How protein structure prediction can play a role in aiding plant science research

Zeti Azura M. H., . (2004) How protein structure prediction can play a role in aiding plant science research. [Proceedings Paper]

The aim of this paper is to explicate the protein structure prediction knowledge in generating models where these models can provide the structural insights that are often needed to understand protein function. Protein models have been proven useful for the rational mutagenesis experiment design and molecular replacement in crystallography and during drug design projects or enzymatic inhibition and allowed the taking of key decisions in compound optimization and chemical synthesis. Models can be classified with reference to their correctness and accuracy which will impact their applicability and usefulness in functional genomics and a variety of situations. Besides describing the protein structure prediction approaches and its importance in other biological field this paper includes the results of structure prediction on the parallel -helix proteins where most of the proteins in this category are involved in plant pathogenesis as well as in plant development. With the aid of the in silico approach the sequences which were likely to adopt the parallel -helix fold from selected protein databases were retrieved. These sequences were clustered into seven families of pectin lyase-like superfamily. By using the comparative modeling and fold recognition approaches models for these families were generated via a large-scale automatic modeling procedure. These models were regarded as high-confidence models due to the very stringent criteria that have been applied on the datasets as well as the meticulous multiple sequence alignments production for the modeling purposes. In addition to models production this research has revealed numerous uncommon conditions in these proteins. These include the possible cysteine stacks at the same equivalent positions of asparagines ladders in the -helix core the identification of common profile in the parallel -helix proteins and the finding of cysteine patterns that showed the occurrence of bridged and unpaired cysteines in the same protein which was previously known as an unusual circumstance. Detailed study should be performed on these findings as there will be some interesting explanation to corroborate the prediction results by the wet-lab experiments. In addition due to their high quality and accuracy these models will also provide a valuable resource for the wet-lab scientists who are interested in this enzyme.

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Abstract

The aim of this paper is to explicate the protein structure prediction knowledge in generating models where these models can provide the structural insights that are often needed to understand protein function. Protein models have been proven useful for the rational mutagenesis experiment design and molecular replacement in crystallography and during drug design projects or enzymatic inhibition and allowed the taking of key decisions in compound optimization and chemical synthesis. Models can be classified with reference to their correctness and accuracy which will impact their applicability and usefulness in functional genomics and a variety of situations. Besides describing the protein structure prediction approaches and its importance in other biological field this paper includes the results of structure prediction on the parallel -helix proteins where most of the proteins in this category are involved in plant pathogenesis as well as in plant development. With the aid of the in silico approach the sequences which were likely to adopt the parallel -helix fold from selected protein databases were retrieved. These sequences were clustered into seven families of pectin lyase-like superfamily. By using the comparative modeling and fold recognition approaches models for these families were generated via a large-scale automatic modeling procedure. These models were regarded as high-confidence models due to the very stringent criteria that have been applied on the datasets as well as the meticulous multiple sequence alignments production for the modeling purposes. In addition to models production this research has revealed numerous uncommon conditions in these proteins. These include the possible cysteine stacks at the same equivalent positions of asparagines ladders in the -helix core the identification of common profile in the parallel -helix proteins and the finding of cysteine patterns that showed the occurrence of bridged and unpaired cysteines in the same protein which was previously known as an unusual circumstance. Detailed study should be performed on these findings as there will be some interesting explanation to corroborate the prediction results by the wet-lab experiments. In addition due to their high quality and accuracy these models will also provide a valuable resource for the wet-lab scientists who are interested in this enzyme.

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Item Type:	Proceedings Paper
Additional Information:	Available at Perpustakaan Sultan Abdul Samad Universiti Putra Malaysia 43400 UPM Serdang Selangor Malaysia. QK710.2 M239 2004 Call Number
AGROVOC Term:	Proteins
AGROVOC Term:	Protein synthesis
AGROVOC Term:	Protein content
AGROVOC Term:	Prediction
AGROVOC Term:	Scientific research
AGROVOC Term:	Laboratory experimentation
AGROVOC Term:	Pathogenesis
AGROVOC Term:	Models
AGROVOC Term:	Plant developmental stages
AGROVOC Term:	Plant pathology
Geographical Term:	MALAYSIA
Depositing User:	Ms. Suzila Mohamad Kasim
Last Modified:	24 Apr 2025 05:15
URI:	http://webagris.upm.edu.my/id/eprint/12840

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