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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

Alignment of S. melongena CC-NBS (query) with CED-4 (template), for homology modeling.
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Related In: Results  -  Collection


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Figure 1: Alignment of S. melongena CC-NBS (query) with CED-4 (template), for homology modeling.

Mentions: Initial CC-NBS structure was modelled with I-TASSER using APAF-1 and CED-4 as multiple templates. Ramachandran plot analysis of I-TASSSER model showed that only 80 percent residues were present in most favoured regions and 5 percent residues in disallowed regions (Table 2 see Table 2). Although I-TASSER failed to develop a satisfactory model but the predicted model guided sequence alignment of S. melongena CC-NBS with CED-4 chain B became an valuable input for further 3D structure modeling with HOMMER and SwissModel (Figure 1).


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)

Alignment of S. melongena CC-NBS (query) with CED-4 (template), for homology modeling.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Alignment of S. melongena CC-NBS (query) with CED-4 (template), for homology modeling.
Mentions: Initial CC-NBS structure was modelled with I-TASSER using APAF-1 and CED-4 as multiple templates. Ramachandran plot analysis of I-TASSSER model showed that only 80 percent residues were present in most favoured regions and 5 percent residues in disallowed regions (Table 2 see Table 2). Although I-TASSER failed to develop a satisfactory model but the predicted model guided sequence alignment of S. melongena CC-NBS with CED-4 chain B became an valuable input for further 3D structure modeling with HOMMER and SwissModel (Figure 1).

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