title: Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms.
abstract: BACKGROUND
  Understanding the basis of protein stability in thermophilic organisms raises a general question: what structural properties of proteins are responsible for the higher thermostability of proteins from thermophilic organisms compared to proteins from mesophilic organisms?
  
  
  RESULTS
  A unique database of 373 structurally well-aligned protein pairs from thermophilic and mesophilic organisms is constructed. Comparison of proteins from thermophilic and mesophilic organisms has shown that the external, water-accessible residues of the first group are more closely packed than those of the second. Packing of interior parts of proteins (residues inaccessible to water molecules) is the same in both cases. The analysis of amino acid composition of external residues of proteins from thermophilic organisms revealed an increased fraction of such amino acids as Lys, Arg and Glu, and a decreased fraction of Ala, Asp, Asn, Gln, Thr, Ser and His. Our theoretical investigation of folding/unfolding behavior confirms the experimental observations that the interactions that differ in thermophilic and mesophilic proteins form only after the passing of the transition state during folding. Thus, different packing of external residues can explain differences in thermostability of proteins from thermophilic and mesophilic organisms.
  
  
  BACKGROUND
  The database of 373 structurally well-aligned protein pairs is available at http://phys.protres.ru/resources/termo_meso_base.html.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Glyakina
authors.forename: Sergiy O
authors.initials: SO
authors.lastname: Garbuzynskiy
authors.forename: Michail Yu
authors.initials: MY
authors.lastname: Lobanov
authors.forename: Oxana V
authors.initials: OV
authors.lastname: Galzitskaya
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D020539:Sequence Analysis, Protein / Q000379:methods*; D013696:Temperature
chemical_list: D001426:Bacterial Proteins