RESUMEN
Structures of many metal-binding proteins are often obtained without structural cations in their apoprotein forms. Missing cation coordinates are usually updated from structural templates constructed from many holoprotein structures. Such templates usually do not include structural water, the important contributor to the ion binding energy. Structural templates are also inconvenient for taking into account structural modifications around the binding site at apo-/holo- transitions. An approach based upon statistical potentials readily takes into account structural modifications associated with binding as well as contribution of structural water molecules. Here, we construct a set of statistical potentials for Mg2+, Ca2+, and Zn2+ contacting with protein atoms of a different type or structural water oxygens. Each type of the cations tends to form tight contacts with protein atoms of specific types. Structural water contributes relatively more into the binding pseudo-energy of Mg2+ and Ca2+ than of Zn2+. We have developed PIONCA (Protein-Ion Calculator), a fast CUDA GPGPU-based algorithm that predicts ion-binding sites in apoproteins. Comparative tests demonstrate that PIONCA outperforms most of the tools based on structural templates or docking. Our software can be also used for locating bound cations in holoprotein structures with missing cation heteroatoms. PIONCA is equipped with an interactive web interface based upon JSmol.
Asunto(s)
Apoproteínas/química , Cationes/química , Metales/química , Agua/química , Algoritmos , Apoproteínas/metabolismo , Sitios de Unión , Cationes/metabolismo , Biología Computacional/métodos , Metales/metabolismo , Unión Proteica , Programas Informáticos , TermodinámicaRESUMEN
Monocytes were isolated from blood of patients belonging to three groups: those with normal intima-media thickness (IMT) of carotid arteries, patients with increased IMT and patients with atherosclerotic plaques. The degree of activation of the macrophages was determined by the concentration of the cytokine TNF-α and chemokine CCL18 in the culture medium. When comparing the average values of the concentrations of TNF-α and CCL18 for patients in all groups dramatic individual differences were revealed. These individual differences were found within each group and in the pool. An inverse relationship between intracellular cholesterol levels and the ability of monocytes to activate was found. To clarify the cause of this relationship, monocytes were cultured with atherogenic modified low-density lipoprotein, causing accumulation of cholesterol in cultured cells. The accumulation of intracellular cholesterol had no effect neither on the secretion of cytokines nor on the expression of their genes. Therefore, individual differences in the activation capacity of monocytes is not determined by the accumulation of intracellular cholesterol caused by atherogenic lipoproteins. The data obtained can be explained by the individual characteristics of the immune response in different patients.
Asunto(s)
Aterosclerosis/sangre , Monocitos/metabolismo , Placa Aterosclerótica/sangre , Aterosclerosis/diagnóstico por imagen , Grosor Intima-Media Carotídeo , Quimiocinas CC/sangre , Colesterol/sangre , Estudios Transversales , Femenino , Humanos , Lipoproteínas LDL/sangre , Masculino , Placa Aterosclerótica/diagnóstico por imagen , Factor de Necrosis Tumoral alfa/sangreRESUMEN
MOTIVATION: Modern experimental methods provide substantial information on protein-DNA recognition. Studying arrangements of transcription factor binding sites (TFBSs) of interacting transcription factors (TFs) advances understanding of the transcription regulatory code. RESULTS: We constructed binding motifs for TFs forming a complex with HIF-1α at the erythropoietin 3(')-enhancer. Corresponding TFBSs were predicted in the segments around transcription start sites (TSSs) of all human genes. Using the genome-wide set of regulatory regions, we observed several strongly preferred distances between hypoxia-responsive element (HRE) and binding sites of a particular cofactor protein. The set of preferred distances was called as a preferred pair distance template (PPDT). PPDT dramatically depended on the TF and orientation of its binding sites relative to HRE. PPDT evaluated from the genome-wide set of regulatory sequences was used to detect significant PPDT-consistent binding site pairs in regulatory regions of hypoxia-responsive genes. We believe PPDT can help to reveal the layout of eukaryotic regulatory segments. CONTACT: ivan.kulakovskiy@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Sitios de Unión/genética , ADN/metabolismo , Regulación de la Expresión Génica/genética , Secuencias Reguladoras de Ácidos Nucleicos/genética , Factores de Transcripción/metabolismo , Secuencias de Aminoácidos/genética , Eritropoyetina/genética , Genoma , Humanos , Subunidad alfa del Factor 1 Inducible por Hipoxia/genética , Subunidad alfa del Factor 1 Inducible por Hipoxia/metabolismo , Motivos de Nucleótidos , Unión Proteica/genética , Proteínas/genética , Proteínas/metabolismo , Factores de Transcripción/genética , Sitio de Iniciación de la TranscripciónRESUMEN
SUMMARY: ChIP-Seq data are a new challenge for motif discovery. Such a data typically consists of thousands of DNA segments with base-specific coverage values. We present a new version of our DNA motif discovery software ChIPMunk adapted for ChIP-Seq data. ChIPMunk is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. ChIPMunk does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences. Comparison with traditional (MEME) or ChIP-Seq-oriented (HMS) motif discovery tools shows that ChIPMunk identifies the correct motifs with the same or better quality but works dramatically faster. AVAILABILITY AND IMPLEMENTATION: ChIPMunk is freely available within the ru_genetika Java package: http://line.imb.ac.ru/ChIPMunk. Web-based version is also available. CONTACT: ivan.kulakovskiy@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Inmunoprecipitación de Cromatina/métodos , Análisis de Secuencia de ADN/métodos , Secuencia de Bases , Sitios de Unión , ADN/química , ADN/metabolismo , Bases de Datos FactualesRESUMEN
MOTIVATION: Transcription regulatory protein factors often bind DNA as homo-dimers or hetero-dimers. Thus they recognize structured DNA motifs that are inverted or direct repeats or spaced motif pairs. However, these motifs are often difficult to identify owing to their high divergence. The motif structure included explicitly into the motif recognition algorithm improves recognition efficiency for highly divergent motifs as well as estimation of motif geometric parameters. RESULT: We present a modification of the Gibbs sampling motif extraction algorithm, SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo), which finds structured motifs of these types, as well as non-structured motifs, in a set of unaligned DNA sequences. It employs improved estimators of motif and spacer lengths. The probability that a sequence does not contain any motif is accounted for in a rigorous Bayesian manner. We have applied the algorithm to a set of upstream regions of genes from two Escherichia coli regulons involved in respiration. We have demonstrated that accounting for a symmetric motif structure allows the algorithm to identify weak motifs more accurately. In the examples studied, ArcA binding sites were demonstrated to have the structure of a direct spaced repeat, whereas NarP binding sites exhibited the palindromic structure. AVAILABILITY: The WWW interface of the program, its FreeBSD (4.0) and Windows 32 console executables are available at http://bioinform.genetika.ru/SeSiMCMC
Asunto(s)
Algoritmos , Proteínas de la Membrana Bacteriana Externa/genética , Proteínas de Unión al ADN/genética , Proteínas de Escherichia coli/genética , Modelos Genéticos , Reconocimiento de Normas Patrones Automatizadas/métodos , Proteínas Represoras/genética , Alineación de Secuencia/métodos , Análisis de Secuencia de ADN/métodos , Secuencia de Bases , Modelos Estadísticos , Datos de Secuencia Molecular , Secuencias Repetitivas de Ácidos Nucleicos/genéticaRESUMEN
UNLABELLED: We present a software system BASIO that allows one to segment a sequence into regions with homogeneous nucleotide composition at a desired length scale. The system can work with arbitrary alphabet and therefore can be applied to various (e.g. protein) sequences. Several sequences of complete genomes of eukaryotes are used to demonstrate the efficiency of the software. AVAILABILITY: The BASIO suite is available for non-commercial users free of charge as a set of executables and accompanying segmentation scenarios from http://www.imb.ac.ru/compbio/basio. To obtain the source code, contact the authors.
Asunto(s)
Genoma , Programas Informáticos , Algoritmos , Animales , Biología Computacional , Genómica/estadística & datos numéricos , Plasmodium falciparum/genética , Saccharomyces cerevisiae/genéticaRESUMEN
The nucleotide contents of the three codon positions show a number of statistical pairwise correlations, some of which are universal for all analysed genomes. Among the most prominent of these correlations are negative correlations between G and T contents found in genes of all species analysed. The pair A/C, which is complementary to G/T shows similar negative correlation in genes of most species. In the genes of several species including all mammalian genes studied, positive correlations between A and T contents, and G and C contents are found. Since these regularities are observed in all three codon positions they are connected with amino-acid content of proteins. Such correlations may origin from features of the mutation process or/and translation reading frame check. The well-known bias of the preference for G in the first codon position and its deficiency in the second is accompanied by opposite bias in T content. In the third codon position there is no general nucleotide preference, but its content is often biased with regard to GC content of the gene. G and T contents in this case are always shifted in the opposite directions Several ideas are drawn to explain this preference.