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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Published on: August 16, 2017

A scheme for multiple sequence alignment optimization--an improvement based on family representative mechanics

Xin Liu1, Ya-Pu Zhao

  • 1The State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, No. 15 Beisihuanxi Road, Beijing 100190, China. liuxin@lnm.imech.ac.cn

Journal of Theoretical Biology
|September 8, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a new method to improve protein sequence alignment by analyzing hydrophobic interactions. This hydrophobic network analysis enhances alignment accuracy, particularly for distantly related proteins.

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

  • Computational Biology
  • Biophysics
  • Bioinformatics

Background:

  • Sequence alignment is crucial for understanding protein structure and function.
  • Existing alignment algorithms can be improved by better incorporating residue correlations.
  • Hydrophobicity plays a key role in protein folding and stability.

Purpose of the Study:

  • To develop a novel scoring scheme that enhances protein sequence alignment quality.
  • To better account for residue-residue correlations using hydrophobic interactions.
  • To improve the performance of multiple sequence alignment algorithms.

Main Methods:

  • A coarse-grained approach was used to model hydrophobic forces between residues.
  • An intramolecular hydrophobic force network was constructed for each protein.
  • The deviation of a protein's network from background networks was used as a score.

Main Results:

  • The hydrophobic force network effectively characterizes protein properties related to hydrophobicity.
  • Homologous proteins share common network features reflecting conserved biological properties.
  • The proposed scoring method significantly improved the identification of structurally similar residue segments (approx. 50% increase at low identity).

Conclusions:

  • The novel scoring scheme, based on intramolecular hydrophobic force networks, enhances multiple sequence alignment.
  • This method offers a complementary approach to existing algorithms, improving their efficiency and accuracy.
  • The findings highlight the importance of hydrophobic interactions in protein evolution and conservation.