NEW METHOD OF EVALUATING RELATIVE THERMAL STABILITIES OF PROTEINS BASED ON THEIR AMINO ACID SEQUENCES: TARGETSTAR

Haejin Kim, Eun-Joung Moon, Sungchul Moon, Ho-Jin Jung, Young-Lyeol Yang, Young-Hoon Park, Muyoung Heo, Mookyung Cheon, Iksoo Chang and Dong-Soo Han ()
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Haejin Kim: Ensoltek Co., Ltd. T122, ICU, Daejeon 305-732, Korea;
Eun-Joung Moon: Ensoltek Co., Ltd. T122, ICU, Daejeon 305-732, Korea
Sungchul Moon: Ensoltek Co., Ltd. T122, ICU, Daejeon 305-732, Korea
Ho-Jin Jung: Ensoltek Co., Ltd. T122, ICU, Daejeon 305-732, Korea
Young-Lyeol Yang: R&D Center for Bioproducts, CJ Corp., Seoul 157-724, Korea
Young-Hoon Park: R&D Center for Bioproducts, CJ Corp., Seoul 157-724, Korea
Muyoung Heo: National Research Laboratory for Computational Proteomics and Biophysics, Department of Physics, Pusan National University, Busan 609-735, Korea
Mookyung Cheon: National Research Laboratory for Computational Proteomics and Biophysics, Department of Physics, Pusan National University, Busan 609-735, Korea
Iksoo Chang: National Research Laboratory for Computational Proteomics and Biophysics, Department of Physics, Pusan National University, Busan 609-735, Korea
Dong-Soo Han: School of Engineering, Information and Communications University, Daejeon 305-714, Korea

International Journal of Modern Physics C (IJMPC), 2007, vol. 18, issue 10, 1513-1526

Abstract: Several computational methods have been developed to solve the problem of protein thermostabilization. One common drawback of them is that they must have the information of a backbone structure of a protein for the generation of a proper amino acid sequence. In this paper, we propose a new method called TargetStar by incorporating computational biology and statistical physics, in which an approximate partition function and a specific heat are used to calculate the folding transition temperature of a protein and then to predict the relative thermal stabilities for given proteins based only on their amino acid sequences. To evaluate the prediction accuracy of TargetStar, we calculated folding transition temperatures of 289 orthologous protein pairs using the proposed method, where each protein pair contains one hyperthermophilic protein and one mesophilic protein. According to our evaluation, hyperthermophilic and mesophilic proteins are distinguished from each other in terms of relative thermal stabilities with 77% prediction accuracy. Thus, TargetStar may serve as an efficient method to design an amino acid sequence of a target protein with the desired thermal stability prior to the expensive and time-consuming mutagenesis experiment.

Keywords: Amino acid sequence; protein thermostabilization; protein energy function; hyperthermophilic; mesophilic; fold-unfolding transition (search for similar items in EconPapers)
Date: 2007
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DOI: 10.1142/S0129183107011534

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