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.
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Abbreviations
- ES:
-
Electrostatic energy
- EST:
-
Time-dependent ES
- ET:
-
Electron transfer
- E13K:
-
Glu13 of WT is replaced by Lys
- E13R:
-
Glu13 replaced by Arg
- E13T:
-
Glu13 replaced by Thr
- E13Q:
-
Glu13 replaced by Gln
- FMN:
-
Flavin mononucleotide
- FBP:
-
Flavin mononucleotide binding protein from Desulfovibrio vulgaris (Miyazaki F)
- MD:
-
Molecular dynamic
- R :
-
Inter-residue distance
- R (t):
-
Time-dependent R
- RES:
-
Residue electrostatic energy
- REST:
-
Time-dependent RES obtained by MD structures
- WT:
-
Wild-type FBP
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Acknowledgements
This research is supported by Ratchadapisek Somphot Fund for Postdoctoral Fellowship, Chulalongkorn University. N.N. acknowledges the Center of Excellence for Innovation in Chemistry (PERCH-CIC), Ministry of Higher Education, Science, Research and Innovation for financial support. S.T. acknowledges the financial support by the JSPS (KAKENHI Grant Number JP18K05050). K.L. acknowledges RGJ Advanced Programme (RAP60K003). The authors are grateful to the Center of Excellence in Computational Chemistry, Chulalongkorn University, for providing computing resources, software packages and computational sources.
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Nunthaboot, N., Lugsanangarm, K., Nueangaudom, A. et al. Protein dynamics of five FMN binding protein isomers revealed by residue electrostatic energies between ionic residues: correlation coefficients. Chem. Pap. 74, 2901–2915 (2020). https://doi.org/10.1007/s11696-020-01128-y
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DOI: https://doi.org/10.1007/s11696-020-01128-y