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Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F15%3A00444348" target="_blank" >RIV/61388963:_____/15:00444348 - isvavai.cz</a>

  • Result on the web

    <a href="http://dx.doi.org/10.1021/ct501168n" target="_blank" >http://dx.doi.org/10.1021/ct501168n</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1021/ct501168n" target="_blank" >10.1021/ct501168n</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    Large-Scale Quantitative Assessment of Binding Preferences in Protein-Nucleic Acid Complexes

  • Original language description

    The growing number of high-quality experimental (X-ray, NMR) structures of protein-DNA complexes has sufficient enough information to assess whether universal rules governing the DNA sequence recognition process apply. While previous studies have investigated the relative abundance of various modes of amino acid-base contacts (van der Waals contacts, hydrogen bonds), relatively little is known about the energetics of these noncovalent interactions. In the present study, we have performed the first large-scale quantitative assessment of binding preferences in protein-DNA complexes by calculating the interaction energies in all 80 possible amino acid-DNA base combinations. We found that several mutual amino acid-base orientations featuring bidentate hydrogen bonds capable of unambiguous one-to-one recognition correspond to unique minima in the potential energy space of the amino acid-base pairs. A clustering algorithm revealed that these contacts form a spatially well-defined group offer

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

  • CEP classification

    CF - Physical chemistry and theoretical chemistry

  • OECD FORD branch

Result continuities

  • Project

    <a href="/en/project/LH11020" target="_blank" >LH11020: Systematic mapping of the conformational space of short peptides through molecular dynamics simulation - a way to understanding of protein structure formation.</a><br>

  • Continuities

    I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Others

  • Publication year

    2015

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Journal of Chemical Theory and Computation

  • ISSN

    1549-9618

  • e-ISSN

  • Volume of the periodical

    11

  • Issue of the periodical within the volume

    4

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    10

  • Pages from-to

    1939-1948

  • UT code for WoS article

    000353176500058

  • EID of the result in the Scopus database

    2-s2.0-84927762269