title: Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks.
abstract: BACKGROUND
  Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability.
  
  
  METHODS
  In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues.
  
  
  RESULTS
  The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs.
  
  
  CONCLUSIONS
  In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. vijay@mbu.iisc.ernet.in
authors.forename: M S
authors.initials: MS
authors.lastname: Vijayabaskar
authors.forename: Saraswathi
authors.initials: S
authors.lastname: Vishveshwara
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins