial regions whose width ranges from 0.5 to 1 nanometers.     

Lysozymes: a chapter of molecular biology

Hen egg-white lysozyme was the first enzyme whose tertiary structure could be elucidated. The peptide chain of this enzyme is arranged in two sections, of approximately equal size, that are separated by a deep cleft. Substrates (and inhibitors) are bound in this cleft via hydrogen bonds and are hydrolyzed under the action of Glu 35 and Asp 52, which form the active site of the enzyme. Although the lysozymes, which occur in many species of animals and plants, exhibit differences in their chemical behavior, they have the same qualitative biological activity; quantitatively important differences have been noted which also concern the specificity. Infection of E. coli with bacteriophages gives rise to a lysozyme whose formation is controlled by the phage DNA. The fact that mutated lysozymes are produced when the phages are treated with mutagens opens new fields of research in molecular biology.     

On the similarity of DNA primary sequences

We consider numerical characterization of graphical representations of DNA primary sequences. In particular we consider graphical representation of DNA of beta-globins of several species, including human, on the basis of the approach of A. Nandy in which nucleic bases are associated with a walk over integral points of a Cartesian x, y-coordinate system. With a so-generated graphical representation of DNA, we associate a distance/distance matrix, the elements of which are given by the quotient of the Euclidean and the graph theoretical distances, that is, through the space and through the bond distances for pairs of bases of graphical representation of DNA. We use eigenvalues of so-constructed matrices to characterize individual DNA sequences. The eigenvalues are used to construct numerical sequences, which are subsequently used for similarity/dissimilarity analysis. The results of such analysis have been compared and combined with similarity tables based on the frequency of occurrence of pairs of bases.     

Predictions of compounds in the family of delafossites

This paper reports the results of our crystal-chemical analysis of structures from the delafossite family A⁺B³⁺X₂, where A and B are cations, and is oxygen. The family is represented by structures of two types, CuFeO₂ and α-NaFeO₂ (R \(\bar 3\) m, Z = 1). Predictions of new compounds are presented. About a hundred new crystals can be synthesized.     

La-Mn-Ni-O催化剂组成、结构、还原性能及氧化活性

用硝酸盐分解法合成了LaMn_(1-x)Ni_xO_3(0≤2≤1.0), 研究了组成、晶体结构及其与还原性能、CO和CH_3OH催化氧化活性的关系。XRD证实在0.0≤x≤1.0范围内, 本体系都生成单一钙钛矿结构: 0.0≤x≤0.4, 0.8相似文献   

Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques

Although the characterization of proteins cannot solely rely upon sequence similarity, it has been widely proved that all-vs-all massive sequence comparisons may be an effective approach and a good basis for the prediction of biochemical functions or for the delineation of common shared properties. The program Cluster-C presented here enables a stand-alone and efficient construction of protein families within whole proteomes. The algorithm, which is based on the detection of cliques, ensures a high level of connectivity within the clusters. As opposed to the single transitive linkage method, Cluster-C allows a large number of sequences to be classified in such a way that the multidomain proteins do not produce a chain-grouping effect resulting in meaningless clusters. Moreover, some proteins can be present in several different but relevant clusters, which is of help in the determination of their functional domains. In the present analysis we used the Z-value, an evaluation of the significance of the similarity score, as the criterion for connecting sequences (the user can freely define the threshold of the similarity criterion). The clusters built with a rather low threshold (Z= 14) include more than 97% of the sequences and are consistent with known protein families and PROSITE patterns.     

Automatic analysis of amino-acid sequences in proteins and peptides

The development of the widely used automatic method from Edman's manual sequence analysis of proteins and peptides has resulted from modification of the procedure and from the use of a physically novel principle. All reaction, centrifugation, extraction, and drying operations are carried out in a rotating vessel. At a minimal cost in time and material, for example, sixty amino acids have been split off consecutively from a single sample of myoglobin.     

Novel features for identifying A-minors in three-dimensional RNA molecules

RNA tertiary interactions or tertiary motifs are conserved structural patterns formed by pairwise interactions between nucleotides. They include base-pairing, base-stacking, and base-phosphate interactions. A-minor motifs are the most common tertiary interactions in the large ribosomal subunit. The A-minor motif is a nucleotide triple in which minor groove edges of an adenine base are inserted into the minor groove of neighboring helices, leading to interaction with a stabilizing base pair. We propose here novel features for identifying and predicting A-minor motifs in a given three-dimensional RNA molecule. By utilizing the features together with machine learning algorithms including random forests and support vector machines, we show experimentally that our approach is capable of predicting A-minor motifs in the given RNA molecule effectively, demonstrating the usefulness of the proposed approach. The techniques developed from this work will be useful for molecular biologists and biochemists to analyze RNA tertiary motifs, specifically A-minor interactions.     

Cs2.91Na1.34Fe3+0.25[Fe3O(SO4)6(H2O)3]·5H2O,a member of the Maus's salt family

The title compound, tricaesium sodium iron(III) μ₃‐oxido‐hexa‐μ₂‐sulfato‐tris[aquairon(III)] pentahydrate, Cs_2.91Na_1.34Fe³⁺_0.25[Fe₃O(SO₄)₆(H₂O)₃]·5H₂O, belongs to the family of Maus's salts, K₅[Fe₃O(SO₄)₆(H₂O)₃]·6H₂O, which is based on the triaqua‐μ₃‐oxido‐hexa‐μ‐sulfato‐triferrate(III) anion, [Fe₃O(SO₄)₆(H₂O)₃]⁵⁻, with Fe in a characteristically distorted octahedral coordination environment, sharing a common corner via an oxide O atom. Cs in four different cation sites, Na in three different cation sites and five water molecules link the anions in three dimensions and set up a crystal structure in which those parts parallel to (001) and within 0.05 < z < 0.95 have a distinct trigonal pseudosymmetry, whereas the cation arrangement and bonding near z∼ 0 generate a clear‐cut noncentrosymmetric polar edifice with the monoclinic space group C2. The structure shows some cation disorder in the region near z ∼ , where one Na atom in octahedral coordination is partly substituted by Fe³⁺, and a Cs atom is substituted by small amounts of Na on a separate nearby site. One Na atom, located on a twofold axis at z = 0 and tetrahedrally coordinated by four sulfate O atoms of two [Fe₃O(SO₄)₆(H₂O)₃]⁵⁻ units, plays a key role in generating the noncentrosymmetric structure. Three of the seven different cation sites are on twofold axes (one Na⁺ site and two Cs⁺ sites), and all other atoms of the structure are in general positions.     

Hidden rearrangement processes in short-lived negative molecular ions

The study of resonant electron capture by nitrobenzene molecules showed that some fragmentary negative ions are unstable toward electron autodetachment. The measured appearance energy of the neutral component of an [M — H]⁻ ion beam does not agree with the energetics of direct dissociation in a molecular ion. The estimation calculations show that the low appearance energy of [M — H]⁰ neutral components is caused by isomerization of a molecular ion of nitrobenzene to the 2-nitrobenzene structure followed by the formation of a phenoxide ion in the autodetachment state. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 367–370, February, 2006.