RESUMO
Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.
Assuntos
Genes de Helmintos/genética , Genes Mitocondriais/genética , Código Genético , Genoma Mitocondrial , Helmintos/genética , Sequências Repetidas Invertidas/genética , Sequência de Aminoácidos , Animais , Composição de Bases , Sequência de Bases , DNA de Helmintos/genética , DNA Ribossômico/genética , Complexo I de Transporte de Elétrons/genética , Evolução Molecular , Feminino , Proteínas de Helminto/genética , Masculino , Consumo de Oxigênio , RNA de Helmintos/genética , RNA Ribossômico 18S/genética , Seleção Genética , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Especificidade da EspécieRESUMO
A comparative analysis of all available structures of complexes of TATA-box binding proteins (TBPs) with DNA is performed. Conserved features of DNA-protein interaction are described, including nine amino acid residues that form conserved hydrogen bonds, 13 residues participating in formation of two conserved hydrophobic clusters at DNA-protein interface, and four conserved water-mediated contacts. Partial symmetry of conserved contacts reflects quasi-symmetry of TBP structure.
Assuntos
Proteína de Ligação a TATA-Box/química , Proteína de Ligação a TATA-Box/metabolismo , Sequência de Aminoácidos , Sequência Conservada , DNA/química , DNA/metabolismo , Ligação de Hidrogênio , Interações Hidrofóbicas e Hidrofílicas , Conformação Proteica , ÁguaRESUMO
The recent upgrade of nucleic acid-protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain-DNA complexes and 17 DNA-protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA-protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family.
Assuntos
Proteínas de Ligação a DNA/química , DNA/química , Bases de Dados Genéticas , DNA/metabolismo , Proteínas de Ligação a DNA/classificação , Proteínas de Ligação a DNA/metabolismo , Conformação de Ácido Nucleico , Estrutura Terciária de ProteínaRESUMO
The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.
Assuntos
Proteínas de Ligação a DNA/química , DNA/química , Bases de Dados de Proteínas , Proteínas de Ligação a RNA/química , RNA/química , Internet , Conformação de Ácido Nucleico , Estrutura Terciária de Proteína , Software , Interface Usuário-Computador , Água/químicaRESUMO
LAGLIDADG family of homing endonucleases are rare-cutting enzymes which recognize long target sequences and are of great interest in genome engineering. Despite advances in homing endonuclease engineering, effective methods of broadening the range of cleaved sequences are still lacking. Here, we present a study of conserved structural features of LAGLIDADG homing endonucleases that might aid further development of such methods. The protein-DNA interface of LAGLIDADG homing endonucleases differs considerably with the particular nuclease, and the analysis of conserved protein-DNA interactions could not identify any residues crucial for DNA binding and common to most nucleases of the family. For the homing endonuclease PI-SceI, a comparison of structural and experimental data derived from literature helped to identify 23 residues that are likely to be important for DNA binding. Analysis of the LAGLIDADG domain dimerization interface allowed the choosing of six positions that contribute to dimerization specificity most, while comparison of 446 sequences of LAGLIDADG endonucleases revealed groups of residues in these positions that appear to be most favorable for dimerization.
Assuntos
DNA/química , DNA/genética , Desoxirribonuclease I/química , Desoxirribonuclease I/genética , Análise de Sequência de DNA/métodos , Análise de Sequência de Proteína/métodos , Sequência de Aminoácidos , Sequência de Bases , Sítios de Ligação , Dados de Sequência Molecular , Ligação ProteicaRESUMO
Water molecules immobilized on a protein or DNA surface are known to play an important role in intramolecular and intermolecular interactions. Comparative analysis of related three-dimensional (3D) structures allows to predict the locations of such water molecules on the protein surface. We have developed and implemented the algorithm WLAKE detecting "conserved" water molecules, i.e. those located in almost the same positions in a set of superimposed structures of related proteins or macromolecular complexes. The problem is reduced to finding maximal cliques in a certain graph. Despite exponential algorithm complexity, the program works appropriately fast for dozens of superimposed structures. WLAKE was used to predict functionally significant water molecules in enzyme active sites (transketolases) as well as in intermolecular (ETS-DNA complexes) and intramolecular (thiol-disulfide interchange protein) interactions. The program is available online at http://monkey.belozersky.msu.ru/~evgeniy/wLake/wLake.html.
