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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Uncover the conserved property underlying sequence-distant and structure-similar proteins
1Department of Bioinformatics and Computer Science, University of the Sciences in Philadelphia, Philadelphia, PA 19104, USA.
Biopolymers
|November 6, 2009
Summary
Proteins with different sequences can share similar 3D structures. Analysis reveals conserved inter-residue interactions, like hydrophobic and hydrogen bonds, are key features in homologous protein structures, aiding protein folding prediction.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Protein structure is generally dictated by amino acid sequence.
- Proteins with low sequence identity can exhibit similar three-dimensional (3D) structures, prompting investigation into conserved properties governing protein folding and stability.
Purpose of the Study:
- To identify conserved properties in homologous protein structures with low sequence identity.
- To enhance understanding of protein folding mechanisms.
- To improve computational protein structure prediction tools.
Main Methods:
- Compiled and analyzed a dataset of 66 soluble protein structure pairs with low sequence identity (16-38%).
- Quantified structure deviation using C(alpha) SiMax values and per-residue potential energy.
- Analyzed inter-residue interactions, focusing on hydrophobic and hydrogen bonds.
Main Results:
- The average number of inter-residue interactions is a conserved feature in homologous structures despite low sequence identity.
- Specific interaction types, including hydrophobic and hydrogen bonds, showed unchanged average numbers between structure pairs.
- Structure deviation was confirmed via C(alpha) SiMax and potential energy per residue analysis.
Conclusions:
- Conserved inter-residue interaction counts are characteristic of homologous protein structures, even with distant sequences.
- Findings support the stability of protein structures through consistent interaction patterns.
- The results can improve homology modeling for proteins with low sequence identity, expanding its utility.
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The primary structure of a protein is its amino acid sequence.
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Overview