Record Details

Structure, Stability and Evolution of Multi-Domain Proteins

Electronic Theses of Indian Institute of Science

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Field Value
 
Title Structure, Stability and Evolution of Multi-Domain Proteins
 
Creator Bhaskara, Ramachandra M
 
Subject Protein Sequence
Protein Structure
Multi-Domain Proteins
GSTO-1
Full-length Proteins
Multi-Domain Proteins - Evolution
Multi-Domain Proteins - Folding
Human Glutathione S-Transferase Omega-1
Multi-Domain Proteins - 3D Modelling
Protein Folding
Proteins - Stability
Amino Acid Sequence
Single Nucleotide Polymophisms (SNPs)
Homologous Protein Structures
Biochemistry
 
Description Analyses of protein sequences from diverse genomes have revealed the ubiquitous nature of multi-domain proteins. They form up to 70% of proteomes of most eukaryotic organisms. Yet, our understanding of protein structure, folding and evolution has been dominated by extensive studies on single-domain proteins. We provide quantitative treatment and proof for prevailing intuitive ideas on the strategies employed by nature to stabilize otherwise unstable domains. We find that domains incapable of independent stability are stabilized by favourable interactions with tethered domains in the multi-domain context. Natural variations (nsSNPs) at these sites alter communication between domains and affect stability leading to disease manifestation. We emphasize this by using explicit all-atom molecular dynamics simulations to study the interface nsSNPs of human Glutathione S-transferase omega 1. We show that domain-domain interface interactions constrain inter-domain geometry (IDG) which is evolutionarily well conserved. The inter-domain linkers modulate the interactions by varying their lengths, conformations and local structure, thereby affecting the overall IDG. These findings led to the development of a method to predict interfacial residues in multi-domain proteins based on difference evolutionary information extracted from at least two diverse domain architectures (single and multi-domain). Our predictions are highly accurate (∼85%) and specific (∼95%). Using predicted residues to constrain domain–domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. Further, we developed and employed an alignment-free approach based on local amino-acid fragment matching to compare sequences of multi-domain proteins. This is especially effective in the absence of proper alignments, which is usually the case for multi-domain proteins. Using this, we were able to recreate the existing Hanks and Hunter classification scheme for protein kinases. We also showed functional relationships among Immunoglobulin sequences. The clusters obtained were functionally distinct and also showed unique domain-architectures. Our analysis provides guidelines toward rational protein and interaction design which have attractive applications in obtaining stable fragments and domain constructs essential for structural studies by crystallography and NMR. These studies enable a deeper understanding of rapport of protein domains in the multi-domain context.
 
Contributor Srinivasan, N
 
Date 2018-04-11T17:01:40Z
2018-04-11T17:01:40Z
2018-04-11
2013
 
Type Thesis
 
Identifier http://etd.iisc.ernet.in/2005/3384
http://etd.iisc.ernet.in/abstracts/4250/G25845-Abs.pdf
 
Language en_US
 
Relation G25845