Protein Thermostabilizing Factors: High Relative Occurrence of Amino Acids, Residual Properties, and Secondary Structure
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Protein Thermostabilizing Factors: High Relative Occurrence of Amino Acids, Residual Properties, and Secondary Structure Type in Different Residual State Seung Pil Pack & Taek Jin Kang & Young Je Yoo
Received: 29 October 2012 / Accepted: 12 March 2013 # Springer Science+Business Media New York 2013
Abstract The relative occurrences of amino acids, residual properties, and secondary structure type found in the residual structure states were compared between thermophilic and mesophilic proteins to find out the protein-thermostabilizing factors. The thermostabilizing patterns in each residual structure state are as follows: (1) in fully exposed state, higher relative occurrences of GLN, ILE, and PHE; (2) in exposed state, higher relative occurrences of ARG, GLU, salt bridges, the residue with low solvation energy, and the residues in 3/10 helix, and lower relative occurrences of ALA, SER, and VAL; (3) in partially exposed state, higher relative occurrence of flexible residue and lower relative occurrence of SER; (4) in buried state, higher relative occurrences of ARG and GLU, and lower relative occurrence of MET; and (5) in well-buried state, higher relative occurrences of ALA, cation–pi interaction, the residues in 3/10 helix, and lower relative occurrences of ASP, GLY, and the residues in the extended beta strand. These findings could be useful for developing protein thermostabilization strategies according to each residual structure state. Keywords Thermostabilizing factors . Residual structure state . Systematical analysis . Thermophilic protein
Seung Pil Pack and Taek Jin Kang equally contributed to this paper. S. P. Pack (*) Department of Biotechnology and Bioinformatics, Korea University, Sejong 339-700, South Korea e-mail: [email protected] T. J. Kang Department of Chemical and Biochemical Engineering, Dongguk University, Seoul 100-715, South Korea Y. J. Yoo (*) School of Chemical and Biological Engineering, Seoul National University, Seoul 151-742, South Korea e-mail: [email protected]
Appl Biochem Biotechnol
Introduction The major goal of protein engineering is to design novel proteins and to develop proteinbased bioprocess required for production of high-value biomolecules in various areas of pharmaceutical, agricultural, industrial, and environmental fields [1]. For industrial application, the engineered protein or enzyme should have highly stable reactivity even under harsh environments such as high temperature, salinity, and acidity [2]. To develop novel proteins for its industrial application via a rational design strategy, the molecule-level mechanisms of protein thermostability should be revealed and understood [3, 4]. As one research approach, analysis of thermostabilizing factors found in the proteins from thermophilic organisms has been performed since thermophilic proteins show substantially higher intrinsic thermostability than their counterparts from mesophilic organisms, while retaining the basic fold characteristic of the particular protein family [5, 6]. Although several comparative studi
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