DbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions.

Ling Liu,Hongyun Gao,Yi Xiong,Julie C Mitchell,Xiaolei Zhu,Dong-Qing Wei

doi:10.1093/database/bay034

Abstract

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. 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. Database URL: http://zhulab.ahu.edu.cn/dbAMEPNI

Highlights

Protein–nucleic acid interactions play essential roles in cellular activities, and they dictate the development of complex multicellular organisms
Alanine scanning mutagenic experiments [1, 2], which measure the effect of alanine substitutions on binding affinity, can be helpful to extrapolate the mechanisms of protein–nucleic acid recognition
We have developed an extensive repository of alanine mutagenic data for protein–nucleic acid interfaces: dbAMEPNI, a database of Alanine Mutagenic Effects for Protein-Nucleic Acids Interaction. dbAMEPNI provides alanine mutagenic effects for over 859 mutations in 217 protein–nucleic acid complexes

Summary

Introduction

Protein–nucleic acid interactions play essential roles in cellular activities, and they dictate the development of complex multicellular organisms. Alanine scanning mutagenesis data can provide ‘hotspot’ information on protein–nucleic acids interfaces. We have developed an extensive repository of alanine mutagenic data for protein–nucleic acid interfaces: dbAMEPNI, a database of Alanine Mutagenic Effects for Protein-Nucleic Acids Interaction (http://zhulab.ahu.edu.cn/ dbAMEPNI).

Results

Conclusion