title: Molecular recognition of avirulence protein (avrxa5) by eukaryotic transcription factor xa5 of rice (Oryza sativa L.): insights from molecular dynamics simulations.
abstract: The avirulence gene avrxa5 of bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) recognized by the resistant rice lines having corresponding resistance (xa5) gene in a gene-for-gene manner. We used a combinatorial approach involving protein-protein docking, molecular dynamics (MD) simulations and binding free energy calculations to gain novel insights into the gene-for-gene mechanism that governs the direct interaction of R-Avr protein. From the best three binding poses predicted by molecular docking, MD simulations were performed to explore the dynamic binding mechanism of xa5 and avrxa5. Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) techniques were employed to calculate the binding free energy and to uncover the thriving force behind the molecular recognition of avrxa5 by eukaryotic transcription factor xa5. Binding free energy analysis revealed van der Waals term as the most constructive component that favors the xa5 and avrxa5 interaction. In addition, hydrogen bonds (H-bonds) and essential electrostatic interactions analysis highlighted amino acid residues Lys54/Asp870, Lys56/Ala868, Lys56/Ala866, Lys56/Glu871, Ile59/His862, Gly61/Phe858, His62/Arg841, His62/Leu856, Ser101/Ala872 and Ser105/Asp870 plays pivotal role for the energetically stability of the R-Avr complex. Insights gained from the present study are expected to unveil the molecular mechanisms that define the transcriptional activator mediated transcriptome modification in host plants.
authors: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India; Department of Life Science and Bioinformatics, Assam University, Silchar -788011, Assam, India. Electronic address: budheswar.dehury@gmail.com.
authors: Budheswar
authors: B
authors: Dehury
authors: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar -751003, Odisha, India.
authors: Jitendra
authors: J
authors: Maharana
authors: Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar -751003, Odisha, India.
authors: Bikash Ranjan
authors: BR
authors: Sahoo
authors: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India.
authors: Jagajjit
authors: J
authors: Sahu
authors: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India.
authors: Priyabrata
authors: P
authors: Sen
authors: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India.
authors: Mahendra Kumar
authors: MK
authors: Modi
authors: Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat -785013, Assam, India. Electronic address: m17barooah@yahoo.co.in.
authors: Madhumita
authors: M
authors: Barooah
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D012275:Oryza / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry*; D011485:Protein Binding; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry*; D014774:Virulence; D014974:Xanthomonas / Q000472:pathogenicity*
chemical_list: D001426:Bacterial Proteins; D010940:Plant Proteins; D014157:Transcription Factors
keywords: Binding free energy; Gene–for–gene; Hypersensitive response (HR); MM/PBSA; Molecular dynamics; Structural biology