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Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal.

Shrivastava D, Nain V, Sahi S, Verma A, Sharma P, Sharma PC, Kumar PA - Bioinformation (2011)

Bottom Line: Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy.Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch.Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

View Article: PubMed Central - PubMed

ABSTRACT
Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED- 4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

No MeSH data available.


Related in: MedlinePlus

A. Superimposition of main chain alpha trace atoms of S. melongena CC-NBS (green) and C. elegans apoptosis regulator (magenta);  B. Identification of cavities on CC-NBS surface; C-D. Interactions of conserved residues present in active site of S. melongena CC-NBS with ADP (C) and ATP (D) using Ligplot.
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Figure 3: A. Superimposition of main chain alpha trace atoms of S. melongena CC-NBS (green) and C. elegans apoptosis regulator (magenta); B. Identification of cavities on CC-NBS surface; C-D. Interactions of conserved residues present in active site of S. melongena CC-NBS with ADP (C) and ATP (D) using Ligplot.

Mentions: The MD trajectories obtained were analysed to study the behaviour of the structure. Figure 2A shows energy plot with respect to time for the complete 5 ns simulation. Comparison of the initial model obtained from homology modeling with the frames from MD trajectories shows that there are pronounced structural fluctuations with root mean square deviations of 2.5-3.0Å (Figure 2B). The frames were then taken from the production phase and analysed further. RMSD for backbone atoms was >1.2 Å revealing that structural fluctuations are not highly pronounced and consistent over frames obtained from production phase (Figure 2C). Overlapping the different conformations from the latter half of the trajectories shows that the molecule is relatively rigid, an indicative of structure stability. The average structure from the production phase frames was taken as the final model. The structural superimposition of Ca trace of CED-4 template and S. melongena CC-NBS shows RMSD of 0.9 A° with an identity score of 0.14 and TM score of 0.52 (Figure 3A).


Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal.

Shrivastava D, Nain V, Sahi S, Verma A, Sharma P, Sharma PC, Kumar PA - Bioinformation (2011)

A. Superimposition of main chain alpha trace atoms of S. melongena CC-NBS (green) and C. elegans apoptosis regulator (magenta);  B. Identification of cavities on CC-NBS surface; C-D. Interactions of conserved residues present in active site of S. melongena CC-NBS with ADP (C) and ATP (D) using Ligplot.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3046036&req=5

Figure 3: A. Superimposition of main chain alpha trace atoms of S. melongena CC-NBS (green) and C. elegans apoptosis regulator (magenta); B. Identification of cavities on CC-NBS surface; C-D. Interactions of conserved residues present in active site of S. melongena CC-NBS with ADP (C) and ATP (D) using Ligplot.
Mentions: The MD trajectories obtained were analysed to study the behaviour of the structure. Figure 2A shows energy plot with respect to time for the complete 5 ns simulation. Comparison of the initial model obtained from homology modeling with the frames from MD trajectories shows that there are pronounced structural fluctuations with root mean square deviations of 2.5-3.0Å (Figure 2B). The frames were then taken from the production phase and analysed further. RMSD for backbone atoms was >1.2 Å revealing that structural fluctuations are not highly pronounced and consistent over frames obtained from production phase (Figure 2C). Overlapping the different conformations from the latter half of the trajectories shows that the molecule is relatively rigid, an indicative of structure stability. The average structure from the production phase frames was taken as the final model. The structural superimposition of Ca trace of CED-4 template and S. melongena CC-NBS shows RMSD of 0.9 A° with an identity score of 0.14 and TM score of 0.52 (Figure 3A).

Bottom Line: Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy.Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch.Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

View Article: PubMed Central - PubMed

ABSTRACT
Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED- 4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

No MeSH data available.


Related in: MedlinePlus