ISSN print edition: 0366-6352 ISSN electronic edition: 1336-9075 Registr. No.: MK SR 9/7 Published monthly

Protein dynamics of five FMN binding protein isomers revealed by residue electrostatic energies between ionic residues: correlation coefficients

Nadtanet Nunthaboot, Kiattisak Lugsanangarm, Arthit Nueangaudom, Somsak Pianwanit, Sirirat Kokpol, Fumio Tanaka, Seiji Taniguchi, and Haik Chosrowjan

Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, Thailand

E-mail: nadtanet.n@msu.ac.th

Received: 17 September 2019  Accepted: 5 March 2020

Abstract:

Dynamics of protein structures of five FMN binding isomers, WT, E13K, E13R, E13T and E13Q, were studied through time-dependent residue electrostatic energies (RESTs) of ionic residues and their correlation coefficients. The Arg86 and Glu119 have high positive correlation coefficients which are higher than 0.7 in most of FBP isomers. The Glu23 and FMN, Asp24 and FMN, and Asp61 and Arg63 pairs displayed relatively high negative coefficients. In these residues, the distributions of RESTs showed a few peaks. REST pairs have high positive coefficients when distribution of REST of one residue overlapped with that of REST of another residue, while the REST pairs displayed high negative coefficients when a peak distribution of REST of one residue overlapped with a minimum distribution of another residue. Correlations of REST pairs were not simple and displayed a few groups. Relationships were examined among the correlation coefficients, inter-residue distance (R) and signs of the charge. In the case of R ≤ 1 nm, the total number of the pairs with high negative coefficients in all FBP isomers was much greater when the pairs possess opposite signs of the charge, compared to that when the pairs possess same signs of the charge.

Keywords: FMN binding protein; FBP; Protein dynamics; Electrostatic energy; Molecular dynamics simulation

Full paper is available at www.springerlink.com.

DOI: 10.1007/s11696-020-01128-y

Chemical Papers 74 (9) 2901–2915 (2020)