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Vahidi SH, Monhemi H, Hassani Sabzevar B, Eftekhari M. Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37965802 DOI: 10.1080/07391102.2023.2280775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Hooman Vahidi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hassan Monhemi
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
| | | | - Mohammad Eftekhari
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
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2
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Wang H, Li H, Lee CK, Mat Nanyan NS, Tay GS. Recent Advances in the Enzymatic Synthesis of Polyester. Polymers (Basel) 2022; 14:polym14235059. [PMID: 36501454 PMCID: PMC9740404 DOI: 10.3390/polym14235059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
Polyester is a kind of polymer composed of ester bond-linked polybasic acids and polyol. This type of polymer has a wide range of applications in various industries, such as automotive, furniture, coatings, packaging, and biomedical. The traditional process of synthesizing polyester mainly uses metal catalyst polymerization under high-temperature. This condition may have problems with metal residue and undesired side reactions. As an alternative, enzyme-catalyzed polymerization is evolving rapidly due to the metal-free residue, satisfactory biocompatibility, and mild reaction conditions. This article presented the reaction modes of enzyme-catalyzed ring-opening polymerization and enzyme-catalyzed polycondensation and their combinations, respectively. In addition, the article also summarized how lipase-catalyzed the polymerization of polyester, which includes (i) the distinctive features of lipase, (ii) the lipase-catalyzed polymerization and its mechanism, and (iii) the lipase stability under organic solvent and high-temperature conditions. In addition, this article also focused on the advantages and disadvantages of enzyme-catalyzed polyester synthesis under different solvent systems, including organic solvent systems, solvent-free systems, and green solvent systems. The challenges of enzyme optimization and process equipment innovation for further industrialization of enzyme-catalyzed polyester synthesis were also discussed in this article.
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Affiliation(s)
- Hong Wang
- Bioresource Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Hongpeng Li
- Tangshan Jinlihai Biodiesel Co. Ltd., Tangshan 063000, China
| | - Chee Keong Lee
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Noreen Suliani Mat Nanyan
- Bioprocess Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Renewable Biomass Transformation Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
| | - Guan Seng Tay
- Bioresource Technology Division, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Green Biopolymer, Coatings & Packaging Cluster, School of Industrial Technology, Universiti Sains Malaysia, Penang USM 11800, Malaysia
- Correspondence:
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Ferrario V, Pleiss J. Simulation of protein diffusion: a sensitive probe of protein-solvent interactions. J Biomol Struct Dyn 2018; 37:1534-1544. [PMID: 29667536 DOI: 10.1080/07391102.2018.1461689] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes (L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein-water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius (RS), which was derived from the diffusion coefficient and the viscosity. RS was compared to the geometric radius (RG) of CALB, which was derived from the protein density. RS and RG differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein-water system sufficiently, and using the complete production run for the determination of the diffusion coefficient.
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Affiliation(s)
- Valerio Ferrario
- a Institute of Biochemistry and Technical Biochemistry , University of Stuttgart , Allmandring 31, Stuttgart 70569 , Germany
| | - Jürgen Pleiss
- a Institute of Biochemistry and Technical Biochemistry , University of Stuttgart , Allmandring 31, Stuttgart 70569 , Germany
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4
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Analysis of Aspergillus sp. lipase immobilization for the application in organic synthesis. Int J Biol Macromol 2018; 108:1165-1175. [DOI: 10.1016/j.ijbiomac.2017.11.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022]
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5
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Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Understanding the activation mechanism ofThermomyces lanuginosuslipase using rational design and tryptophan-induced fluorescence quenching. EUR J LIPID SCI TECH 2016. [DOI: 10.1002/ejlt.201600059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | | | | | - Morten J. Bjerrum
- Department of Chemistry; University of Copenhagen; Copenhagen Denmark
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6
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Lid dynamics of porcine pancreatic lipase in non-aqueous solvents. Biochim Biophys Acta Gen Subj 2016; 1860:2326-34. [DOI: 10.1016/j.bbagen.2016.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 01/06/2023]
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7
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Skjold-Jørgensen J, Vind J, Moroz OV, Blagova E, Bhatia VK, Svendsen A, Wilson KS, Bjerrum MJ. Controlled lid-opening in Thermomyces lanuginosus lipase- An engineered switch for studying lipase function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:20-27. [PMID: 27693248 DOI: 10.1016/j.bbapap.2016.09.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/09/2016] [Accepted: 09/26/2016] [Indexed: 11/16/2022]
Abstract
Here, we present a lipase mutant containing a biochemical switch allowing a controlled opening and closing of the lid independent of the environment. The closed form of the TlL mutant shows low binding to hydrophobic surfaces compared to the binding observed after activating the controlled switch inducing lid-opening. We directly show that lipid binding of this mutant is connected to an open lid conformation demonstrating the impact of the exposed amino acid residues and their participation in binding at the water-lipid interface. The switch was created by introducing two cysteine residues into the protein backbone at sites 86 and 255. The crystal structure of the mutant shows the successful formation of a disulfide bond between C86 and C255 which causes strained closure of the lid-domain. Control of enzymatic activity and binding was demonstrated on substrate emulsions and natural lipid layers. The locked form displayed low enzymatic activity (~10%) compared to wild-type. Upon release of the lock, enzymatic activity was fully restored. Only 10% binding to natural lipid substrates was observed for the locked lipase compared to wild-type, but binding was restored upon adding reducing agent. QCM-D measurements revealed a seven-fold increase in binding rate for the unlocked lipase. The TlL_locked mutant shows structural changes across the protein important for understanding the mechanism of lid-opening and closing. Our experimental results reveal sites of interest for future mutagenesis studies aimed at altering the activation mechanism of TlL and create perspectives for generating tunable lipases that activate under controlled conditions.
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Affiliation(s)
- Jakob Skjold-Jørgensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark; Novozymes A/S, Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Jesper Vind
- Novozymes A/S, Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Olga V Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK
| | | | | | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
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Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Lipases That Activate at High Solvent Polarities. Biochemistry 2015; 55:146-56. [PMID: 26645098 DOI: 10.1021/acs.biochem.5b01114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermomyces lanuginosus lipase (TlL) and related lipases become activated in low-polarity environments that exist at the water-lipid interface where a structural change of the "lid" region occurs. In this work, we have investigated the activation of TlL (Lipase_W89) and certain lid mutants, containing either a single positive charge mutation, E87K (Lipase_K87_W89), within the lid region or a lid residue composition of both lipase and esterase character (Hybrid_W89) as a function of solvent polarity. Activation differences between the variants and TlL were studied by a combination of biophysical and theoretical methods. To investigate the structural changes taking place in the lid region upon lipase activation, we used a fluorescence-based method measuring the efficiency of Trp89 in the lid to quench the fluorescence of a bimane molecule attached in front (C255) and behind (C61) the lid. These structural changes were compared to the enzymatic activity of each variant at the water-substrate interface and to theoretical calculations of the energies associated with lid opening as a function of the dielectric constant (ε) of the environment. Our results show that the lid in Lipase_K87_W89 undergoes a pronounced structural transition toward an open conformation around ε = 50, whereas only small changes are detected for Lipase_W89 ascribed to the stabilizing effect of the positive charge mutation on the open lid conformation. Interestingly, Hybrid_W89, with the same charge as Lipase_W89, shows a stabilization of the open lid even more pronounced at high solvent polarities than that of Lipase_K87_W89, allowing activation at ε < 80. This is further indicated by measurement of the lipase activity for each variant showing that Hybrid_W89 is more quickly activated at the water-lipid interface of a true, natural substrate. Combined, we show that a correlation exists between structural changes and enzymatic activities detected on one hand and theoretical calculations on lid opening energies on the other. These results highlight the key role that the lid plays in determining the polarity-dependent activation of lipases.
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Affiliation(s)
- Jakob Skjold-Jørgensen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark.,Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Jesper Vind
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
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9
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Lorch S, Capponi S, Pieront F, Bondar AN. Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II. J Phys Chem B 2015; 119:12172-81. [DOI: 10.1021/acs.jpcb.5b06594] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastian Lorch
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Sara Capponi
- Department
of Physiology and Biophysics, University of California at Irvine, Medical Sciences I, Irvine, California 92697, United States
| | - Florian Pieront
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
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10
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Fogarty AC, Potestio R, Kremer K. Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties. J Chem Phys 2015; 142:195101. [DOI: 10.1063/1.4921347] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aoife C. Fogarty
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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11
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Shinobu A, Agmon N. The Hole in the Barrel: Water Exchange at the GFP Chromophore. J Phys Chem B 2015; 119:3464-78. [DOI: 10.1021/jp5127255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ai Shinobu
- The Fritz
Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Noam Agmon
- The Fritz
Haber Research
Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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12
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Benson SP, Pleiss J. Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B. J Chem Theory Comput 2014; 10:5206-14. [DOI: 10.1021/ct500791e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Mohammad Latif MA, Micaêlo NM, Abdul Rahman MB. Influence of anion–water interactions on the behaviour of lipases in room temperature ionic liquids. RSC Adv 2014. [DOI: 10.1039/c4ra07460b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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14
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Villo L, Metsala A, Tamp S, Parve J, Vallikivi I, Järving I, Samel N, Lille Ü, Pehk T, Parve O. Thermomyces lanuginosusLipase with Closed Lid Catalyzes Elimination of Acetic Acid from 11-Acetyl-Prostaglandin E2. ChemCatChem 2014. [DOI: 10.1002/cctc.201400019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Sharma S, Kanwar SS. Organic solvent tolerant lipases and applications. ScientificWorldJournal 2014; 2014:625258. [PMID: 24672342 PMCID: PMC3929378 DOI: 10.1155/2014/625258] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 10/31/2013] [Indexed: 11/23/2022] Open
Abstract
Lipases are a group of enzymes naturally endowed with the property of performing reactions in aqueous as well as organic solvents. The esterification reactions using lipase(s) could be performed in water-restricted organic media as organic solvent(s) not only improve(s) the solubility of substrate and reactant in reaction mixture but also permit(s) the reaction in the reverse direction, and often it is easy to recover the product in organic phase in two-phase equilibrium systems. The use of organic solvent tolerant lipase in organic media has exhibited many advantages: increased activity and stability, regiospecificity and stereoselectivity, higher solubility of substrate, ease of products recovery, and ability to shift the reaction equilibrium toward synthetic direction. Therefore the search for organic solvent tolerant enzymes has been an extensive area of research. A variety of fatty acid esters are now being produced commercially using immobilized lipase in nonaqueous solvents. This review describes the organic tolerance and industrial application of lipases. The main emphasis is to study the nature of organic solvent tolerant lipases. Also, the potential industrial applications that make lipases the biocatalysts of choice for the present and future have been presented.
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Affiliation(s)
- Shivika Sharma
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 171 005, India
| | - Shamsher S. Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla 171 005, India
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16
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Monhemi H, Housaindokht MR, Moosavi-Movahedi AA, Bozorgmehr MR. How a protein can remain stable in a solvent with high content of urea: insights from molecular dynamics simulation of Candida antarctica lipase B in urea : choline chloride deep eutectic solvent. Phys Chem Chem Phys 2014; 16:14882-93. [DOI: 10.1039/c4cp00503a] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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17
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Park HJ, Park K, Yoo YJ. Understanding the effect of tert-butanol onCandida antarcticalipase B using molecular dynamics simulations. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.758850] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Park HJ, Joo JC, Park K, Kim YH, Yoo YJ. Prediction of the solvent affecting site and the computational design of stable Candida antarctica lipase B in a hydrophilic organic solvent. J Biotechnol 2013. [DOI: 10.1016/j.jbiotec.2012.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Lousa D, Baptista AM, Soares CM. A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys Chem Chem Phys 2013; 15:13723-36. [DOI: 10.1039/c3cp51761f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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How enzymes can remain active and stable in a compressed gas? New insights into the conformational stability of Candida antarctica lipase B in near-critical propane. J Supercrit Fluids 2012. [DOI: 10.1016/j.supflu.2012.08.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Specific Enzyme-Catalyzed Hydrolysis and Synthesis in Aqueous and Organic Medium Using Biocatalysts with Lipase Activity from Aspergillus niger MYA 135. Catal Letters 2012. [DOI: 10.1007/s10562-012-0901-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Shi JH, Fan CH. FT-IR study on interactions between medroxyprogesterone acetate and solvent in CHCl₃/cyclo-C6H₁₂ and CCl₄/cyclo-C6H₁₂ binary solvent systems. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 95:230-234. [PMID: 22634415 DOI: 10.1016/j.saa.2012.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 05/01/2012] [Indexed: 06/01/2023]
Abstract
The intermolecular interactions between medroxyprogesterone acetate (MPA) and CHCl(3) and CCl(4) solvent in CHCl(3)/cyclo-C(6)H(12) and CCl(4)/cyclo-C(6)H(12) binary solvent systems have been studied by Fourier transform infrared spectroscopy (FT-IR). The experimental results showed that there are hydrogen bonding interactions between oxygen atoms of all carbonyl groups in MPA and hydrogen atom of CHCl(3) so as to form 1:3 complex of MPA with CHCl(3) and produce three new absorption bands at 1728.9-1736.1, 1712.7-1717.4 and 1661.9-1673.8 cm(-1), respectively. And, 1:1 complex of MPA with CCl(4) is formed in CCl(4)/cyclo-C(6)H(12) binary solvent as a result of hydrogen bonding interaction between C3 carbonyl group and empty d-orbital in chlorine atom of CCl(4) leading to producing new absorption band at 1673.2-1674.2 cm(-1). However, all free carbonyl and associated carbonyl stretching vibrations of MPA in CHCl(3)/cyclo-C(6)H(12) and CCl(4)/cyclo-C(6)H(12) binary solvent systems shift to lower wavenumbers with the increasing of volume fraction of CHCl(3) and CCl(4) in binary solvent systems owing to the dipole-dipole interaction and the dipole-induced dipole interaction between MPA and solvents.
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Affiliation(s)
- Jie-hua Shi
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310032, China.
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23
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Wedberg R, Abildskov J, Peters GH. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation. J Phys Chem B 2012; 116:2575-85. [DOI: 10.1021/jp211054u] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rasmus Wedberg
- Department of Chemical and Biochemical
Engineering, Technical University of Denmark, Søltofts Plads, Building 229, DTU, 2800 Kongens Lyngby, Denmark
| | - Jens Abildskov
- Department of Chemical and Biochemical
Engineering, Technical University of Denmark, Søltofts Plads, Building 229, DTU, 2800 Kongens Lyngby, Denmark
| | - Günther H. Peters
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Building
207, DTU, 2800 Kongens Lyngby, Denmark
- MEMPHYS−Center for Biomembrane Physics
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24
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Barbe S, Cortés J, Siméon T, Monsan P, Remaud-Siméon M, André I. A mixed molecular modeling-robotics approach to investigate lipase large molecular motions. Proteins 2011; 79:2517-29. [DOI: 10.1002/prot.23075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/18/2011] [Accepted: 04/19/2011] [Indexed: 11/07/2022]
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25
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Rehm S, Trodler P, Pleiss J. Solvent-induced lid opening in lipases: a molecular dynamics study. Protein Sci 2011; 19:2122-30. [PMID: 20812327 DOI: 10.1002/pro.493] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In most lipases, a mobile lid covers the substrate binding site. In this closed structure, the lipase is assumed to be inactive. Upon activation of the lipase by contact with a hydrophobic solvent or at a hydrophobic interface, the lid opens. In its open structure, the substrate binding site is accessible and the lipase is active. The molecular mechanism of this interfacial activation was studied for three lipases (from Candida rugosa, Rhizomucor miehei, and Thermomyces lanuginosa) by multiple molecular dynamics simulations for 25 ns without applying restraints or external forces. As initial structures of the simulations, the closed and open structures of the lipases were used. Both the closed and the open structure were simulated in water and in an organic solvent, toluene. In simulations of the closed lipases in water, no conformational transition was observed. However, in three independent simulations of the closed lipases in toluene the lid gradually opened. Thus, pathways of the conformational transitions were investigated and possible kinetic bottlenecks were suggested. The open structures in toluene were stable, but in water the lid of all three lipases moved towards the closed structure and partially unfolded. Thus, in all three lipases opening and closing was driven by the solvent and independent of a bound substrate molecule.
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Affiliation(s)
- Sascha Rehm
- Institute of Technical Biochemistry, University of Stuttgart, D-70569 Stuttgart, Germany
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26
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Li C, Tan T, Zhang H, Feng W. Analysis of the conformational stability and activity of Candida antarctica lipase B in organic solvents: insight from molecular dynamics and quantum mechanics/simulations. J Biol Chem 2010; 285:28434-41. [PMID: 20601697 PMCID: PMC2937868 DOI: 10.1074/jbc.m110.136200] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/29/2010] [Indexed: 11/06/2022] Open
Abstract
The conformational stability and activity of Candida antarctica lipase B (CALB) in the polar and nonpolar organic solvents were investigated by molecular dynamics and quantum mechanics/molecular mechanics simulations. The conformation change of CALB in the polar and nonpolar solvents was examined in two aspects: the overall conformation change of CALB and the conformation change of the active site. The simulation results show that the overall conformation of CALB is stable in the organic solvents. In the nonpolar solvents, the conformation of the active site keeps stable, whereas in the polar solvents, the solvent molecules reach into the active site and interact intensively with the active site. This interaction destroys the hydrogen bonding between Ser(105) and His(224). In the solvents, the activation energy of CALB and that of the active site region were further simulated by quantum mechanics/molecular mechanics simulation. The results indicate that the conformation change in the region of active sites is the main factor that influences the activity of CALB.
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Affiliation(s)
- Cong Li
- From the Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- From the Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- From the Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- From the Beijing Key Lab of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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27
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Thirumuruganandham SP, Urbassek HM. Evaporation of solvent molecules by ultrafast heating: effect on conformation of solvated protein. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:349-354. [PMID: 20049882 DOI: 10.1002/rcm.4396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Using molecular dynamics simulation, we compare two cases of ultrafast heating of a small water droplet containing a solvated protein (echistatin). If the water temperature after irradiation is above the critical temperature, explosive boiling liberates the protein within some 10 ps of its hydration shell, while its temperature remains relatively low. By comparing with the case where the water shell is heated to the same final temperature, but without complete evaporation, we demonstrate that the protein conformation is governed by the hydration shell rather than by the protein temperature.
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28
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Insights into lid movements ofBurkholderia cepacialipase inferred from molecular dynamics simulations. Proteins 2009; 77:509-23. [DOI: 10.1002/prot.22462] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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29
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Orrenius C, Hbffner F, Rotticci D, öhrner N, Norin T, Hult K. Chiral Recognition Of Alcohol Enantiomers In Acyl Transfer Reactions Catalysed ByCandida AntarcticaLipase B. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242429809040107] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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30
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Trodler P, Schmid RD, Pleiss J. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC STRUCTURAL BIOLOGY 2009; 9:38. [PMID: 19476626 PMCID: PMC2695465 DOI: 10.1186/1472-6807-9-38] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 05/28/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. Interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. While for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. Therefore, molecular dynamics simulations of a closed homology model and an open crystal structure of Burkholderia cepacia lipase in water and toluene were performed to investigate the influence of solvents on structure, dynamics, and the conformational transition of the lid. RESULTS The conformational transition of B. cepacia lipase was dependent on the solvent. In simulations of closed B. cepacia lipase in water no conformational transition was observed, while in three independent simulations of the closed lipase in toluene the lid gradually opened during the first 10-15 ns. The pathway of conformational transition was accessible and a barrier was identified, where a helix prevented the lid from opening to the completely open conformation. The open structure in toluene was stabilized by the formation of hydrogen bonds.In simulations of open lipase in water, the lid closed slowly during 30 ns nearly reaching its position in the closed crystal structure, while a further lid opening compared to the crystal structure was observed in toluene. While the helical structure of the lid was intact during opening in toluene, it partially unfolded upon closing in water. The closing of the lid in water was also observed, when with eight intermediate structures between the closed and the open conformation as derived from the simulations in toluene were taken as starting structures. A hydrophobic beta-hairpin was moving away from the lid in all simulations in water, which was not observed in simulations in toluene. The conformational transition of the lid was not correlated to the motions of the beta-hairpin structure. CONCLUSION Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing were driven by the solvent and independent of a bound substrate molecule.
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Affiliation(s)
- Peter Trodler
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany.
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31
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Hu Z, Jiang J. Comment on 'Diffusion of water and sodium counter-ions in nanopores of a β-lactoglobulin crystal: a molecular dynamics study'. NANOTECHNOLOGY 2008; 19:438001. [PMID: 21832716 DOI: 10.1088/0957-4484/19/43/438001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Malek et al (2005 Nanotechnology 16 S522) studied the diffusion of water and sodium counter-ions in a β-lactoglobulin (βLG) crystal from a 5 ns molecular dynamics simulation. They presented water density in the main pore, and water mobility in the core and surface zones. Unfortunately, their results were incorrect and misleading. In this comment, we provide the results from our analysis for the same system.
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Affiliation(s)
- Zhongqiao Hu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117576, Singapore
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32
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Díaz-Vergara N, Piñeiro Á. Molecular Dynamics Study of Triosephosphate Isomerase from Trypanosoma cruzi in Water/Decane Mixtures. J Phys Chem B 2008; 112:3529-39. [DOI: 10.1021/jp7102275] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Norma Díaz-Vergara
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
| | - Ángel Piñeiro
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, UNAM, Ciudad Universitaria 04510, México D.F., Mexico
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33
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Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC STRUCTURAL BIOLOGY 2008; 8:9. [PMID: 18254946 PMCID: PMC2262892 DOI: 10.1186/1472-6807-8-9] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 02/06/2008] [Indexed: 11/22/2022]
Abstract
Background The structure and flexibility of Candida antarctica lipase B in water and five different organic solvent models was investigated using multiple molecular dynamics simulations to describe the effect of solvents on structure and dynamics. Interactions of the solvents with the protein and the distribution of water molecules at the protein surface were examined. Results The simulated structure was independent of the solvent, and had a low deviation from the crystal structure. However, the hydrophilic surface of CALB in non-polar solvents decreased by 10% in comparison to water, while the hydrophobic surface is slightly increased by 1%. There is a large influence on the flexibility depending on the dielectric constant of the solvent, with a high flexibility in water and a low flexibility in organic solvents. With decreasing dielectric constant, the number of surface bound water molecules significantly increased and a spanning water network with an increasing size was formed. Conclusion The reduced flexibility of Candida antarctica lipase B in organic solvents is caused by a spanning water network resulting from less mobile and slowly exchanging water molecules at the protein-surface. The reduced flexibility of Candida antarctica lipase B in organic solvent is not only caused by the interactions between solvent-protein, but mainly by the formation of a spanning water network.
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34
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Guzzi R, Arcangeli C, Bizzarri AR. A molecular dynamics simulation study of the solvent isotope effect on copper plastocyanin. Biophys Chem 2007; 82:9-22. [PMID: 17030337 DOI: 10.1016/s0301-4622(99)00097-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/1999] [Revised: 07/29/1999] [Accepted: 07/29/1999] [Indexed: 11/24/2022]
Abstract
The effect of heavy water on the structure and dynamics of copper plastocyanin as well as on some aspects of the solvent dynamics at the protein-solvent interfacial region have been investigated by molecular dynamics simulation. The simulated system has been analyzed in terms of the atomic root mean square deviation and fluctuations, intraprotein H-bond pattern, dynamical cross-correlation map and the results have been compared with those previously obtained for plastocyanin in H2O (Ciocchetti et al. Biophys. Chem. 69 (1997), 185-198). The simulated plastocyanin structure in the two solvents, averaging 1 ns, is very similar along the beta-structure regions, while the most significant differences are registered, analogous to the turns and the regions likely involved in the electron transfer pathway. Moreover, plastocyanin in D2O shows an increase in the number of both the intraprotein H-bonds and the residues involved in correlated motions. An analysis of the protein-solvent coupling evidenced that D2O makes the H-bond formation more difficult with the solvent molecules for positively charged and polar residues, while an opposite trend is observed for negatively charged residues. On the other hand, the frequency of exchange of the solvent molecules involved in the protein-solvent H-bond formation is significantly depressed in D2O. The results are discussed also in connection with protein functionality and briefly with some experimental results connected with the thermostability of proteins in D2O.
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Affiliation(s)
- R Guzzi
- Unita' INFM, Dipartimento di Fisica, Universita' della Calabria, I-87030 Rende, Italy.
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35
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Abstract
A comprehensive study of the hydration mechanism of an enzyme in nonaqueous media was done using molecular dynamics simulations in five organic solvents with different polarities, namely, hexane, 3-pentanone, diisopropyl ether, ethanol, and acetonitrile. In these solvents, the serine protease cutinase from Fusarium solani pisi was increasingly hydrated with 12 different hydration levels ranging from 5% to 100% (w/w) (weight of water/weight of protein). The ability of organic solvents to 'strip off' water from the enzyme surface was clearly dependent on the nature of the organic solvent. The rmsd of the enzyme from the crystal structure was shown to be lower at specific hydration levels, depending on the organic solvent used. It was also shown that organic solvents determine the structure and dynamics of water at the enzyme surface. Nonpolar solvents enhance the formation of large clusters of water that are tightly bound to the enzyme, whereas water in polar organic solvents is fragmented in small clusters loosely bound to the enzyme surface. Ions seem to play an important role in the stabilization of exposed charged residues, mainly at low hydration levels. A common feature is found for the preferential localization of water molecules at particular regions of the enzyme surface in all organic solvents: water seems to be localized at equivalent regions of the enzyme surface independently of the organic solvent employed.
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Affiliation(s)
- Nuno M Micaêlo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisoba, Oeiras, Portugal
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36
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Micaêlo NM, Soares CM. Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS J 2007. [DOI: 10.1111/j.0014-2956.2007.05781.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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GANDHI NEENAN, PATIL NITINS, SAWANT SUDHIRPRAKASHB, JOSHI JYESHTHARAJB, WANGIKAR PRAMODP, MUKESH D. Lipase-Catalyzed Esterification. CATALYSIS REVIEWS-SCIENCE AND ENGINEERING 2007. [DOI: 10.1081/cr-100101953] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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38
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Dominy BN. Parameterization and Application of an Implicit Solvent Model for Macromolecules. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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39
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Kurkal V, Daniel RM, Finney JL, Tehei M, Dunn RV, Smith JC. Enzyme activity and flexibility at very low hydration. Biophys J 2005; 89:1282-7. [PMID: 15894640 PMCID: PMC1366612 DOI: 10.1529/biophysj.104.058677] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent measurements have demonstrated enzyme activity at hydrations as low as 3%. This raises the question of whether hydration-induced enzyme flexibility is important for activity. Here, to address this, picosecond dynamic neutron scattering experiments are performed on pig liver esterase powders at 0%, 3%, 12%, and 50% hydration by weight and at temperatures ranging from 120 to 300 K. At all temperatures and hydrations, significant quasielastic scattering intensity is found in the protein, indicating the presence of anharmonic, diffusive motion. As the hydration increases, a temperature-dependent dynamical transition appears and strengthens involving additional diffusive motion. The implication of these results is that, although the additional hydration-induced diffusive motion in the protein detected here may be related to increased activity, it is not required for the enzyme to function.
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Affiliation(s)
- V Kurkal
- Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Germany
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40
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Tejo BA, Salleh AB, Pleiss J. Structure and dynamics of Candida rugosa lipase: the role of organic solvent. J Mol Model 2004; 10:358-66. [PMID: 15597204 DOI: 10.1007/s00894-004-0203-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2004] [Accepted: 07/13/2004] [Indexed: 11/27/2022]
Abstract
The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (C(alpha) rms deviation 1-1.3 A). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 A, organic solvent reduced flexibility to 0.9 A. This increase rigidity was caused by two salt bridges (Lys85-Asp284, Lys75-Asp79) and a stable hydrogen bond (Lys75-Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. [figure: see text]. Superimposition of open (black, PDB entry 1CRL) and closed (gray, PDB entry 1TRH) conformers of C. rugosa lipase. The mobile lid is indicated.
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Affiliation(s)
- Bimo Ario Tejo
- Department of Biochemistry and Microbiology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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41
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Dastidar SG, Mukhopadhyay C. Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2003; 68:021921. [PMID: 14525020 DOI: 10.1103/physreve.68.021921] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2003] [Indexed: 05/24/2023]
Abstract
The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.
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Affiliation(s)
- Shubhra Ghosh Dastidar
- Department of Chemistry, University of Calcutta, 92. A.P.C. Road, Kolkata, 700 009, India
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42
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Soares CM, Teixeira VH, Baptista AM. Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys J 2003; 84:1628-41. [PMID: 12609866 PMCID: PMC1302733 DOI: 10.1016/s0006-3495(03)74972-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Protein structure and dynamics in nonaqueous solvents are here investigated using molecular dynamics simulation studies, by considering two model proteins (ubiquitin and cutinase) in hexane, under varying hydration conditions. Ionization of the protein groups is treated assuming "pH memory," i.e., using the ionization states characteristic of aqueous solution. Neutralization of charged groups by counterions is done by considering a counterion for each charged group that cannot be made neutral by establishing a salt bridge with another charged group; this treatment is more physically reasonable for the nonaqueous situation, contrasting with the usual procedures. Our studies show that hydration has a profound effect on protein stability and flexibility in nonaqueous solvents. The structure becomes more nativelike with increasing values of hydration, up to a certain point, when further increases render it unstable and unfolding starts to occur. There is an optimal amount of water, approximately 10% (w/w), where the protein structure and flexibility are closer to the ones found in aqueous solution. This behavior can explain the experimentally known bell-shaped dependence of enzyme catalysis on hydration, and the molecular reasons for it are examined here. Water and counterions play a fundamental and dynamic role on protein stabilization, but they also seem to be important for protein unfolding at high percentages of bound water.
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Affiliation(s)
- Cláudio M Soares
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, Apartado 127, 2781-901 Oeiras, Portugal.
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43
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Bizzarri AR, Cannistraro S. Molecular Dynamics of Water at the Protein−Solvent Interface. J Phys Chem B 2002. [DOI: 10.1021/jp020100m] [Citation(s) in RCA: 440] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Rita Bizzarri
- Unita' INFM, Dipartimento di Scienze Ambientali, Universita’ della Tuscia, I-01100 Viterbo, Italy
| | - Salvatore Cannistraro
- Unita' INFM, Dipartimento di Scienze Ambientali, Universita’ della Tuscia, I-01100 Viterbo, Italy
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44
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Stabilization mechanism of MPEG modified trypsin based on thermal inactivation kinetic analysis and molecular modeling computation. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s1381-1177(00)00241-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Pencreac'h G, Baratti JC. Comparison of hydrolytic activity in water and heptane for thirty-two commercial lipase preparations. Enzyme Microb Technol 2001; 28:473-479. [PMID: 11240208 DOI: 10.1016/s0141-0229(00)00355-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The protein content and the rates of hydrolysis of p-nitrophenyl palmitate (pNPP) in water (soluble enzyme and emulsified substrate) and in heptane (soluble substrate and insoluble enzyme) were measured for thirty-two commercial lipase preparations. The protein content of the powders varied in a wide range as well as the activity on emulsified pNPP showing the high heterogeneity of the commercial samples. Activity in heptane also varied but to a lesser extent than that in water. There was no direct correlation between activities in water and in heptane as assayed with the same hydrolytic reaction. The ratio of activity in heptane to that in water, R(O/A) ratio, was introduced to characterize activity in organic media. Six lipases showed R(O/A) values higher than 1 demonstrating a higher activity in organic solvent than in water. A linear correlation of R(O/A) with activity in water (log plot) suggested the strong influence of diffusional limitations on activity of solid enzyme suspended in organic solvents.
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Affiliation(s)
- G Pencreac'h
- Université de la Méditerranée, Faculté des Sciences de Luminy, Biocatalyse et Chimie Fine, CNRS UMR 6111, Marseille, France
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46
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Cajal Y, Svendsen A, De Bolós J, Patkar SA, Alsina MA. Effect of the lipid interface on the catalytic activity and spectroscopic properties of a fungal lipase. Biochimie 2000; 82:1053-61. [PMID: 11099802 DOI: 10.1016/s0300-9084(00)01189-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Lipase from the fungi Thermomyces (formerly Humicola) lanuginosa (TlL) is widely used in industry. This interfacial enzyme is inactive under aqueous conditions, but catalytic activation is induced on binding to a lipid-water interface. In order for protein engineering to design more efficient mutants of TlL for specific applications, it is important to characterize its interfacial catalysis. A complete analysis of steady-state kinetics for the hydrolysis of a soluble substrate by TlL has been developed using an interface different from the substrate. Small vesicles of 1-palmitoyl-2-oleoylglycero-sn-3-phosphoglycerol (POPG) or other anionic phospholipids are a neutral diluent interface for the partitioning of substrate and enzyme. TlL binds to these interfaces in an active or open form, thus implying a displacement of the helical lid away from the active site. A study of the influence of substrate and diluent concentration dependence of the rate of hydrolysis provides a basis for the determination of the primary interfacial catalytic parameters. The interfacial activation is not supported by zwitterionic vesicles or by large anionic vesicles of 100 nm diameter, although TlL binds to these interfaces. Using a combination of fluorescence-based techniques applied to several mutants of TlL with different tryptophan residues we have shown that TlL binds to phospholipid vesicles in different forms rendering different catalytic activities, and that the open lid conformation is achieved and stabilized by a combination of electrostatic and hydrophobic interactions between the enzyme's lipid-binding face and the interface.
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Affiliation(s)
- Y Cajal
- Physical Chemistry Department, School of Pharmacy, University of Barcelona, Avn. Joan XXIII s/n, 08028, Barcelona, Spain.
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47
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Choi JH, Lee S. Correlation between the roughness degree of a protein surface and the mobility of solvent molecules on the surface. J Chem Phys 2000. [DOI: 10.1063/1.1309527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Higo J, Kono H, Nakamura H, Sarai A. Solvent density and long-range dipole field around a DNA-binding protein studied by molecular dynamics. Proteins 2000; 40:193-206. [PMID: 10842336 DOI: 10.1002/(sici)1097-0134(20000801)40:2<193::aid-prot30>3.0.co;2-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The distribution and orientation of solvent around a DNA-binding protein, 434 Cro, were investigated by molecular dynamics simulations with a periodic-boundary condition. The protein was treated in two states: charged and neutral. The computed high-density sites of the solvent around the protein correlated well with the experimentally determined crystal-water sites, in both the charged and neutral states. A local density map, introduced to investigate the solvent density around the highly mobile regions of the protein, showed a hydration shell around hydrophobic sidechains and hydrogen-bondable sites around hydrophilic sidechains, and also showed that the solvent density is sensitive to the slight concaves of the sidechain surface. The long-range solvent-dipole field was observed around the protein, where the pattern of the dipole ordering was considerably different between the charged and neutral states. A local solvent-dipole field was introduced, and the pattern of the dipole ordering was different between the hydrophobic and hydrophilic sidechains. The dipole field from the charged state provided a higher correlation to the electrostatic field obtained from the Poisson-Boltzmann's equation than that from the neutral state, although the correlation become weak quickly for the both states with increasing the protein-solvent distance.
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Affiliation(s)
- J Higo
- Biomolecular Engineering Research Institute (BERI), Suita, Osaka, Japan.
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49
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Walser R, Mark AE, van Gunsteren WF, Lauterbach M, Wipff G. The effect of force-field parameters on properties of liquids: Parametrization of a simple three-site model for methanol. J Chem Phys 2000. [DOI: 10.1063/1.481680] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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50
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Herrgård S, Gibas CJ, Subramaniam S. Role of an electrostatic network of residues in the enzymatic action of the Rhizomucor miehei lipase family. Biochemistry 2000; 39:2921-30. [PMID: 10715112 DOI: 10.1021/bi9916980] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have used continuum electrostatic methods to investigate the role of electrostatic interactions in the structure, function, and pH-dependent stability of the fungal Rhizomucor miehei lipase (RmL) family. We identify a functionally important electrostatic network which includes residues S144, D203, H257, Y260, H143, Y28, R80, and D91 (residue numbering is from RmL). This network consists of residues belonging to the catalytic triad (S144, D203, H257), residues located in proximity to the active site (Y260), residues stabilizing the geometry of the active site (Y28, H143), and residues located in the lid (D91) or close to the first hinge (R80). The lid and the first hinge are associated with the interfacial activation of lipases, where an alpha-helical lid opens up by rotating around two hinge regions. All network residues are well conserved in a set of 12 lipase homologues, and 6 of the network residues are located in sequence motifs. We observe that the effects of modeled mutations R86L, D91N, and H257F on the pH-dependent electrostatic free energies differ significantly in the closed and open conformations of RmL. Mutation R86L is especially interesting since it stabilizes the closed conformation but destabilizes the open one. Site-site electrostatic interaction energies reveal that interactions between R86 and D61, D113, and E117 stabilize the open conformation.
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Affiliation(s)
- S Herrgård
- Department of Molecular and Integrative Physiology, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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