Rational Design to Improve Protein Thermostability: Recent Advances and Prospects
Haiquan Yang
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorLong Liu
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorJianghua Li
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorJian Chen
National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.
Search for more papers by this authorCorresponding Author
Guocheng Du
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.Search for more papers by this authorHaiquan Yang
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorLong Liu
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorJianghua Li
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Search for more papers by this authorJian Chen
National Engineering of Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi 214122, China.
Search for more papers by this authorCorresponding Author
Guocheng Du
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.Search for more papers by this authorAbstract
Research on proteins is in rapid development, but the use of wild-type proteins under industrial conditions has limitations, low thermostability in particular. Thermal stability includes three types: thermodynamic, kinetic, and process stability. Several factors (e.g., hydrophobic interactions and hydrogen bonds) affect the thermostability of proteins. The use of rational design to improve protein thermal stability is a hot topic in the field of computational biology and protein engineering. Several methods have been applied successfully to improve the thermal stability of protein, including introducing the number of disulfide bonds, optimizing protein surface charge, homologous comparison, and optimizing the free energy of unfolding. This review summarizes recent advances in our understanding of the factors influencing protein thermostability, highlights its effective improvement strategies, and discusses future prospects in this field.
References
- 1 U. T. Bornscheuer, G. W. Huisman, R. J. Kazlauskas, S. Lutz, J. C. Moore, K. Robins, Nature 2012, 485, 185–194.
- 2 H. J. Wijma, R. J. Floor, D. B. Janssen, Curr. Opin. Struct. Biol. 2013, 23, 588–594.
- 3 S. Ferdjani, M. Ionita, B. Roy, M. Dion, Z. Djeghaba, C. Rabiller, C. Tellier, Biotechnol. Lett. 2011, 33, 1215–1219.
- 4 Z. M. Deng, H. Q. Yang, J. H. Li, H.-D. Shin, G. C. Du, L. Liu, J. Chen, Appl. Microbiol. Biotechnol. 2014, 98, 3997–4007.
- 5 L. Liu, Z. M. Deng, H. Q. Yang, J. H. Li, H.-D. Shin, R. R. Chen, G. C. Du, J. Chen, Appl. Environ. Microbiol. 2014, 80, 798–807.
- 6 A. S. Bommarius, M. F. Paye, Chem. Soc. Rev. 2013, 42, 6534–6565.
- 7 K. M. Polizzi, A. S. Bommarius, J. M. Broering, J. F. Chaparro-Riggers, Curr. Opin. Chem. Biol. 2007, 11, 220–225.
- 8 H. Q. Yang, X. Y. Lu, L. Liu, J. H. Li, H.-D. Shin, R. R. Chen, G. C. Du, J. Chen, Appl. Environ. Microbiol. 2013, 79, 3049–3058.
- 9 H. Q. Yang, L. Liu, J. H. Li, G. C. Du, J. Chen, Biotechnol. Prog. 2012, 28, 1271–1277.
- 10 H. Q. Yang, L. Liu, M. X. Wang, J. H. Li, N. S. Wang, G. C. Du, J. Chen, Appl. Environ. Microbiol. 2012, 78, 7519–7526.
- 11 J. V. Rodrigues, V. Prosinecki, I. Marrucho, L. P. N. Rebelo, C. M. Gomes, Phys. Chem. Chem. Phys. 2011, 13, 13614–13616.
- 12 G. A. Senisterra, P. J. Finerty, Mol. BioSyst. 2009, 5, 217–223.
- 13 J. K. Blum, M. D. Ricketts, A. S. Bommarius, J. Biotechnol. 2012, 160, 214–221.
- 14 S.-Y. Huang, Y. H. P. Zhang, J.-J. Zhong, Appl. Microbiol. Biotechnol. 2012, 93, 2403–2410.
- 15 T. A. Rogers, A. S. Bommarius, Chem. Eng. Sci. 2010, 65, 2118–2124.
- 16 C. Li, W. Li, T. P. Holler, Z. Gu, Z. Li, Food Chem. 2014, 164, 17–22.
- 17 T. A. Rogers, R. M. Daniel, A. S. Bommarius, ChemCatChem 2009, 1, 131–137.
- 18 W. T. Chen, T. Chen, C. S. Cheng, W. Y. Huang, X. Wang, H. S. Yin, Chem. Commun. 2014, 50, 4248–4250.
- 19 K. Wang, H. Y. Luo, J. Tian, O. Turunen, H. Q. Huang, P. J. Shi, H. F. Hua, C. H. Wang, S. H. Wang, B. Yao, Appl. Environ. Microbiol. 2014, 80, 2158–2165.
- 20 T.-H. Wu, C.-C. Chen, Y.-S. Cheng, T.-P. Ko, C.-Y. Lin, H.-L. Lai, T.-Y. Huang, J.-R. Liu, R.-T. Guo, J. Biotechnol. 2014, 175, 1–6.
- 21 H. R. Yu, H. Huang, Biotechnol. Adv. 2014, 32, 308–315.
- 22 X. Yin, Y. Yao, M. C. Wu, T. D. Zhu, Y. Zeng, Q. F. Pang, Biochem. Moscow 2014, 79, 531–537.
- 23 D. S. Vieira, L. Degreve, Mol. Phys. 2009, 107, 59–69.
- 24 J.-P. Wu, M. Li, Y. Zhou, L.-R. Yang, G. Xu, Biotechnol. Lett. 2014, 37 (2), 403–407. DOI: 10.1007/s10529-014-1683-2
- 25 A. S. Mahadevi, G. N. Sastry, Chem. Rev. 2013, 113, 2100–2138.
- 26 W. F. Li, X. X. Zhou, P. Lu, Biotechnol. Adv. 2005, 23, 271–281.
- 27 B. Folch, M. Rooman, Y. Dehouck, J. Biomol. Struct. Dyn. 2007, 24, 764–764.
- 28 B. Folch, M. Rooman, Y. Dehouck, J. Chem. Inf. Model. 2008, 48, 119–127.
- 29 C. You, Q. Huang, H. P. Xue, Y. Xu, H. Lu, Biotechnol. Bioeng. 2010, 105, 861–870.
- 30 S. Chakravarty, R. Varadarajan, Biochem. 2002, 41, 8152–8161.
- 31 A. Korkegian, M. E. Black, D. Baker, B. L. Stoddard, Science 2005, 308, 857–860.
- 32 H. Q. Yang, J. H. Li, H. D. Shin, G. C. Du, L. Liu, J. Chen, Appl. Microbiol. Biotechnol. 2014, 98, 23–29.
- 33 S. Sharma, G. Kumar, H. Vinod, J. Kaur, Res. J. Pharm., Biol. Chem. Sci. 2012, 3, 183–191.
- 34 S.-J. Gao, J.-Q. Wang, M.-C. Wu, H.-M. Zhang, X. Yin, J.-F. Li, Biotechnol. Bioeng. 2013, 110, 1028–1038.
- 35 Y. B. Ruiz-Blanco, Y. Marrero-Ponce, W. Paz, Y. Garcia, J. Salgado, J. Theor. Biol. 2013, 321, 44–53.
- 36 R. D. Socha, N. Tokuriki, FEBS J. 2013, 280, 5582–5595.
- 37 H. T. Ding, F. Gao, D. F. Liu, Z. L. Li, X. H. Xu, M. Wu, Y. H. Zhao, Enzyme Microb. Technol. 2013, 53, 365–372.
- 38 S. Kaushik, D. Mohanty, A. Surolia, J. Biomol. Struct. Dyn. 2012, 29, 905–920.
- 39 H. Liu, K. May, mAbs 2012, 4, 17–23.
- 40 L. L. Ning, J. J. Guo, N. Z. Jin, H. X. Liu, X. J. Yao, J. Mol. Model. 2014, 20, 2.
- 41 T. N. Vinther, M. Norrman, U. Ribel, K. Huus, M. Schlein, D. B. Steensgaard, T. A. Pedersen, I. Pettersson, S. Ludvigsen, T. Kjeldsen, K. J. Jensen, F. Hubalek, Protein Sci. 2013, 22, 296–305.
- 42 Y. W. Wang, Z. Fu, H. Q. Huang, H. S. Zhang, B. Yao, H. R. Xiong, O. Turunen, Bioresour. Technol. 2012, 112, 275–279.
- 43 Q. A. T. Le, J. C. Joo, Y. J. Yoo, Y. H. Kim, Biotechnol. Bioeng. 2012, 109, 867–876.
- 44 P. K. Sharma, R. Kumar, R. Kumar, O. Mohammad, R. Singh, J. Kaur, Gene 2012, 491, 264–271.
- 45 N. V. Paz, S. M. C. Alqueres, M. S. Almeida, R. V. Almeida, O. B. Martins, D. Foguel, Biophys. J. 2010, 98, 447A–447A.
- 46 L. J. Zhang, X. M. Tang, D. B. Cui, Z. Q. Yao, B. Gao, S. Q. Jiang, B. Yin, Y. A. Yuan, D. Wei, Protein Sci. 2014, 23, 110–116.
- 47 A. A. Howard, N. Webb, T. K. S. Kumar, C. D. Heyes, Biophys. J. 2013, 104, 217A–217A.
- 48 A. V. Gribenko, M. M. Patel, J. Liu, S. A. McCallum, C. Wang, G. I. Makhatadze, PNAS 2009, 106, 2601–2606.
- 49 A. V. Gribenko, G. I. Makhatadze, J. Mol. Biol. 2007, 366, 842–856.
- 50 K. L. Schweiker, A. Zarrine-Afsar, A. R. Davidson, G. I. Makhatadze, Protein Sci. 2007, 16, 2694–2702.
- 51 S. H. Ackerman, D. L. Gatti, PLoS ONE 2011, 6, 3.
- 52 A. Barzegar, A. A. Moosavi-Movahedi, J. Z. Pedersen, M. Miroliaei, Enzyme Microb. Technol. 2009, 45, 73–79.
- 53 X. Jiang, J. Kowalski, J. W. Kelly, Protein Sci. 2001, 10, 1454–1465.
- 54 A. C. F. Alvim, E. D. Taillard, Eur. J. Oper. Res. 2009, 192, 396–413.
- 55 D. Gilis, M. Rooman, Protein Eng. 2000, 13, 849–856.
- 56 Y. Dehouck, J. M. Kwasigroch, D. Gilis, M. Rooman, BMC Bioinf. 2011, 12.
- 57 S.-B. Zhang, Z.-L. Wu, Bioresour. Technol. 2011, 102, 2093–2096.
- 58 X. H. Qi, Q. Guo, Y. T. Wei, H. Xu, R. B. Huang, Biotechnol. Lett. 2012, 34, 339–346.
- 59 B. H. Liu, J. Zhang, Z. Fang, L. Gu, X. R. Liao, G. C. Du, J. Chen, J. Ind. Microbiol. Biotechnol. 2013, 40, 697–704.
- 60 M. T. Reetz, J. D. Carballeira, Nat. Protoc. 2007, 2, 891–903.
- 61 I. R. Silva, C. Jers, H. Otten, C. Nyffenegger, D. M. Larsen, P. M. F. Derkx, A. S. Meyer, J. D. Mikkelsen, S. Larsen, Appl. Microbiol. Biotechnol. 2014, 98, 4521–4531.
- 62 H. S. Kim, Q. A. T. Lee, Y. H. Kim, Enzyme Microb. Technol. 2010, 47, 1–5.
- 63 J.-H. Zhang, Y. Lin, Y.-F. Sun, Y.-R. Ye, S.-P. Zheng, S.-Y. Han, Enzyme Microb. Technol. 2012, 50, 325–330.
- 64 Y. Xie, J. An, G. Yang, G. Wu, Y. Zhang, L. Cui, Y. Feng, J. Biol. Chem. 2014, 289, 7994–8006.
- 65 A. K. Pandey, D. Naduthambi, K. M. Thomas, N. J. Zondlo, J. Am. Chem. Soc. 2013, 135, 4333–4363.
- 66 L. Moroder, N. Budisa, ChemPhysChem 2010, 11, 1181–1187.
- 67 M. D. Shoulders, K. A. Satyshur, K. T. Forest, R. T. Raines, Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 559–564.
- 68 H.-C. Tang, Y.-J. Lin, J.-C. Horng, Proteins: Struct., Funct., Bioinf. 2014, 82, 67–76.
- 69 P. Heinzelman, C. D. Snow, M. A. Smith, X. Yu, A. Kannan, K. Boulware, A. Villalobos, S. Govindarajan, J. Minshull, F. H. Arnold, J. Biol. Chem. 2009, 284, 26229–26233.
- 70 P. A. Romero, E. Stone, C. Lamb, L. Chantranupong, A. Krause, A. E. Miklos, R. A. Hughes, B. Fechtel, A. D. Ellington, F. H. Arnold, G. Georgiou, ACS Synth. Biol. 2012, 1, 221–228.
- 71 R. J. Floor, H. J. Wijma, D. I. Colpa, A. Ramos-Silva, P. A. Jekel, W. Szymanski, B. L. Feringa, S. J. Marrink, D. B. Janssen, ChemBioChem 2014, 15, 1659–1671.
- 72 L.-Z. Li, T.-H. Xie, H.-J. Li, C. Qing, G.-M. Zhang, M.-S. Sun, Enzyme Microb. Technol. 2007, 41, 523–527.
- 73 S. P. Voutilainen, H. Boer, M. Alapuranen, J. Janis, J. Vehmaanpera, A. Koivula, Appl. Microbiol. Biotechnol. 2009, 83, 261–272.
- 74 G. A. Kotzia, N. E. Labrou, FEBS J. 2009, 276, 1750–1761.
- 75 Z. Xiao, H. Bergeron, S. Grosse, M. Beauchemin, M.-L. Garron, D. Shaya, T. Sulea, M. Cygler, P. C. K. Lau, Appl. Environ. Microbiol. 2008, 74, 1183–1189.
- 76 S. Edwardraja, S. Sriram, R. Govindan, N. Budisa, S.-G. Lee, Mol. Biosyst. 2011, 17, 258–265.