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Title: dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acid complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.
Authors:
 [1] ;  [2] ;  [3] ;  [2] ;  [4] ;  [1]
  1. Anhui Univ., Hefei, Anhui (China). School of Life Sciences
  2. Shanghai Jiao Tong Univ. (China). State Key Lab. of Microbial Metabolism and School of Life Sciences and Biotechnology
  3. Dalian Univ., Dalian, Liaoning (China). Information and Engineering College
  4. Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry; Univ. of Wisconsin, Madison, WI (United States). Dept. of Mathematics; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
Publication Date:
Grant/Contract Number:
AC05-00OR22725
Type:
Accepted Manuscript
Journal Name:
Database
Additional Journal Information:
Journal Volume: 2018; Journal Issue: 1; Related Information: See also https://academic.oup.com/database/article/doi/10.1093/database/bay034/4959188; Journal ID: ISSN 1758-0463
Publisher:
Oxford University Press
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE; National Natural Science Foundation of China (NNSFC)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1435258

Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., and Zhu, Xiaolei. dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions. United States: N. p., Web. doi:10.1093/database/bay034.
Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., & Zhu, Xiaolei. dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions. United States. doi:10.1093/database/bay034.
Liu, Ling, Xiong, Yi, Gao, Hongyun, Wei, Dong-Qing, Mitchell, Julie C., and Zhu, Xiaolei. 2018. "dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions". United States. doi:10.1093/database/bay034. https://www.osti.gov/servlets/purl/1435258.
@article{osti_1435258,
title = {dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions},
author = {Liu, Ling and Xiong, Yi and Gao, Hongyun and Wei, Dong-Qing and Mitchell, Julie C. and Zhu, Xiaolei},
abstractNote = {Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acid complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.},
doi = {10.1093/database/bay034},
journal = {Database},
number = 1,
volume = 2018,
place = {United States},
year = {2018},
month = {4}
}