RESUMEN
A method and software tool to develop patterns of protein families has been designed. These patterns are intended for the identification of local similarities in arbitrary amino acid sequences with proteins of the SWISS-PROT bank. The method is based on the physical, chemical and structural properties of amino acids. It assembles a 'best set' of elements (a pattern) for a given group of aligned related proteins. These elements provide discrimination between proteins of a family and representatives of other families or random sequences. The method combines the advantages of BLOCKS (automatic generation of multiple elements for protein groups), PROSITE (simplicity of element presentation) and matrices/profiles (different distinctions between amino acids for different positions of aligned sequences). Using our method, a data bank of protein family patterns, PROF_PAT, is produced. This data bank is based on the 27,752 amino acid sequences of SWISS-PROT bank release 24. The characteristics of patterns of 743 related protein groups are described. The results of comparisons of PROF_PAT patterns with the proteins of the SWISS-PROT bank are discussed.
Asunto(s)
Bases de Datos Factuales , Proteínas/genética , Programas Informáticos , Algoritmos , Secuencia de Aminoácidos , Animales , Humanos , Datos de Secuencia Molecular , Alineación de Secuencia , Homología de Secuencia de AminoácidoRESUMEN
A bank of images of protein families (PROF IMAGE bank) is developed using early published method and amino acid sequences of 24-th release SWISS-PROT bank (27752 sequences). The method relies on physical-chemical and structural properties of amino acids and on the choice of fragments of protein families for the most discriminate distinction of amino acid sequences of a family from representatives of other families or random sequences. Specifications of the algorithms of building the images, principles of amino acid sequences selection to form protein families, the structure of the bank, and characteristics of images of 163 protein families are described. The data are illustrated by the image of alpha-interferon precursors family. The results of the images comparison with all proteins of the SWISS-PROT bank and ways to use the PROF IMAGE bank for determination of possible functions of amino acid sequences are discussed.
Asunto(s)
Sistemas de Información , Proteínas/química , Algoritmos , Secuencia de Aminoácidos , Datos de Secuencia Molecular , Proteínas/metabolismo , Relación Estructura-ActividadRESUMEN
A new theoretical approach to elaboration of an information-analytical integrated knowledge base containing data on regulation and function of biological systems is presented. The knowledge base incorporates: (i) a reference database containing experimental data on the structural-functional organization of a biological system; (ii) a dynamic mathematical model for analysis of the evolution of the system over time; and (iii) an interpretation module of simulation results. Application of this approach to theoretical investigation of the interferon system in the case of viral infection is discussed. The approach is specific in that it uses mathematical modeling technology, which allows one to generate mathematical models of different degrees of complexity in the analysis of the diverse aspects of biological system behavior. This approach allows one not only to store and to treat available experimental data, but also to acquire new knowledge about the behavior of a biological system. The proposed approach is implemented as a computer system for the IBM PC and compatibles.
Asunto(s)
Inteligencia Artificial , Regulación de la Expresión Génica , Interferones/genética , Algoritmos , Gráficos por Computador , Computadores , Interferones/biosíntesis , Interferones/fisiología , Modelos TeóricosRESUMEN
A method to develop images of protein families for fast comparison with any amino acid sequences is proposed. The method is based on physico-chemical properties of amino acids and on the choice of fragments of amino acid sequences of protein families that maximally distinguish the sequences from members of other families or random sequences. The efficiency of the method is demonstrated on comparison of images developed for protein families of alpha-interferons, alpha-hemoglobins, long neurotoxins, and DNA polymerases with the SWISS-PROT data bank.
Asunto(s)
Proteínas/química , Homología de Secuencia de Aminoácido , ADN Polimerasa Dirigida por ADN/química , Hemoglobinas/química , Interferones/química , Neurotoxinas/químicaAsunto(s)
Genoma , Análisis de Secuencia de ADN , Análisis de Secuencia de ADN/métodos , Algoritmos , Secuencia de Aminoácidos , Secuencia de Bases , ADN/genética , Matemática , Modelos Genéticos , Datos de Secuencia Molecular , Secuencias Repetitivas de Ácidos Nucleicos , Análisis de Secuencia de ADN/estadística & datos numéricos , Homología de Secuencia de Ácido Nucleico , Teoría de SistemasAsunto(s)
Genoma , Análisis de Secuencia de ADN/métodos , Secuencia de Aminoácidos , Secuencia de Bases , ADN/genética , Modelos Genéticos , Datos de Secuencia Molecular , Secuencias Repetitivas de Ácidos Nucleicos , Análisis de Secuencia de ADN/estadística & datos numéricos , Homología de Secuencia de Ácido Nucleico , Teoría de SistemasRESUMEN
The suggested earlier complexity approach for detecting structural regularities in primary structures of nucleic acids is illustrated by using lambda phage as an example. Among the most interesting regularities detected in the lambda phage genome are the following: (a) the presence of "extended homology zones" i.e. fragments in which block transpositions of duplicative type predominate explicitly; (b) the abundance of palindrome-hairpin structures and duplications in the origins and termini of many genes; (c) the hierarchy in the repeats and inversions organization.
Asunto(s)
Bacteriófago lambda/genética , Biblioteca Genómica , Homología de Secuencia de Ácido Nucleico , Secuencia de Bases , Genes Virales , Datos de Secuencia Molecular , Conformación de Ácido NucleicoRESUMEN
A new computer method for detecting local structural regularities in genomes of different microorganisms is described. The method is based on the concepts of complexity and complexity profile of a finite sequence. The complexity measure taking into account the specificity of genetic texts (presence of repeats, symmetries, inversions) is proposed. The genomes of different viruses and bacteriophages contained in Genbank were processed. The classification and interpretation of structural regularities were carried out.
Asunto(s)
Biblioteca Genómica , Bacteriófagos/genética , Secuencia de Bases , Genes Virales , Datos de Secuencia Molecular , Regiones Promotoras Genéticas , Virus/genéticaRESUMEN
The mathematical formalization of the conceptual model for antiviral immune response regulation described in the preceding report was carried out. The mathematical model is presented as a system of 30 ordinary nonlinear differential equations with delays. The algorithm for numerical integration of the mathematical model is based on Gear's methods of variable step and variable order. Initial conditions and parameters, as well as intervals of plausible values for them, were chosen for adaptation of the model for description of acute hepatitis B.
Asunto(s)
Hepatitis B/inmunología , Modelos Biológicos , Subgrupos de Linfocitos T/inmunología , Linfocitos T Colaboradores-Inductores/inmunología , Enfermedad Aguda , Anticuerpos contra la Hepatitis B/biosíntesis , Virus de la Hepatitis B/inmunología , Humanos , Interleucina-1/biosíntesis , Interleucina-2/biosíntesis , Interleucina-4/biosíntesis , Células Asesinas Naturales/inmunología , Activación de MacrófagosRESUMEN
Genes encoding virus-specific late proteins with molecular mass 36 kDa and 12 kDa were mapped in HindIII-P DNA fragment of vaccinia virus strain L-IVP by hybrid selection of RNA to cloned DNA fragments followed by in vitro translation. RNA origin site of the 36K protein was detected in HindIII-J fragment. Nucleotide sequences of these genes were determined. Amino acid sequences of the 36K and 12K polypeptides were compared with the protein bank PIR.
Asunto(s)
ADN Viral/genética , Genes Virales , Virus Vaccinia/genética , Proteínas Virales/genética , Secuencia de Aminoácidos , Secuencia de Bases , Southern Blotting , Desoxirribonucleasa HindIII , Datos de Secuencia Molecular , Peso Molecular , ARN Viral/genética , Mapeo Restrictivo , Proteínas Virales/químicaRESUMEN
Based on the protein sequence data bank (PIR), the "variable fragment" bank, comprising pairs of closely related proteins, containing one or more strongly differing sites of primary structures was formed. The bank includes 465 "variable fragments" of 383 protein pairs. Amino acid residues composition of "variable fragments" was examined and indexes of potential amino acid residues variability was formed. An analysis of amino acid fragments replaceability was carried out by substituting the N-, C-terminal, or middle part of a chain), the fragments length differences and physico-chemical properties of residues, such as volume, hydrophobicity, polarity, isoelectric point, etc. Some general empirical rules of peptide insertions in carrier-proteins were created based on these analyses. The rules are directed for performing modifications maintaining the common structure and function of the carrier-protein molecule. The selection scheme for determining the regions suitable for modification and the criteria for defining the width of acceptable modifications in this regions were suggested. The use of potential variability profile for detecting regions suitable for peptide insertion was considered on the model of hepatitis B surface protein.
Asunto(s)
Fragmentos de Péptidos/análisis , Ingeniería de Proteínas , Vacunas Sintéticas , Vacunas , Secuencia de Aminoácidos , Datos de Secuencia Molecular , Homología de Secuencia de Ácido NucleicoRESUMEN
Based on protein sequence databank (PIR), the 'variable fragment' bank, comprising pairs of closely-related proteins, containing one or more strongly differing sites of primary structures, was formed. The bank includes 465 'variable fragments' in 383 protein pairs. The amino acid composition of 'variable fragments' was examined and indices of potential amino acid residue variability were formed. An analysis of the interchangeability of amino acid fragments depending on the substitution site (N- or C-terminal, or middle part of a chain), the fragment length differences and physico-chemical properties of residues, such as volume, hydrophobicity, polarity and isoelectric point, was carried out. Based on this analysis some general empirical rules of peptide insertions in carrier proteins were created. The rules are directed at performing modifications leaving the general structure and function of the carrier protein molecule unchanged. The selection scheme for the regions suitable for modification and the criteria for determination of the range of acceptable variations in these regions were suggested. The use of the potential variability profile for detecting regions suitable for peptide insertion was considered using surface protein of hepatitis B virus as an example.
Asunto(s)
Fragmentos de Péptidos , Ingeniería de Proteínas , Vacunas Sintéticas , Vacunas , Secuencia de Aminoácidos , Aminoácidos/análisis , Datos de Secuencia Molecular , Homología de Secuencia de Ácido NucleicoRESUMEN
Frequency distributions of adjacent ARs in the primary structures of 320 globular proteins out of different superfamilies were investigated. ARs of every type were compared with the occurrence frequencies of 20 canonic residues at the distances of 1-20 residues according to their primary structure. Amino acid residues were found to be divided into groups of interchangeable residues in the course of globular protein evolution according to the distribution kinds and in terms of Euclidean distances. The use of pancreatic RNases of mammals showed that the approximate preservation of frequency adjacent (1-4 residues according to their primary structure) and characteristics in 5-15 residues mid-interactions may be used in studying the supposed amino acid substitutions in globular protein.
Asunto(s)
Aminoácidos/genética , Mutación , Proteínas/genética , Secuencia de Aminoácidos , Aminoácidos/análisis , Animales , Humanos , Matemática , Modelos Moleculares , Datos de Secuencia Molecular , Proteínas/análisisRESUMEN
A correlation of the localization of functionally important regions with places having low and high values on twelve profiles built on a basis of amino acid sequences was analysed using a broad set of proteins. The profiles of hydrophilicity, resemblance to the sequences of human proteins, flexibility, mutability and others were considered. The resemblance profile was plotted by the program fixing short similar fragments in the testing protein and 92 human ones. The active centres were shown to be located in the primary structure regions having relatively low values on the resemblance profiles. Similar effect was observed in the mutability and alpha-helicity profiles. The potential functionally important sites of the human leukocyte interferon and interleukin-2 isolated on the basis of the analysis of this profiles were in accord with the available literary data.
Asunto(s)
Aminoácidos , Proteínas , Sitios de Unión , Evolución Biológica , Humanos , Mutación , Conformación ProteicaRESUMEN
Using gene fragments encoding the leader peptide of E. coli tryptophane operon (as duplicated fragment HhaI-140) or M13 phage coat protein (as TaqI-381 or HaeIII-1623 fragments) and basing on pDS1 family of plasmids, expression vectors have been constructed which contained transcription promoters Ptrp, PVIII, and Pv + PVIII, respectively. An artificial gene for human leukocyte interferon alpha 2 (ifn-alpha 2) has been cloned into these plasmids, so that its transcription was a part of polycistronic mRNA and preceding translation was terminated upstream to the ribosome binding site and starting codon of the interferon gene. E. coli cells harbouring these recombinant plasmids provided high level of the interferon biosynthesis. The effect of the mRNA length on the amount of protein synthesised under control of the M13 coat protein transcription-translation signals has been found.
Asunto(s)
Genes Sintéticos , Genes , Vectores Genéticos , Operón , Plásmidos , Secuencia de Bases , Colifagos/genética , Escherichia coli/genética , Regulación de la Expresión Génica , Genes Bacterianos , Genes Virales , Datos de Secuencia Molecular , Señales de Clasificación de Proteína/genética , ARN Mensajero/genética , Recombinación Genética , Triptófano/genética , Proteínas del Envoltorio Viral/genéticaRESUMEN
Using a chemically synthesised adapter, the coding part of an artificial gene for human leukocyte alpha 2 interferon (ifn-alpha 2) has been duplicated. The adapter contained a termination signal of the first gene (TAA) within the Shine-Dalgarno sequence of the second gene (TAAGGA), distance between the terminating codon and starting codon of the second gene being 11 nucleotides. In another case this distance was 69 nucleotides, with the same SD sequence. The expression of the tandems as a part of polycistrons has been studied under control of promoters Plac, (Ptrp)2 of E. coli, and PVIII of M13 phage. It was found that tandems of ifn-alpha 2 genes in polycistronic structures trp L-ifn-ifn and IX-VIII-ifn-ifn under control of promoters (Ptrp)2 and PVIII, respectively, provided high level of the interferon biosynthesis, thus differing from the tandem under Plac promoter control, which had only ifn-ifn translation coupling.
Asunto(s)
Regulación de la Expresión Génica , Genes Sintéticos , Interferón Tipo I/genética , Familia de Multigenes , Biosíntesis de Proteínas , Escherichia coli/genética , Genes , Humanos , Plásmidos , ARN Mensajero/genéticaRESUMEN
For automation of segmental solid-phase synthesis a simple approach leading to the optimal scheme of synthesis of a large numbers of oligonucleotides in one reaction vessel has been proposed. An advantage of the scheme as compared with synthesis in four reaction vessels is a lower number of condensation steps and increased economy of the process. Sixteen oligodeoxyribonucleotides constituting promoter fragment of the viral genome have been synthesised by the modified segmental method on "Victoriya-2" synthesizer according to the optimal scheme.