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In-Silico Characterization and Homology Modelling of Membrane Bound Proteins in Different Rice Cultivars

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Title In-Silico Characterization and Homology Modelling of Membrane Bound Proteins in Different Rice Cultivars
Not Available
 
Creator S. Kumar, Arup Kumar Mukherjee, S.R. Dash
 
Subject UniprotKB, SWISS model, homology modeling, Phospholipase D.
 
Description Not Available
Various stresses which include majorly drought, salt and metal ions present in the
soil adversely affects the growth and survival of the rice cultivars produced by various methods.
To combat these researchers and scientist with the help of computational and systems biology
are characterizing proteins involved for the resistance of these stresses to have the availability
and reach of the rice cultivar across the globe with cost effectiveness keeping in mind. There are
many of the proteins which are yet to be discovered, and many of them which have been
discovered do not have their 3-D structure determined. So, there comes the application of
homology modelling. Another reason for choosing homology modelling is, since proteins which
are targeted here are membrane bound, they are hard to crystallize hence homology modelling
becomes the most suitable way to determine and study their functionality. Proteins such as
remorin 1.4, Phospholipase D, HIR protein LT1A, LT1B are some of the proteins which came
into light after some research from already uploaded data from various journals and protein
databases such as the UniprotKB. Using the database proteins were characterized based on
biotic and abiotic stresses and proceeded accordingly. For modelling, an online software named
SWISS Model was used to select the template and even helped in making the whole model with
required scores to assess the quality of the model, respectively. To further refine the model
modrefiner online software was used to refine the model to the extent where its score is better
with bad angles and bonds removed respectively hence giving us a refined version of the model
compared to the ones made by SWISS model directly. Templates or reference sequences were
chosen based on ideal characteristics seen in Arabidopsis thaliana also seeing their sequence
similarity which were automatically shown in the SWISS Model. Managed to model three of the
total proteins mentioned which showed great scores after refining models. ERRAT online
software was also used to give us the verification of the structure obtained.
Not Available
 
Date 2023-04-10T11:33:19Z
2023-04-10T11:33:19Z
2023-01-01
 
Type Research Paper
 
Identifier S. Kumar, A.K. Mukherjee, S.R. Dash(2023).In-Silico Characterization and Homology Modelling of Membrane Bound Proteins in Different Rice Cultivars. Grenze International Journal of Engineering and Technology 9(1):1561-1567.
2395-5287
http://krishi.icar.gov.in/jspui/handle/123456789/76785
 
Language English
 
Relation Not Available;
 
Publisher GRENZE Scientific Society