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Méndez-Zamora A, Diaz-Vidal T, Robles-Machuca M, Pereira-Santana A, Casas-Godoy L. Unveiling potential PET degrading eukaryotes through in silico bioprospecting of PETases. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174978. [PMID: 39047840 DOI: 10.1016/j.scitotenv.2024.174978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 07/05/2024] [Accepted: 07/21/2024] [Indexed: 07/27/2024]
Abstract
This study addresses the environmental problem of PET plastic through in silico bioprospecting for the identification and experimental validation of novel PET degrading eukaryotes through the in silico bioprospectingI of PETases, employing a methodology that combines Hidden Markov Models (HMMs), clustering techniques, molecular docking, and dynamic simulations. A total of 424 putative PETase sequences were identified from 219 eukaryotic organisms, highlighting six sequences with low affinity energies. The Aspergillus luchuensis sequence showed the lowest Gibbs free energy and exhibited stability at different temperatures in molecular dynamics assays. Experimental validation, through a plate clearance assay and HPLC, confirmed PETase activity in three wild-type fungal strains, with A. luchuensis showing the highest efficiency. The results obtained demonstrate the effectiveness of combining computational and experimental approaches as proof of concept to discover and validate eukaryotes with PET-degrading capabilities opening new perspectives for the sustainable management of this type of waste and contributing to its environmental mitigation.
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Affiliation(s)
- Andrés Méndez-Zamora
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida Normalistas 800, Col. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, Mexico
| | - Tania Diaz-Vidal
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Avenida Normalistas 800, Col. Colinas de la Normal, C.P. 44270 Guadalajara, Jalisco, Mexico
| | - Marcela Robles-Machuca
- Tecnologia de alimentos, Secretaría de Investigación y Posgrado, Universidad Autónoma de Nayarit, Ciudad de la Cultura s/n, C.P. 63000 Tepic, Nayarit, Mexico
| | - Alejandro Pereira-Santana
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Parque Científico Tecnológico de Yucatán, 97302 Mérida, Yucatán, Mexico.
| | - Leticia Casas-Godoy
- CONAHCYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Camino Arenero 1227, El Bajío, 45019 Zapopan, Jalisco, Mexico.
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2
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Er-Rajy M, El Fadili M, Faris A, Zarougui S, Elhallaoui M. Design of potential anti-cancer agents as COX-2 inhibitors, using 3D-QSAR modeling, molecular docking, oral bioavailability proprieties, and molecular dynamics simulation. Anticancer Drugs 2024; 35:117-128. [PMID: 38018861 DOI: 10.1097/cad.0000000000001492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Modeling the structural properties of novel morpholine-bearing 1, 5-diaryl-diazole derivatives as potent COX-2 inhibitor, two proposed models based on CoMFA and CoMSIA were evaluated by external and internal validation methods. Partial least squares analysis produced statistically significant models with Q 2 values of 0.668 and 0.652 for CoMFA and CoMSIA, respectively, and also a significant non-validated correlation coefficient R² with values of 0.882 and 0.878 for CoMFA and CoMSIA, respectively. Both models met the requirements of Golbraikh and Tropsha, which means that both models are consistent with all validation techniques. Analysis of the CoMFA and CoMSIA contribution maps and molecular docking revealed that the R1 substituent has a very significant effect on their biological activity. The most active molecules were evaluated for their thermodynamic stability by performing MD simulations for 100 ns; it was revealed that the designed macromolecular ligand complex with 3LN1 protein exhibits a high degree of structural and conformational stability. Based on these results, we predicted newly designed compounds, which have acceptable oral bioavailability properties and would have high synthetic accessibility.
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Affiliation(s)
- Mohammed Er-Rajy
- LIMAS Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
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3
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Li Z, Zhao C, Li D, Wang L. Enhancing the thermostability of Streptomyces cyaneofuscatus strain Ms1 tyrosinase by multi-factors rational design and molecular dynamics simulations. PLoS One 2023; 18:e0288929. [PMID: 37471348 PMCID: PMC10358999 DOI: 10.1371/journal.pone.0288929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
This study presents a multi-factor rational design strategy combined with molecular dynamics simulation to improve the thermostability of Streptomyces cyaneofuscatus strain Ms1 tyrosinase. Candidate mutation sites were identified using Discovery Studio and FoldX software, and the double mutant G124W/G137W was obtained. The mutant was heterogeneously expressed in Escherichia coli strain Rosetta2 (DE3), and its thermostability was verified. Results indicate that the rational design method, combined with molecular dynamics simulation and protein energy calculation, improved the enzyme's thermostability more accurately and effectively. The double mutant G124W/G137W had an optimum temperature of 60°C, about 5.0°C higher than that of the wild-type TYRwt, and its activity was 171.06% higher than the wild-type TYRwt. Its thermostability was enhanced, 42.78% higher than the wild-type at 50°C. These findings suggest that the rational design strategy applied in this study can facilitate the application of industrial enzymes in the pharmaceutical industry.
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Affiliation(s)
- Zhengtao Li
- School of Pharmacy, Qingdao University, Qingdao City, Shandong Province, China
| | - Chen Zhao
- School of Pharmacy, Chengdu University, Chengdu City, Sichuan Province, China
| | - Duanhua Li
- School of Pharmacy, Chengdu University, Chengdu City, Sichuan Province, China
| | - Lu Wang
- School of Pharmacy, Qingdao University, Qingdao City, Shandong Province, China
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4
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Wang F, Zhang L, Zhang D, Wu X, Deng S. Binding of Anionic Polyacrylamide with Amidase and Laccase under 298, 303, and 308 K: Docking and Molecular Dynamics Simulation Studies Combined with Experiments. ACS OMEGA 2023; 8:10040-10050. [PMID: 36969392 PMCID: PMC10034835 DOI: 10.1021/acsomega.2c07380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Amidase and laccase play a key role in the degradation process of anionic polyacrylamide (HPAM). However, the largest challenge of HPAM enzymatic degradation is whether the enzyme can bind with a substrate for a period of time. Here, the most suitable complexes, namely, Rh Amidase-HPAM-2 and Bacillus subtilis (B. subtilis) laccase-HPAM-3, were obtained by docking, and they were carried out for molecular dynamics simulation (MDS) under 298, 303, and 308 K. MDS result analysis showed that Rh Amidase-HPAM-2 was the most stable at 298 K mainly due to a salt bridge and a hydrogen bond, and B. subtilis laccase-HPAM-3 was the most stable at 298 K mainly due to two electrostatic and hydrogen bonds. The LYS96 in Rh Amidase-HPAM-2 and LYS135 in B. subtilis laccase-HPAM-3 had been the most important in their binding process. The binding of Rh Amidase-HPAM-2 and B. subtilis laccase-HPAM-3 was optimal at 303 and 298 K, respectively. HPAM was degraded by mixed bacteria, and the optimal conditions were determined to be 308 K, initial pH = 7, and an inoculated dosage of 2 mL. Under these conditions, the degradation ratio reached 39.24%. The effect of parameters on the HPAM degradation ratio followed a decreasing order of temperature > initial pH > inoculated dosage. The HPAM codegradation mechanism was supposed by mixed bacteria according to test data. The mixed bacteria secreted both amidase and laccase, and they interacted jointly with HPAM. These results lay a theoretical foundation to design and modify the enzyme through mutation experiments in the future.
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Affiliation(s)
- Fanglue Wang
- School
of Bioengineering, Huainan Normal University, Huainan 232038, China
| | - Liwen Zhang
- School
of Mechanical and Electrical Engineering, Huainan Normal University, Huainan 232038, China
| | - Dongchen Zhang
- School
of Materials Science and Engineering, Anhui
University of Science and Technology, Huainan 232001, China
| | - Xuefeng Wu
- School
of Food and Bioengineering, Hefei University
of Technology, Hefei 230009, China
| | - Shengsong Deng
- School
of Food and Bioengineering, Hefei University
of Technology, Hefei 230009, China
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5
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Van Wyk JC, Sewell BT, Danson MJ, Tsekoa TL, Sayed MF, Cowan DA. Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase. Curr Res Struct Biol 2022; 4:256-270. [PMID: 36106339 PMCID: PMC9465369 DOI: 10.1016/j.crstbi.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/27/2022] [Accepted: 07/19/2022] [Indexed: 11/20/2022] Open
Abstract
Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4–7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15–1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising. Random mutagenesis yields a 15-fold increase in nitrile hydratase thermostability. Salt bridges and hydrogen bonds improves nitrile hydratase thermostability. Water-mediated hydrogen bonds improves protein thermostability.
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6
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Mitra D, Das Mohapatra PK. Discovery of Novel Cyclic Salt Bridge in Thermophilic Bacterial Protease and Study of its Sequence and Structure. Appl Biochem Biotechnol 2021; 193:1688-1700. [PMID: 33683551 DOI: 10.1007/s12010-021-03547-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/26/2021] [Indexed: 11/30/2022]
Abstract
The plausible explanation behind the stability of thermophilic protein is still yet to be defined more clearly. Here, an in silico study has been undertaken by investigating the sequence and structure of protease from thermophilic (tPro) bacteria and mesophilic (mPro) bacteria. Results showed that charged and uncharged polar residues have higher abundance in tPro. In extreme environment, the tPro is stabilized by high number of isolated and network salt bridges. A novel cyclic salt bridge is also found in a structure of tPro. High number of metal ion-binding site also helps in protein stabilization of thermophilic protease. Aromatic-aromatic interactions also play a crucial role in tPro stabilization. Formation of long network aromatic-aromatic interactions also first time reported here. Finally, the present study provides a major insight with a newly identified cyclic salt bridge in the stability of the enzyme, which may be helpful for protein engineering. It is also used in industrial applications for human welfare.
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Affiliation(s)
- Debanjan Mitra
- Department of Microbiology, Raiganj University, Raiganj, WB, India
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7
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Cheng Z, Lan Y, Guo J, Ma D, Jiang S, Lai Q, Zhou Z, Peplowski L. Computational Design of Nitrile Hydratase from Pseudonocardia thermophila JCM3095 for Improved Thermostability. Molecules 2020; 25:molecules25204806. [PMID: 33086715 PMCID: PMC7587978 DOI: 10.3390/molecules25204806] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 11/16/2022] Open
Abstract
High thermostability and catalytic activity are key properties for nitrile hydratase (NHase, EC 4.2.1.84) as a well-industrialized catalyst. In this study, rational design was applied to tailor the thermostability of NHase from Pseudonocardia thermophila JCM3095 (PtNHase) by combining FireProt server prediction and molecular dynamics (MD) simulation. Site-directed mutagenesis of non-catalytic residues provided by the rational design was subsequentially performed. The positive multiple-point mutant, namely, M10 (αI5P/αT18Y/αQ31L/αD92H/βA20P/βP38L/βF118W/βS130Y/βC189N/βC218V), was obtained and further analyzed. The Melting temperature (Tm) of the M10 mutant showed an increase by 3.2 °C and a substantial increase in residual activity of the enzyme at elevated temperatures was also observed. Moreover, the M10 mutant also showed a 2.1-fold increase in catalytic activity compared with the wild-type PtNHase. Molecular docking and MD simulations demonstrated better substrate affinity and improved thermostability for the mutant.
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Affiliation(s)
- Zhongyi Cheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Yao Lan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Junling Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Dong Ma
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Shijin Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Qianpeng Lai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (Z.C.); (Y.L.); (J.G.); (D.M.); (S.J.); (Q.L.)
- Jiangnan University (Rugao) Food Biotechnology Research Institute, Rugao 226500, China
- Correspondence: (Z.Z.); (L.P.)
| | - Lukasz Peplowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Torun, Grudziadzka 5, 87-100 Torun, Poland
- Correspondence: (Z.Z.); (L.P.)
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8
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Enhanced Thermostability and Enzymatic Activity of Cel6A Variants from Thermobifida fusca by Empirical Domain Engineering (Short Title: Domain Engineering of Cel6A). BIOLOGY 2020; 9:biology9080214. [PMID: 32784797 PMCID: PMC7464639 DOI: 10.3390/biology9080214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (Cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as Cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant Cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of Cel6A.CBC which revealed thermostability of Cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of Cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass.
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9
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Cheng Z, Xia Y, Zhou Z. Recent Advances and Promises in Nitrile Hydratase: From Mechanism to Industrial Applications. Front Bioeng Biotechnol 2020; 8:352. [PMID: 32391348 PMCID: PMC7193024 DOI: 10.3389/fbioe.2020.00352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 03/30/2020] [Indexed: 12/21/2022] Open
Abstract
Nitrile hydratase (NHase, EC 4.2.1.84) is one type of metalloenzyme participating in the biotransformation of nitriles into amides. Given its catalytic specificity in amide production and eco-friendliness, NHase has overwhelmed its chemical counterpart during the past few decades. However, unclear catalytic mechanism, low thermostablity, and narrow substrate specificity limit the further application of NHase. During the past few years, numerous studies on the theoretical and industrial aspects of NHase have advanced the development of this green catalyst. This review critically focuses on NHase research from recent years, including the natural distribution, gene types, posttranslational modifications, expression, proposed catalytic mechanism, biochemical properties, and potential applications of NHase. The developments of NHase described here are not only useful for further application of NHase, but also beneficial for the development of the fields of biocatalysis and biotransformation.
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Affiliation(s)
| | | | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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10
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Jiao S, Li F, Yu H, Shen Z. Advances in acrylamide bioproduction catalyzed with Rhodococcus cells harboring nitrile hydratase. Appl Microbiol Biotechnol 2019; 104:1001-1012. [DOI: 10.1007/s00253-019-10284-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023]
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11
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Barros EP, Schiffer JM, Vorobieva A, Dou J, Baker D, Amaro RE. Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:5703-5715. [PMID: 31442033 DOI: 10.1021/acs.jctc.9b00483] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Custom-designed ligand-binding proteins represent a promising class of macromolecules with exciting applications toward the design of new enzymes or the engineering of antibodies and small-molecule recruited proteins for therapeutic interventions. However, several challenges remain in designing a protein sequence such that the binding site organization results in high affinity interaction with a bound ligand. Here, we study the dynamics of explicitly solvated designed proteins through all-atom molecular dynamics (MD) simulations to gain insight into the causes that lead to the low affinity or instability of most of these designs, despite the prediction of their success by the computational design methodology. Simulations ranging from 500 to 1000 ns per replicate were conducted on 37 designed protein variants encompassing two distinct folds and a range of ligand affinities, resulting in more than 180 μs of combined sampling. The simulations provide retrospective insights into the properties affecting ligand affinity that can prove useful in guiding further steps of design optimization. Features indicate that entropic components are particularly important for affinity, which are not easily incorporated in the empirical models often used in design protocols. Additionally, we demonstrate that the application of machine learning approaches built upon the output from the simulations can help discriminate between successful and failed binders, such that MD could act as a screening step in protein design, resulting in a more efficient process.
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Affiliation(s)
| | - Jamie M Schiffer
- Janssen Pharmaceuticals, Inc. , San Diego , California 92121 , United States
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12
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Tang L, Yang J, Chen J, Zhang J, Yu H, Shen Z. Design of salt-bridge cyclization peptide tags for stability and activity enhancement of enzymes. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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13
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Xu Q, Ming D, Shi C, Lu D, Tang S, Jiang L, Huang H. Catcher/Tag cyclization introduces electrostatic interaction mediated protein-protein interactions to enhance the thermostability of luciferase. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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14
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Xu Q, Si M, Zhang Z, Li Z, Jiang L, Huang H. Rational Side-Chain Amino Acid Substitution in Firefly Luciferase for Improved Thermostability. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683819010204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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15
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Pei X, Wang J, Wu Y, Zhen X, Tang M, Wang Q, Wang A. Evidence for the participation of an extra α-helix at β-subunit surface in the thermal stability of Co-type nitrile hydratase. Appl Microbiol Biotechnol 2018; 102:7891-7900. [DOI: 10.1007/s00253-018-9191-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/23/2022]
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16
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Muneeswaran G, Kartheeswaran S, Muthukumar K, Karunakaran C. Temperature-dependent conformational dynamics of cytochrome c: Implications in apoptosis. J Mol Graph Model 2017; 79:140-148. [PMID: 29161635 DOI: 10.1016/j.jmgm.2017.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 11/29/2022]
Abstract
Heat, electric shock, and burn injuries induce apoptosis by releasing cytochrome c (cyt-c) from mitochondria and by subsequently activating the death protease, caspases-3. During apoptosis, cyt-c undergoes changes in the secondary structure that have been suggested to increase its peroxidase activity. Information about these structural changes will provide better understanding of the apoptotic mechanism. Hence, temperature-dependent conformational dynamics of cyt-c has been investigated through molecular dynamics (MD) simulations to explain the structural changes and to correlate them with its apoptotic behavior. We observe that, at lower temperatures (223, 248, and 300K), the secondary structure of cyt-c, remains stable, while at higher temperatures (323, 373, 423, and 473K), the secondary structural regions change significantly. Further, our MD results indicate that these structural changes are mainly localized on α-helices, turns, β-sheets, and important loops that were involved in the stabilization of the heme conformation. This conformational transition between specific regions of secondary structure of cyt-c directly affects the electron tunneling properties of the proteins as observed experimentally. We quantify and compare these changes and explain that the temperature plays a vital role in assuring the structural stability of cyt-c and thus its functions. Our findings from this MD study reproduce experimental results at high temperatures and provide evidence for the alteration of the heme through the disruption of the H-bonding interactions between specific regions of cyt-c, thereby enhancing its peroxidase activity which plays a crucial role in the apoptotic process.
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Affiliation(s)
- Gurusamy Muneeswaran
- Biomedical Research Lab, Department of Chemistry, VHNSN College (Autonomous), Virudhunagar, 626 001, Tamilnadu, India; Department of Chemistry, School of Advanced Sciences, Kalasalingam Academy of Research and Education, Krishnanakoil, 626 126, Tamil Nadu, India
| | - Subramanian Kartheeswaran
- Department of Master of Computer Applications, School of Computing, Kalasalingam Academy of Research and Education, Krishnanakoil, 626 126, Tamil Nadu, India
| | | | - Chandran Karunakaran
- Biomedical Research Lab, Department of Chemistry, VHNSN College (Autonomous), Virudhunagar, 626 001, Tamilnadu, India.
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17
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Molecular dynamic simulation studies of bacterial thermostable mannanase unwinding the enzymatic catalysis. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Satish L, Millan S, Bera K, Mohapatra S, Sahoo H. A spectroscopic and molecular dynamics simulation approach towards the stabilizing effect of ammonium-based ionic liquids on bovine serum albumin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02900d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Experimental and theoretical evidence in support of the stabilizing effect of ammonium-based ionic liquids on thermal unfolding/refolding of bovine serum albumin is provided in this article.
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Affiliation(s)
- Lakkoji Satish
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Sabera Millan
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Krishnendu Bera
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Sujata Mohapatra
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
| | - Harekrushna Sahoo
- Department of Chemistry
- National Institute of Technology Rourkela
- Sundergarh
- India
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Xia Y, Cui W, Liu Z, Zhou L, Cui Y, Kobayashi M, Zhou Z. Construction of a subunit-fusion nitrile hydratase and discovery of an innovative metal ion transfer pattern. Sci Rep 2016; 6:19183. [PMID: 26755342 PMCID: PMC4709657 DOI: 10.1038/srep19183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 12/07/2015] [Indexed: 01/10/2023] Open
Abstract
Metallochaperones are metal-binding proteins designed to deliver the appropriate metal to a target protein. The metal is usually transferred between different proteins. In this study, we discovered that metal was transferred between the same subunit of a mutant nitrile hydratase (NHase). Various “activator proteins” mediate the trafficking of metal ions into NHases. We constructed fusion NHases by fusing the β- and α-subunits and/or the “activator proteins” of the NHase from Pseudomonas putida. The fusion NHases exhibited higher thermostability and tolerance to high concentrations of the product amide. The mechanism of the cobalt incorporation changed from a self-subunit swapping pattern to an apoprotein-specific molecular chaperone pattern in vivo and a metallochaperone pattern in vitro. Notably, the cobalt transfer occurred between the same α-subunit in the metallochaperone pattern. These results not only demonstrated the superiority of fusion-type NHases, but also revealed an innovative metal ion transfer pattern in metalloprotein biosynthesis.
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Affiliation(s)
- Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Youtian Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Michihiko Kobayashi
- Institute of Applied Biochemistry, and Graduate School of Life and Environmental Sciences, The University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Gong JS, Shi JS, Lu ZM, Li H, Zhou ZM, Xu ZH. Nitrile-converting enzymes as a tool to improve biocatalysis in organic synthesis: recent insights and promises. Crit Rev Biotechnol 2015; 37:69-81. [DOI: 10.3109/07388551.2015.1120704] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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21
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The Stability Enhancement of Nitrile Hydratase from Bordetella petrii by Swapping the C-terminal Domain of β subunit. Appl Biochem Biotechnol 2015; 178:1481-7. [DOI: 10.1007/s12010-015-1961-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/14/2015] [Indexed: 10/22/2022]
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22
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Rational Substitution of Surface Acidic Residues for Enhancing the Thermostability of Thermolysin. Appl Biochem Biotechnol 2015; 178:725-38. [DOI: 10.1007/s12010-015-1905-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/21/2015] [Indexed: 11/26/2022]
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23
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Zhang PP, Zhao L, Long SY, Tian P. The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study. J Mol Model 2015; 21:72. [PMID: 25750022 DOI: 10.1007/s00894-015-2625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 02/15/2015] [Indexed: 11/24/2022]
Abstract
Human cytosolic sulfotransferases (hSULTs) are important phase II metabolic enzymes. They catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the hydroxyl or primary amine moieties of a large number of endogenous and xenobiotic substrates. Broad selectivity and specificity of binding and activity within the sulfortransferases family could be detected by thermal denaturation assays, which have been made more and more suitable for high throughput screening based on recent technical advances. Here molecular dynamics simulations were used to explore the effect of the cofactor (PAPS) and substrate (LCA) on the thermal stability of the enzyme. It was found that the apo-enzyme unfolded fastest upon heating. The holo-enzyme with bound substrate LCA unfolded slowest. This thermo-denaturation order is consistent with that observed in experiments. Further it was found that the cofactor and substrate will pronouncedly increase the thermal stability of the active pocket regions that interact directly with the ligands. In addition, cofactor and substrate show noticeable synergy effect on the thermal stability of the enzyme.
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Affiliation(s)
- Pu-pu Zhang
- School of Life Sciences, Jilin University, Changchun, China
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24
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Singh B, Bulusu G, Mitra A. Understanding the thermostability and activity of Bacillus subtilis lipase mutants: insights from molecular dynamics simulations. J Phys Chem B 2015; 119:392-409. [PMID: 25495458 DOI: 10.1021/jp5079554] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Improving the thermostability of industrial enzymes is an important protein engineering challenge. Point mutations, induced to increase thermostability, affect the structure and dynamics of the target protein in several ways and thus can also affect its activity. There appears to be no general rules for improving the thermostabilty of enzymes without adversely affecting their enzymatic activity. We report MD simulations, of wild type Bacillus subtilis lipase (WT) and its six progressively thermostable mutants (2M, 3M, 4M, 6M, 9M, and 12M), performed at different temperatures, to address this issue. Less thermostable mutants (LTMs), 2M to 6M, show WT-like dynamics at all simulation temperatures. However, the two more thermostable mutants (MTMs) show the required flexibility at appropriate temperature ranges and maintain conformational stability at high temperature. They show a deep and rugged free-energy landscape, confining them within a near-native conformational space by conserving noncovalent interactions, and thus protecting them from possible aggregation. In contrast, the LTMs having marginally higher thermostabilities than WT show greater probabilities of accessing non-native conformations, which, due to aggregation, have reduced possibilities of reverting to their respective native states under refolding conditions. Our analysis indicates the possibility of nonadditive effects of point mutations on the conformational stability of LTMs.
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Affiliation(s)
- Bipin Singh
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology Hyderabad (IIIT-H) , Gachibowli, Hyderabad, 500032, India
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25
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Yu H, Zhao Y, Guo C, Gan Y, Huang H. The role of proline substitutions within flexible regions on thermostability of luciferase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:65-72. [PMID: 25448017 DOI: 10.1016/j.bbapap.2014.10.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 10/19/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022]
Abstract
Improving the stability of firefly luciferase has been a critical issue for its wider industrial applications. Studies about hyperthermophile proteins show that flexibility could be an effective indicator to find out weak spots to engineering thermostability of proteins. However, the relationship among flexibility, activity and stability in most of proteins is unclear. Proline is the most rigid residue and can be introduced to rigidify flexible regions to enhance thermostability of proteins. We firstly apply three different methods, molecular dynamics (MD) simulation, B-FITTER and framework rigidity optimized dynamics algorithm (FRODA) to determine the flexible regions of Photinus pyralis luciferase: Fragment 197-207; Fragment 471-481 and Fragment 487-495. Then, introduction of proline is used to rigidify these flexible regions. Two mutants D476P and H489P within most flexible regions are finally designed. In the results, H489P mutant shows improved thermostability while maintaining its catalytic efficiency compared to that of wild type luciferase. Flexibility analysis confirms that the overall rigidity and local rigidity of H489P mutant are greatly strengthened. D476P mutant shows decreased thermosatbility and the reason for this is elucidated at the molecular level. S307P mutation is randomly chosen outside the flexible regions as a control. Thermostability analysis shows that S307P mutation has decreased kinetic stability and enhanced thermodynamic stability.
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Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yang Zhao
- National Institutes for Food and Drug Control (NIFDC), Beijing 100050, PR China
| | - Chao Guo
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - Yiru Gan
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300072, PR China; Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin 300072, PR China; Collaborative Innovation Center of Chemical Science and Engineering, Tianjin PR China.
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26
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Shao H, Xu L, Yan Y. Biochemical characterization of a carboxylesterase from the archaeon Pyrobaculum sp. 1860 and a rational explanation of its substrate specificity and thermostability. Int J Mol Sci 2014; 15:16885-910. [PMID: 25250909 PMCID: PMC4200780 DOI: 10.3390/ijms150916885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 08/20/2014] [Accepted: 09/11/2014] [Indexed: 11/16/2022] Open
Abstract
In this work, genome mining was used to identify esterase/lipase genes in the archaeon Pyrobaculum sp. 1860. A gene was cloned and functionally expressed in Escherichia coli as His-tagged protein. The recombinant enzyme (rP186_1588) was verified by western blotting and peptide mass fingerprinting. Biochemical characterization revealed that rP186_1588 exhibited optimum activity at pH 9.0 and 80 °C towards p-nitrophenyl acetate (K(m): 0.35 mM, k(cat): 11.65 s⁻¹). Interestingly, the purified rP186_1588 exhibited high thermostability retaining 70% relative activity after incubation at 90 °C for 6 h. Circular dichroism results indicated that rP186_1588 showed slight structure alteration from 60 to 90 °C. Structural modeling showed P186_1588 possessed a typical α/β hydrolase's fold with the catalytic triad consisting of Ser97, Asp147 and His172, and was further confirmed by site-directed mutagenesis. Comparative molecular simulations at different temperatures (300, 353, 373 and 473 K) revealed that its thermostability was associated with its conformational rigidity. The binding free energy analysis by MM-PBSA method revealed that the van der Waals interaction played a major role in p-NP ester binding for P186_1588. Our data provide insights into the molecular structures of this archaeal esterase, and may help to its further protein engineering for industrial applications.
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Affiliation(s)
- Hua Shao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Li Xu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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27
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Chen S, Gao H, Chen J, Wu J. Surface modification of polyacrylonitrile fibre by nitrile hydratase from Corynebacterium nitrilophilus. Appl Biochem Biotechnol 2014; 174:2058-66. [PMID: 25163886 DOI: 10.1007/s12010-014-1186-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 08/15/2014] [Indexed: 11/24/2022]
Abstract
Previously, nitrile hydratase (NHase) from Corynebacterium nitrilophilus was obtained and showed potential in polyacrylonitrile (PAN) fibre modification. In the present study, the modification conditions of C. nitrilophilus NHase on PAN were investigated. In the optimal conditions, the wettability and dyeability (anionic and reactive dyes) of PAN treated by C. nitrilophilus NHase reached a similar level of those treated by alkali. In addition, the chemical composition and microscopically observable were changed in the PAN surface after NHase treatment. Meanwhile, it revealed that cutinase combined with NHase facilitates the PAN hydrolysis slightly because of the ester existed in PAN as co-monomer was hydrolyzed. All these results demonstrated that C. nitrilophilus NHase can modify PAN efficiently without textile structure damage, and this study provides a foundation for the further application of C. nitrilophilus NHase in PAN modification industry.
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Affiliation(s)
- Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Ave., Wuxi, Jiangsu, 214122, China
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28
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Improvement of stability of nitrile hydratase via protein fragment swapping. Biochem Biophys Res Commun 2014; 450:401-8. [DOI: 10.1016/j.bbrc.2014.05.127] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 05/27/2014] [Indexed: 11/21/2022]
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29
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Gao X, Liu Z, Cui W, Zhou L, Tian Y, Zhou Z. Enhanced thermal stability and hydrolytic ability of Bacillus subtilis aminopeptidase by removing the thermal sensitive domain in the non-catalytic region. PLoS One 2014; 9:e92357. [PMID: 24633010 PMCID: PMC3954873 DOI: 10.1371/journal.pone.0092357] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/20/2014] [Indexed: 11/18/2022] Open
Abstract
Besides the catalytic ability, many enzymes contain conserved domains to perform some other physiological functions. However, sometimes these conserved domains were unnecessary or even detrimental to the catalytic process for industrial application of the enzymes. In this study, based on homology modeling and molecular dynamics simulations, we found that Bacillus subtilis aminopeptidase contained a thermal sensitive domain (protease-associated domain) in the non-catalytic region, and predicted that deletion of this flexible domain can enhance the structure stability. This prediction was then verified by the deletion of protease-associated domain from the wild-type enzyme. The thermal stability analysis showed that deletion of this domain improved the T50 (the temperature required to reduce initial activity by 50% in 30 min) of the enzyme from 71 °C to 77 °C. The melting temperature (Tm) of the enzyme also increased, which was measured by thermal denaturation experiments using circular dichroism spectroscopy. Further studies indicated that this deletion did not affect the activity and specificity of the enzyme toward aminoacyl-p-nitroanilines, but improved its hydrolytic ability toward a 12-aa-long peptide (LKRLKRFLKRLK) and soybean protein. These findings suggested the possibility of a simple technique for enzyme modification and the artificial enzyme obtained here was more suitable for the protein hydrolysis in food industry than the wild-type enzyme.
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Affiliation(s)
- Xinxing Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yaping Tian
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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30
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Yu H, Huang H. Engineering proteins for thermostability through rigidifying flexible sites. Biotechnol Adv 2013; 32:308-15. [PMID: 24211474 DOI: 10.1016/j.biotechadv.2013.10.012] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 09/04/2013] [Accepted: 10/29/2013] [Indexed: 01/06/2023]
Abstract
Engineering proteins for thermostability is an exciting and challenging field since it is critical for broadening the industrial use of recombinant proteins. Thermostability of proteins arises from the simultaneous effect of several forces such as hydrophobic interactions, disulfide bonds, salt bridges and hydrogen bonds. All of these interactions lead to decreased flexibility of polypeptide chain. Structural studies of mesophilic and thermophilic proteins showed that the latter need more rigid structures to compensate for increased thermal fluctuations. Hence flexibility can be an indicator to pinpoint weak spots for enhancing thermostability of enzymes. A strategy has been proven effective in enhancing proteins' thermostability with two steps: predict flexible sites of proteins firstly and then rigidify these sites. We refer to this approach as rigidify flexible sites (RFS) and give an overview of such a method through summarizing the methods to predict flexibility of a protein, the methods to rigidify residues with high flexibility and successful cases regarding enhancing thermostability of proteins using RFS.
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Affiliation(s)
- Haoran Yu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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31
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Housaindokht MR, Monhemi H, Hosseini HE, Sadeghi Googheri MS, Najafabadi RI, Ashraf N, Gholizadeh M. It is explored that ionic liquids can be suitable solvents for nitrile hydratase catalyzed reactions: A gift of the molecular modeling for the industry. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2013.05.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Stability mechanisms of a thermophilic laccase probed by molecular dynamics. PLoS One 2013; 8:e61985. [PMID: 23658618 PMCID: PMC3639223 DOI: 10.1371/journal.pone.0061985] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
Abstract
Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching Topt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes.
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Chen J, Yu H, Liu C, Liu J, Shen Z. Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions. J Biotechnol 2013; 164:354-62. [DOI: 10.1016/j.jbiotec.2013.01.021] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 01/26/2013] [Accepted: 01/28/2013] [Indexed: 01/29/2023]
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34
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Engineering of Rhodococcus cell catalysts for tolerance improvement by sigma factor mutation and active plasmid partition. ACTA ACUST UNITED AC 2012; 39:1421-30. [DOI: 10.1007/s10295-012-1146-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022]
Abstract
Abstract
Tolerance to various stresses is a key phenotype for cell catalysts, which are used widely in bioproduction of diverse valuable chemicals. Using the Rhodococcus ruber TH strain, which exhibits high nitrile hydratase activity, as the target cell catalyst for acrylamide production, we established a method to improve cell tolerance by stably introducing global transcription perturbation. The σ70 gene (sigA) of R. ruber was cloned and randomly mutated. An R. ruber TH3/pNV-sigAM library containing additional sigA mutants was constructed and used for survival selection. The TH3/M4N1-59 mutant was selected by acrylonitrile/acrylamide double stress and exhibited a 160 % extension of the half-life of nitrile hydratase upon exposure to 40 % acrylamide. A redesigned parDEM gene was introduced to Rhodococcus to accomplish stable inheritance of plasmids. A two-batch acrylonitrile hydration reaction was performed using the engineered cells as a catalyst. Compared to TH3, the acrylamide productivity of TH3/M4N1-59DEM catalysis increased by 27.8 and 37.5 % in the first and second bioreaction batches, respectively. These data suggest a novel method for increasing the bioconversion productivity of target chemicals through sigA mutation of the cell catalyst.
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35
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Priyakumar UD. Role of Hydrophobic Core on the Thermal Stability of Proteins—Molecular Dynamics Simulations on a Single Point Mutant of Sso7d. J Biomol Struct Dyn 2012; 29:961-71. [DOI: 10.1080/07391102.2012.10507415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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Comparison of the structural basis for thermal stability between archaeal and bacterial proteins. Extremophiles 2011; 16:67-78. [PMID: 22015540 DOI: 10.1007/s00792-011-0406-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 10/07/2011] [Indexed: 10/16/2022]
Abstract
In this study, the structural basis for thermal stability in archaeal and bacterial proteins was investigated. There were many common factors that confer resistance to high temperature in both archaeal and bacterial proteins. These factors include increases in the Lys content, the bends and blanks of secondary structure, the Glu content of salt bridge; decreases in the number of main-side chain hydrogen bond and exposed surface area, and changes in the bends and blanks of amino acids. Certainly, the utilization of charged amino acids to form salt bridges is a primary factor. In both heat-resistant archaeal and bacterial proteins, most Glu and Asp participate in the formation of salt bridges. Other factors may influence either archaeal or bacterial protein thermostability, which includes the more frequent occurrence of shorter 3(10)-helices and increased hydrophobicity in heat-resistant archaeal proteins. However, there were increases in average helix length, the Glu content in salt bridges, temperature factors and decreases in the number of main-side chain hydrogen bonds, uncharged-uncharged hydrogen bonds, hydrophobicity, and buried and exposed polar surface area in heat-resistant bacterial proteins. Evidently, there are few similarities and many disparities between the heat-resistant mechanisms of archaeal and bacterial proteins.
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Matsutani M, Hirakawa H, Nishikura M, Soemphol W, Ali IAI, Yakushi T, Matsushita K. Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100. Biochem Biophys Res Commun 2011; 409:120-4. [PMID: 21554859 DOI: 10.1016/j.bbrc.2011.04.126] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Accepted: 04/26/2011] [Indexed: 11/30/2022]
Abstract
Thermotolerant acetic acid bacteria (AAB), Acetobacter tropicalis SKU1100, can grow above 40°C. To investigate the basis of its thermotolerance, we compared the genome of A. tropicalis SKU1100 with that of mesophilic AAB strain Acetobacter pasteurianus IFO3283-01. The comparative genomic study showed that amino acid substitutions from large to small residue and Lys to Arg occur in many orthologous genes. Furthermore, comparative modeling study was carried out with the orthologous proteins between SKU1100 and IFO3283-01 strains, indicating that the number of Arg-based salt bridges increased in protein models. Since it has been reported that Arg-based salt bridges are important factor for thermo-stability of protein structure, our results strongly suggest that the increased number of Arg-based salt bridges may contributes to the thermotolerance of A. tropicalis SKU1100 (the thermo-stability of proteins in A. tropicalis SKU1100).
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Affiliation(s)
- Minenosuke Matsutani
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, Japan
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38
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Nitrile hydratases (NHases): At the interface of academia and industry. Biotechnol Adv 2010; 28:725-41. [DOI: 10.1016/j.biotechadv.2010.05.020] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Revised: 05/16/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022]
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39
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Tian J, Wang P, Gao S, Chu X, Wu N, Fan Y. Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation. FEBS J 2010; 277:4901-8. [PMID: 20977676 DOI: 10.1111/j.1742-4658.2010.07895.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein thermostability can be increased by some glycine to proline mutations in a target protein. However, not all glycine to proline mutations can improve protein thermostability, and this method is suitable only at carefully selected mutation sites that can accommodate structural stabilization. In this study, homology modeling and molecular dynamics simulations were used to select appropriate glycine to proline mutations to improve protein thermostability, and the effect of the selected mutations was proved by the experiments. The structure of methyl parathion hydrolase (MPH) from Ochrobactrum sp. M231 (Ochr-MPH) was constructed by homology modeling, and molecular dynamics simulations were performed on the modeled structure. A profile of the root mean square fluctuations of Ochr-MPH was calculated at the nanosecond timescale, and an eight-amino acid loop region (residues 186-193) was identified as having high conformational fluctuation. The two glycines nearest to this region were selected as mutation targets that might affect protein flexibility in the vicinity. The structures and conformational fluctuations of two single mutants (G194P and G198P) and one double mutant (G194P/G198P) were modeled and analyzed using molecular dynamics simulations. The results predicted that the mutant G194P had the decreased conformational fluctuation in the loop region and might increase the thermostability of Ochr-MPH. The thermostability and kinetic behavior of the wild-type and three mutant enzymes were measured. The results were consistent with the computational predictions, and the mutant G194P was found to have higher thermostability than the wild-type enzyme.
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Affiliation(s)
- Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Meharenna YT, Poulos TL. Using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes P450. Biochemistry 2010; 49:6680-6. [PMID: 20593793 DOI: 10.1021/bi100929x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-temperature molecular dynamics (MD) has been used to assess if MD can be employed as a useful tool for probing the structural basis for enhanced stability in thermal stable cytochromes P450. CYP119, the most thermal stable P450 known, unfolds more slowly during 500 K MD simulations than P450s that melt at lower temperatures, P450cam and P450cin. A comparison of the 500 K MD trajectories shows that the Cys ligand loop, a critically important structural feature just under the heme, in both P450cin and P450cam completely unfolds while this region is quite stable in CYP119. In CYP119, this region is stabilized by tight nonpolar interactions involving Tyr26 and Leu308. The corresponding residues in P450cam are Gly and Thr, respectively. The in silico generated Y26A/L308A CYP119 double mutant is substantially less stable than wild-type CYP119, and the Cys ligand loop unfolds in a manner similar to that of P450cam. The MD thus has identified a potential "hot spot" important for stability. As an experimental test of the MD results, the Y26A/L308A double mutant was prepared, and thermal melting curves show that the double mutant exhibits a melting temperature (T(m)) 16 degrees C lower than that of wild-type CYP119. Control mutations that were predicted by MD not to destabilize the protein were also generated, and the experimental melting temperature was not significantly different from that of the wild-type enzyme. Therefore, high-temperature MD is a useful tool in predicting the structural underpinnings of thermal stability in P450s.
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Affiliation(s)
- Yergalem T Meharenna
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA
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Merkley ED, Parson WW, Daggett V. Temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold. Protein Eng Des Sel 2010; 23:327-36. [PMID: 20083491 PMCID: PMC2851445 DOI: 10.1093/protein/gzp090] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 12/17/2009] [Accepted: 12/18/2009] [Indexed: 11/13/2022] Open
Abstract
A widely held hypothesis regarding the thermostability of thermophilic proteins states asserts that, at any given temperature, thermophilic proteins are more rigid than their mesophilic counterparts. Many experimental and computational studies have addressed this question with conflicting results. Here, we compare two homologous enzymes, one mesophilic (Escherichia coli FMN-dependent nitroreductase; NTR) and one thermophilic (Thermus thermophilus NADH oxidase; NOX), by multiple molecular dynamics simulations at temperatures from 5 to 100 degrees C. We find that the global rigidity/flexibility of the two proteins, assessed by a variety of metrics, is similar on the time scale of our simulations. However, the thermophilic enzyme retains its native conformation to a much greater degree at high temperature than does the mesophilic enzyme, both globally and within the active site. The simulations identify the helix F-helix G 'arm' as the region with the greatest difference in loss of native contacts between the two proteins with increasing temperature. In particular, a network of electrostatic interactions holds helix F to the body of the protein in the thermophilic protein, and this network is absent in the mesophilic counterpart.
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Affiliation(s)
- Eric D. Merkley
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195-7350, USA
| | - William W. Parson
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195-7350, USA
| | - Valerie Daggett
- Department of Biochemistry, University of Washington, Box 357350, Seattle, Washington 98195-7350, USA
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, USA
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42
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Kundu S, Roy D. Structural study of carboxylesterase from hyperthermophilic bacteria Geobacillus stearothermophilus by molecular dynamics simulation. J Mol Graph Model 2010; 28:820-7. [PMID: 20347362 DOI: 10.1016/j.jmgm.2010.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 02/25/2010] [Accepted: 03/01/2010] [Indexed: 11/27/2022]
Abstract
Carboxylesterases are ubiquitous enzymes with important physiological, industrial and medical applications such as synthesis and hydrolysis of stereo specific compounds, including the metabolic processing of drugs, and antimicrobial agents. Here, we have performed molecular dynamics simulations of carboxylesterase from hyperthermophilic bacterium Geobacillus stearothermophilus (GsEst) for 10ns each at five different temperatures namely at 300K, 343K, 373K, 473K and 500K. Profiles of root mean square fluctuation (RMSF) identify thermostable and thermosensitive regions of GsEst. Unfolding of GsEst initiates at the thermosensitive alpha-helices and proceeds to the thermostable beta-sheets. Five ion-pairs have been identified as critical ion-pairs for thermostability and are maintained stably throughout the higher temperature simulations. A detailed investigation of the active site residues of this enzyme suggests that the geometry of this site is well preserved up to 373K. Furthermore, the hydrogen bonds between Asp188 and His218 of the active site are stably maintained at higher temperatures imparting stability of this site. Radial distribution functions (RDFs) show similar pattern of solvent ordering and water penetration around active site residues up to 373K. Principal component analysis suggests that the motion of the entire protein as well as the active site is similar at 300K, 343K and 373K. Our study may help to identify the factors responsible for thermostability of GsEst that may endeavor to design enzymes with enhanced thermostability.
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Priyakumar UD, Ramakrishna S, Nagarjuna KR, Reddy SK. Structural and Energetic Determinants of Thermal Stability and Hierarchical Unfolding Pathways of Hyperthermophilic Proteins, Sac7d and Sso7d. J Phys Chem B 2010; 114:1707-18. [DOI: 10.1021/jp909122x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - S. Ramakrishna
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - K. R. Nagarjuna
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - S. Karunakar Reddy
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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