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Wu H, Yi M, Wu X, Ding Y, Pu M, Wen L, Cheng Y, Zhang W, Mu W. Engineering the thermostability of d-lyxose isomerase from Caldanaerobius polysaccharolyticus via multiple computer-aided rational design for efficient synthesis of d-mannose. Synth Syst Biotechnol 2023; 8:323-330. [PMID: 37168606 PMCID: PMC10165151 DOI: 10.1016/j.synbio.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023] Open
Abstract
d-Mannose is an attractive functional sugar that exhibits many physiological benefits on human health. The demand for low-calorie sugars and sweeteners in foods are increasingly available on the market. Some sugar isomerases, such as d-lyxose isomerase (d-LIase), can achieve an isomerization reaction between d-mannose and d-fructose. However, the weak thermostability of d-LIase limits its efficient conversion from d-fructose to d-mannose. Nonetheless, few studies are available that have investigated the molecular modification of d-LIase to improve its thermal stability. In this study, computer-aided tools including FireProt, PROSS, and Consensus Finder were employed to jointly design d-LIase mutants with improved thermostability for the first time. Finally, the obtained five-point mutant M5 (N21G/E78P/V58Y/C119Y/K170P) showed high thermal stability and catalytic activity. The half-life of M5 at 65 °C was 10.22 fold, and the catalytic efficiency towards 600 g/L of d-fructose was 2.6 times to that of the wild type enzyme, respectively. Molecular dynamics simulation and intramolecular forces analysis revealed a thermostability mechanism of highly rigidity conformation, newly formed hydrogen bonds and π-cation interaction between and within protein domains, and redistributed surface electrostatic charges for the mutant M5. This research provided a promising d-LIase mutant for the industrial production of d-mannose from d-fructose.
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Affiliation(s)
- Hao Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Ming Yi
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Xiaoyi Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Yating Ding
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Minghui Pu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Li Wen
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Yunhui Cheng
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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Asadi M, Oanca G, Warshel A. Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. J Am Chem Soc 2022; 144:1251-1257. [PMID: 35023734 PMCID: PMC10349665 DOI: 10.1021/jacs.1c10494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The cleavage of protein inside cell membranes regulates pathological pathways and is a subject of major interest. Thus, the nature of the coupling between the physical environment and the function of such proteins has recently attracted significant experimental and theoretical efforts. However, it is difficult to determine the nature of this coupling uniquely by experimental and theoretical studies unless one can separate the chemical and the environmental factors. This work describes calculations of the activation barriers of the intramembrane rhomboid protease in neutral and charged lipid bilayers and in detergent micelle, trying to explore the environmental effect. The calculations of the chemical barrier are done using the empirical valence bond (EVB) method. Additionally, the renormalization method captures the energetics and dynamical effects of the conformational change. The simulations indicate that the physical environment around the rhomboid protease is not a major factor in changing the chemical catalysis and that the conformational and substrate dynamics do not exhibit long-time coupling. General issues about the action of membrane-embedded enzymes are also considered.
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Affiliation(s)
- Mojgan Asadi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Gabriel Oanca
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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Pulling Simulations and Hydrogen Sorption Modelling on Carbon Nanotube Bundles. C — JOURNAL OF CARBON RESEARCH 2020. [DOI: 10.3390/c6010011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent progress in molecular simulation technology has developed an interest in modernizing the usual computational methods and approaches. For instance, most of the theoretical work on hydrogen adsorption on carbon nanotubes was conducted a decade ago. It should be insightful to reinvestigate the field and take advantage of code improvements and features implemented in contemporary software. One example of such features is the pulling simulation modules now available in many molecular dynamics programs. We conduct pulling simulations on pairs of carbon nanotubes and measure the inter-tube distance before they dissociate in water. We use this distance to set the interval size between adjacent nanotubes as we arrange them in bundle configurations. We consider bundles with triangular, intermediate and honeycomb patterns, and armchair nanotubes with a chiral index from n = 5 to n = 10. Then, we simulate low pressure hydrogen adsorption isotherms at 77 K, using the grand canonical Monte Carlo method. The different bundle configurations adsorb great hydrogen amounts that may exceed 2% wt at ambient pressures. The computed hydrogen capacities are considered large for physisorption on carbon nanostructures and attributed to the ultra-microporous network and extraordinary high surface area of the configured models.
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Soares RF, Antunes D, Santos LHS, Rocha GV, Bastos LS, Guimarães ACR, Caffarena ER. Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior. J Biomol Struct Dyn 2019; 38:2047-2056. [PMID: 31184542 DOI: 10.1080/07391102.2019.1626769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Trypanosoma cruzi ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas' disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11+‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102+), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102+, and exclusive suboptimal paths for His11+‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further in silico drug discovery studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael F Soares
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Deborah Antunes
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Lucianna H S Santos
- Laboratório de Modelagem Molecular e Planejamento de Fármacos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brasil
| | - Gisele Vieira Rocha
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Leonardo Soares Bastos
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
| | - Ana Carolina R Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Ernesto R Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fiocruz, Rio de Janeiro, Brasil
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Wang L, Zhang L, Feng RR, Dong X, Lu HZ, Zhang JJ. Unravelling the binding affinity between model transport protein and a prospective tuberculosis therapeutic agent: a spectroscopic and theoretical simulation exploration. J Biomol Struct Dyn 2019; 37:4507-4521. [DOI: 10.1080/07391102.2018.1552624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Leng Wang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Li Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Rui Rui Feng
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Xue Dong
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Hui Zhe Lu
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
| | - Jian Jun Zhang
- Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, China
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