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Protein Organization01:24

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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A Protocol for Computer-Based Protein Structure and Function Prediction
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Systematic and Comparative Evaluation of Software Programs for Template-Based Modeling of Protein Structures.

Woo Dae Jang1, Sang Mi Lee2, Hyun Uk Kim2,3,4

  • 1Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.

Biotechnology Journal
|March 5, 2020
PubMed
Summary

Profile-based methods like PSI-BLAST excel in template-based modeling (TBM) for protein structure prediction. Model building software choice has minimal impact, except for challenging membrane protein cases.

Keywords:
model building programspairwise alignment methodsprotein structure modelingsoluble and membrane proteinstemplate-based modeling

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Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Structure Prediction

Background:

  • Protein structure modeling is essential for understanding protein function in biological and biotechnological applications.
  • Template-based modeling (TBM) is a widely adopted and reliable method for protein structure prediction.
  • Selecting optimal software for pairwise alignment and model building in TBM remains a challenge.

Purpose of the Study:

  • To compare the performance of different pairwise alignment methods for template-based modeling.
  • To evaluate the impact of different model building programs on protein structure model quality.
  • To provide guidance for accurate implementation of template-based modeling.

Main Methods:

  • Comparative analysis of pairwise alignment methods using comprehensive datasets.
  • Datasets include 6185 domain sequences from Structural Classification of Proteins (SCOP) and 259 Protein Data Bank (PDB) entries for membrane proteins.
  • Evaluation of structure model quality generated by alignment methods and model building programs (MODELLER, SWISS-MODEL).

Main Results:

  • Profile-based alignment methods, particularly PSI-BLAST, demonstrated consistently high performance across all datasets and evaluation metrics.
  • The choice between MODELLER and SWISS-MODEL for model building did not significantly impact model quality for most proteins.
  • A minor effect on model quality was observed for the 'Hard' group of membrane proteins when using different building programs.

Conclusions:

  • PSI-BLAST is recommended as a high-performing pairwise alignment tool for template-based modeling.
  • The selection of model building software has a limited impact on the overall quality of predicted protein structures.
  • These findings will aid in the more accurate and efficient application of template-based modeling techniques.