Comparison of DNA binding across protein superfamilies

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Comparison of DNA binding across protein superfamilies Running title: Analysis of DNA-binding superfamilies

Specific protein-DNA interactions are central to a wide group of processes in the cell and have been studied both experimentally and computationally over the years. Despite the increasing collection of protein-DNA complexes, so far only a few studies have aimed at dissecting the structural characteristics of DNA binding among evolutionarily related proteins. Some questions that remain to be ans...

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Comparative Investigation of R213G Mutation in DNA-Binding Domain of P53 Protein via Molecular Dynamics Simulation

Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...

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Physical origins of protein superfamilies.

In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using a standard exact three-dimensional lattice model we evolve sequences starting from random ones and determine the exact native structure after each mutation. Acceptance of mutations is biased to select for stable proteins. We found that certain str...

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ژورنال

عنوان ژورنال: Proteins: Structure, Function, and Bioinformatics

سال: 2009

ISSN: 0887-3585

DOI: 10.1002/prot.22525