Amino Acid Interaction (INTAA) web server

Abstract

Large biomolecules—proteins and nucleic acids—are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein–DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein–DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid–deoxyribonucleotide pairs found at the protein–DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations.

A Missense Mutation in the UGDH Gene Is Associated With Developmental Delay and Axial Hypotonia

“…Arg317 locates to α13 (294-321) of the inter-subunit dimerization-associated three-helical bundle (α11-α13) of the hUGDH and is conserved across the homologs (Figure 3C). Analysis of the hUGDH, (PDB ID: 2Q3E) structure by Amino Acid Interaction (INTAA) web server (36) allowed us to calculate the Arg317 Interaction Energy Matrix (IEM) in the protein (36). The IEM analysis highlighted that Arg317 forms multiple contacts with the residues in the neighboring structural elements with strongest interactions being formed with Glu460, Thr461, Phe314, and Phe439 ( Figure 3D).…”

Novel molecular insights into the anti‐oxidative stress response and structure–function of a salt‐inducible cyanobacterial Mn‐catalase

“…Analysis of cavities in the protein structures were performed using CASTp 3.0 server (http://sts.bioe.uic.edu/castp/; Tian, Chen, Lei, Zhao, & Liang, ). INTAA web server (http://bioinfo.uochb.cas.cz/INTAA/) was used for calculation of the pairwise interaction energies in KatBWT or KatBF2V (Galgonek, Vymetal, Jakubec, & Vondrášek, ).…”

Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide-based inhibitor design

“…To determine the prodomain inhibitory mechanism, residue interactions between prodomain and catalytic domain of plasmodial and human partial zymogen complexes were evaluated using the Protein Interaction Calculator (PIC) web server [78]. The interaction energy of identified residues was evaluated using the amino acid interaction (AAI) web server [79]. PyMOL was used to visualise the resulting interactions.…”