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Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions

The NADPH-dependent HC-toxin reductases (HCTR1 and 2) encoded by enzymatic class of disease resistance homologous genes (Hm1 and Hm2) protect maize by detoxifying a cyclic tetrapeptide, HC-toxin, secreted by the fungus Cochliobolus carbonum race 1(CCR1). Unlike the other classes' resistance (R)...

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Autores principales: Dehury, Budheswar, Patra, Mahesh Chandra, Maharana, Jitendra, Sahu, Jagajjit, Sen, Priyabrata, Modi, Mahendra Kumar, Choudhury, Manabendra Dutta, Barooah, Madhumita
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029905/
https://www.ncbi.nlm.nih.gov/pubmed/24847713
http://dx.doi.org/10.1371/journal.pone.0097852
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author Dehury, Budheswar
Patra, Mahesh Chandra
Maharana, Jitendra
Sahu, Jagajjit
Sen, Priyabrata
Modi, Mahendra Kumar
Choudhury, Manabendra Dutta
Barooah, Madhumita
author_facet Dehury, Budheswar
Patra, Mahesh Chandra
Maharana, Jitendra
Sahu, Jagajjit
Sen, Priyabrata
Modi, Mahendra Kumar
Choudhury, Manabendra Dutta
Barooah, Madhumita
author_sort Dehury, Budheswar
collection PubMed
description The NADPH-dependent HC-toxin reductases (HCTR1 and 2) encoded by enzymatic class of disease resistance homologous genes (Hm1 and Hm2) protect maize by detoxifying a cyclic tetrapeptide, HC-toxin, secreted by the fungus Cochliobolus carbonum race 1(CCR1). Unlike the other classes' resistance (R) genes, HCTR-mediated disease resistance is an inimitable mechanism where the avirulence (Avr) component from CCR1 is not involved in toxin degradation. In this study, we attempted to decipher cofactor (NADPH) recognition and mode of HC-toxin binding to HCTRs through molecular docking, molecular dynamics (MD) simulations and binding free energy calculation methods. The rationality and the stability of docked complexes were validated by 30-ns MD simulation. The binding free energy decomposition of enzyme-cofactor complex was calculated to find the driving force behind cofactor recognition. The overall binding free energies of HCTR1-NADPH and HCTR2-NADPH were found to be −616.989 and −16.9749 kJ mol(−1) respectively. The binding free energy decomposition revealed that the binding of NADPH to the HCTR1 is mainly governed by van der Waals and nonpolar interactions, whereas electrostatic terms play dominant role in stabilizing the binding mode between HCTR2 and NADPH. Further, docking analysis of HC-toxin with HCTR-NADPH complexes showed a distinct mode of binding and the complexes were stabilized by a strong network of hydrogen bond and hydrophobic interactions. This study is the first in silico attempt to unravel the biophysical and biochemical basis of cofactor recognition in enzymatic class of R genes in cereal crop maize.
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spelling pubmed-40299052014-05-28 Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions Dehury, Budheswar Patra, Mahesh Chandra Maharana, Jitendra Sahu, Jagajjit Sen, Priyabrata Modi, Mahendra Kumar Choudhury, Manabendra Dutta Barooah, Madhumita PLoS One Research Article The NADPH-dependent HC-toxin reductases (HCTR1 and 2) encoded by enzymatic class of disease resistance homologous genes (Hm1 and Hm2) protect maize by detoxifying a cyclic tetrapeptide, HC-toxin, secreted by the fungus Cochliobolus carbonum race 1(CCR1). Unlike the other classes' resistance (R) genes, HCTR-mediated disease resistance is an inimitable mechanism where the avirulence (Avr) component from CCR1 is not involved in toxin degradation. In this study, we attempted to decipher cofactor (NADPH) recognition and mode of HC-toxin binding to HCTRs through molecular docking, molecular dynamics (MD) simulations and binding free energy calculation methods. The rationality and the stability of docked complexes were validated by 30-ns MD simulation. The binding free energy decomposition of enzyme-cofactor complex was calculated to find the driving force behind cofactor recognition. The overall binding free energies of HCTR1-NADPH and HCTR2-NADPH were found to be −616.989 and −16.9749 kJ mol(−1) respectively. The binding free energy decomposition revealed that the binding of NADPH to the HCTR1 is mainly governed by van der Waals and nonpolar interactions, whereas electrostatic terms play dominant role in stabilizing the binding mode between HCTR2 and NADPH. Further, docking analysis of HC-toxin with HCTR-NADPH complexes showed a distinct mode of binding and the complexes were stabilized by a strong network of hydrogen bond and hydrophobic interactions. This study is the first in silico attempt to unravel the biophysical and biochemical basis of cofactor recognition in enzymatic class of R genes in cereal crop maize. Public Library of Science 2014-05-21 /pmc/articles/PMC4029905/ /pubmed/24847713 http://dx.doi.org/10.1371/journal.pone.0097852 Text en © 2014 Dehury et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Dehury, Budheswar
Patra, Mahesh Chandra
Maharana, Jitendra
Sahu, Jagajjit
Sen, Priyabrata
Modi, Mahendra Kumar
Choudhury, Manabendra Dutta
Barooah, Madhumita
Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title_full Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title_fullStr Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title_full_unstemmed Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title_short Structure-Based Computational Study of Two Disease Resistance Gene Homologues (Hm1 and Hm2) in Maize (Zea mays L.) with Implications in Plant-Pathogen Interactions
title_sort structure-based computational study of two disease resistance gene homologues (hm1 and hm2) in maize (zea mays l.) with implications in plant-pathogen interactions
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4029905/
https://www.ncbi.nlm.nih.gov/pubmed/24847713
http://dx.doi.org/10.1371/journal.pone.0097852
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