Literature DB >> 25414269

Structure-based modeling of protein: DNA specificity.

Adam P Joyce, Chi Zhang, Philip Bradley, James J Havranek.   

Abstract

Protein:DNA interactions are essential to a range of processes that maintain and express the information encoded in the genome. Structural modeling is an approach that aims to understand these interactions at the physicochemical level. It has been proposed that structural modeling can lead to deeper understanding of the mechanisms of protein:DNA interactions, and that progress in this field can not only help to rationalize the observed specificities of DNA-binding proteins but also to allow researchers to engineer novel DNA site specificities. In this review we discuss recent developments in the structural description of protein:DNA interactions and specificity, as well as the challenges facing the field in the future.
© The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Keywords:  Binding specificity; Molecular modeling; Protein:DNA interactions; Structural modeling; Structure prediction; Transcription factor binding sites

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Substances：

Year:  2014        PMID： 25414269      PMCID： PMC4366589          DOI： 10.1093/bfgp/elu044

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN： 2041-2649            Impact factor:   4.241


  72 in total

1.  A systems approach to measuring the binding energy landscapes of transcription factors.

Authors:  Sebastian J Maerkl; Stephen R Quake
Journal:  Science       Date:  2007-01-12       Impact factor: 47.728

2.  Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.

Authors:  Michael F Berger; Anthony A Philippakis; Aaron M Qureshi; Fangxue S He; Preston W Estep; Martha L Bulyk
Journal:  Nat Biotechnol       Date:  2006-09-24       Impact factor: 54.908

Review 3.  The evolutionary significance of cis-regulatory mutations.

Authors:  Gregory A Wray
Journal:  Nat Rev Genet       Date:  2007-03       Impact factor: 53.242

Review 4.  Potential energy functions for protein design.

Authors:  F Edward Boas; Pehr B Harbury
Journal:  Curr Opin Struct Biol       Date:  2007-03-26       Impact factor: 6.809

5.  Molecular flexibility in protein-DNA interactions.

Authors:  Stefan Günther; Kristian Rother; Cornelius Frömmel
Journal:  Biosystems       Date:  2006-02-20       Impact factor: 1.973

Review 6.  Water at biomolecular binding interfaces.

Authors:  Zheng Li; Themis Lazaridis
Journal:  Phys Chem Chem Phys       Date:  2006-11-24       Impact factor: 3.676

7.  Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Authors:  Raluca Gordân; Ning Shen; Iris Dror; Tianyin Zhou; John Horton; Remo Rohs; Martha L Bulyk
Journal:  Cell Rep       Date:  2013-04-04       Impact factor: 9.423

8.  Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

Authors:  Trevor W Siggers; Barry Honig
Journal:  Nucleic Acids Res       Date:  2007-01-30       Impact factor: 16.971

9.  Quantifying similarity between motifs.

Authors:  Shobhit Gupta; John A Stamatoyannopoulos; Timothy L Bailey; William Stafford Noble
Journal:  Genome Biol       Date:  2007       Impact factor: 13.583

10.  PiDNA: Predicting protein-DNA interactions with structural models.

Authors:  Chih-Kang Lin; Chien-Yu Chen
Journal:  Nucleic Acids Res       Date:  2013-05-22       Impact factor: 16.971
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  5 in total

1.  Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.

Authors:  Abigail R Lambert; Jazmine P Hallinan; Rachel Werther; Dawid Głów; Barry L Stoddard
Journal:  Structure       Date:  2020-04-30       Impact factor: 5.006

Review 2.  DNA-protein interaction: identification, prediction and data analysis.

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Journal:  Mol Biol Rep       Date:  2019-03-26       Impact factor: 2.316

Review 3.  Transcription factor-DNA binding: beyond binding site motifs.

Authors:  Sachi Inukai; Kian Hong Kock; Martha L Bulyk
Journal:  Curr Opin Genet Dev       Date:  2017-03-27       Impact factor: 5.578

4.  The Non-continuum Nature of Eukaryotic Transcriptional Regulation.

Authors:  Gregory M K Poon
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

5.  The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Authors:  Rebecca F Alford; Andrew Leaver-Fay; Jeliazko R Jeliazkov; Matthew J O'Meara; Frank P DiMaio; Hahnbeom Park; Maxim V Shapovalov; P Douglas Renfrew; Vikram K Mulligan; Kalli Kappel; Jason W Labonte; Michael S Pacella; Richard Bonneau; Philip Bradley; Roland L Dunbrack; Rhiju Das; David Baker; Brian Kuhlman; Tanja Kortemme; Jeffrey J Gray
Journal:  J Chem Theory Comput       Date:  2017-05-12       Impact factor: 6.006
  5 in total

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