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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Multiresolution analysis uncovers hidden conservation of properties in structurally and functionally similar proteins
Gek-Huey Chua1, Arun Krishnan, Kuo-Bin Li
1Bioinformatics Institute, 30, Biopolis Street, #07-01, Matrix, Singapore.
Journal of Bioinformatics and Computational Biology
|January 25, 2007
Summary
This study reveals that physicochemical properties are conserved in protein kinase functional domains, even with varying sequences. Multiresolution analysis uncovers hidden characteristics and aids in identifying similar protein sequences.
Area of Science:
- Biochemistry
- Bioinformatics
- Structural Biology
Background:
- Protein structure and function depend on amino acid physicochemical properties.
- Current methods often average these properties, masking domain-specific variations.
- Understanding property conservation is key to deciphering protein function.
Purpose of the Study:
- To investigate the conservation of physicochemical properties within the protein kinase family.
- To apply a novel multiresolution analysis (MRA) technique to uncover hidden characteristics.
- To assess the utility of MRA in identifying functionally similar protein sequences.
Main Methods:
- Application of a novel wavelet-based multiresolution analysis (MRA).
- Analysis of physicochemical property conservation across the protein kinase family.
- Development of a prediction model for sequence similarity.
Main Results:
- Identified conserved physicochemical properties in the catalytic domain of protein kinases, independent of sequence identity.
- Observed property conservation at multiple frequency levels, correlating with known subdomain structures and functions.
- Detected structural differences reflected in waveform variations and mutations causing waveform distortions.
- Achieved high performance (93.7% recall, 96.75% precision) in cross-validation for sequence identification.
Conclusions:
- Multiresolution analysis effectively reveals conserved physicochemical properties in protein families.
- This approach enhances understanding of protein structure-function relationships and subdomain characteristics.
- The method shows significant potential for identifying functionally similar protein sequences, especially in challenging sequence similarity zones.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
02:26Conservation of Protein Domains
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
01:49Conserved Binding Sites
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
01:24Protein Organization
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.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
01:22Protein Folding
Overview
01:25Protein Folding
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...