%0 Journal Article
%T Comparative void-volume analysis of psychrophilic and mesophilic enzymes: Structural bioinformatics of psychrophilic enzymes reveals sources of core flexibility
%A Diana I Paredes
%A Kyle Watters
%A Derek J Pitman
%A Christopher Bystroff
%A Jonathan S Dordick
%J BMC Structural Biology
%D 2011
%I BioMed Central
%R 10.1186/1472-6807-11-42
%X We examine twenty homologous enzyme pairs from psychrophiles and mesophiles to investigate flexibility as a key characteristic for cold adaptation. B-factors in protein X-ray structures are one way to measure flexibility. Comparing psychrophilic to mesophilic protein B-factors reveals that psychrophilic enzymes are more flexible in 5-turn and strand secondary structures. Enzyme cavities, identified using CASTp at various probe sizes, indicate that psychrophilic enzymes have larger average cavity sizes at probe radii of 1.4-1.5 £¿, sufficient for water molecules. Furthermore, amino acid side chains lining these cavities show an increased frequency of acidic groups in psychrophilic enzymes.These findings suggest that embedded water molecules may play a significant role in cavity flexibility, and therefore, overall protein flexibility. Thus, our results point to the important role enzyme flexibility plays in adaptation to cold environments.Life exists over a wide temperature range, from as low as -15¡ãC to as high as 122¡ãC [1]. On the upper end of the temperature spectrum, thermophiles and hyperthermophiles have been studied extensively by the scientific community, particularly the molecular mechanisms that support protein structure and function at high temperatures. For example, compact and strong hydrophobic packing is typically found in most cores of thermophilic proteins, which increases the energy needed to unfold the protein, making it possible for thermophilic proteins to retain native structure at high temperatures [2]. Indeed, a strong correlation exists between high core packing density and thermostability [2-4]. We are also intrigued by the obverse - organisms that survive optimally at cold temperatures; harsh environments with restricted molecular mobility and reduced reaction kinetics that hinder myriad cellular and biomolecular processes [5-7].Psychrophiles, "cold-loving" microorganisms, have adapted to life at low temperatures by using a variety of mechani
%U http://www.biomedcentral.com/1472-6807/11/42