Elucidating the protein cold-adaptation: Investigation of the parameters enhancing protein psychrophilicity

Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures

“…This can probably be explained by Fleming et al's finding that packing density is in general similar for conserved domains of homologous proteins within a protein family, while for buried residues in these domains the packing densities are not the same because of distinct secondary structure at different loci (Fleming and Richards, 2000). While in our previous study we have detected only slight changes in the helical content of psychrophilic compared to mesophilic proteins, it can be inferred that packing density may not be significantly different between the psychrophilic-mesophilic homologous protein pairs (Jahandideh et al, 2008). Nevertheless, psychrophilicity rules are completely different from thermophilicity of proteins to expect less compact density for psychrophilic proteins compared to thermophilic proteins (Robinson-Rechavi and Godzik, 2005).…”

“…To investigate the differences, we compared several structural properties; molecular weight (MW) per residues Q7 , radius of gyration (ROG), hydrogen bond (HB), packing density (PD), accessible surface area (ASA), buried surface area (BSA), and number of cavities. These global parameters are assigned to general structures of psychrophilic/mesophilic pairs, while in our previous studies, local parameters attributed to specific locations of proteins have been discussed (Jahandideh et al, 2007a(Jahandideh et al, , 2007b(Jahandideh et al, , 2008. The results suggest some possible general rules for protein design experiments aimed to produce enzymes catalytically more effective at low temperatures.…”

“…significant difference in total open β-turn content, substitution of amino acids, distribution of amino acids in secondary structures, etc. (Jahandideh et al, 2007a(Jahandideh et al, , 2007b(Jahandideh et al, , 2008. In this study, we extended our previous database to 30 pairs of structurally defined proteins categorized as psychrophilic and mesophilic to examine a few physicochemical parameters involved in protein cold adaptation.…”

“…To address some of those important studies, comparative genomics studies for amino acid composition in some cold adapted organisms have shown higher content of noncharged polar amino acids and a lower content of hydrophobic amino acids as well as more propensity in solvent accessible area for some hydrophobic residues (Casanueva et al, 2010;Saunders et al, 2003). In addition, many researches have reported the difference in occurrence of some amino acid substitutions in psychrophilic proteins as a likely adaptation strategy by psychrophiles (Jahandideh et al, 2008;Methe et al, 2005). As for structural characterization of psychrophilic proteins and their pertinent adaptation process, cavities and clefts are indispensable factors to consider in cold-adaptation (Paredes et al, 2011).…”

Dynamic properties of extremophilic subtilisin-like serine-proteases

“…Moreover, an inventory of structural and molecular characteristics related to temperature adaptation in extremophilic enzymes came from several comparative statistical studies of cold-and heat-active enzymes (Berezovsky and Shakhnovich, 2005;Gianese et al, 2002;Jahandideh et al, 2008), pointing out that general theories cannot be formulated. Gu and Hilser (2009) also showed that there is no uniform modulation of conformational flexibility and stability across the components of the proteome of organisms adapted to different environmental conditions, as well as that apparent mechanisms of thermal adaptation differ from protein to protein.…”