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Cui H, Vedder M, Schwaneberg U, Davari MD. Using Molecular Simulation to Guide Protein Engineering for Biocatalysis in Organic Solvents. Methods Mol Biol 2022; 2397:179-202. [PMID: 34813065 DOI: 10.1007/978-1-0716-1826-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biocatalysis in organic solvents (OSs) is very appealing for the industry in producing bulk and/or fine chemicals, such as pharmaceuticals, biodiesel, and fragrances. The poor performance of enzymes in OSs (e.g., reduced activity, insufficient stability, and deactivation) negates OSs' excellent solvent properties. Molecular dynamics (MD) simulations provide a complementary method to study the relationship between enzymes dynamics and the stability in OSs. Here we describe computational procedure for MD simulation of enzymes in OSs with an example of Bacillus subtilis lipase A (BSLA) in dimethyl sulfoxide (DMSO) cosolvent with software GROMACS. We discuss main essential practical issues considered (such as choice of force field, parameterization, simulation setup, and trajectory analysis). The core part of this protocol (enzyme-OS system setup, analysis of structural-based and solvation-based observables) is transferable to other enzymes and any OS systems. Combining with experimental studies, the obtained molecular knowledge is most likely to guide researchers to access rational protein engineering approaches to tailor OS resistant enzymes and expand the scope of biocatalysis in OS media. Finally, we discuss potential solutions to overcome the remaining challenges of computational biocatalysis in OSs and briefly draw future directions for further improvement in this field.
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Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Markus Vedder
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
- DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.
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2
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Anand S, Swami P, Goel G, Gupta S. Zwitterions for impedance spectroscopy: The new buffers in town. Anal Chim Acta 2021; 1166:338547. [PMID: 34022999 DOI: 10.1016/j.aca.2021.338547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/03/2021] [Accepted: 04/05/2021] [Indexed: 11/29/2022]
Abstract
Studying the role of buffers in impedance spectroscopy is a relatively unexplored area. We demonstrate a special class of biologically relevant buffers known as Good's zwitterionic buffers that show improved performance over standard electrolyte buffers (e.g. PBS) currently widely used in impedance spectroscopy measurements of bacterial suspensions. Our theoretical and experimental comparisons of conductivity of classical and zwitterionic buffers at various different concentrations show that ion-ion interaction effects are significantly higher in zwitterionic buffers as compared to classical buffers at the concentrations at which they are used. This and the fact that zwitterions have larger sizes leads to the lowering of their conductivity which significantly improves their impedance sensing ability. We illustrate through an example of heat-induced ionic release in model S. typhi and S. aureus bacteria that having a low conductivity buffer is indeed beneficial for biological impedance measurements. In fact, the best buffer for impedance studies can be chosen solely based on their electrical properties as long as they are also biologically compatible. This gives Good's zwitterionic buffers an edge over conventional media as they satisfy both these criteria.
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Affiliation(s)
- Satyam Anand
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Pragya Swami
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Gaurav Goel
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India.
| | - Shalini Gupta
- Dept. of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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3
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Alencar L, Passos L, Martins M, Barreto I, Soares C, Lima A, Souza R. Complete process for the selective recovery of textile dyes using aqueous two-phase system. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.117502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Egorov GI, Makarov DM. Densities and thermal expansions of (water + tetrahydrofuran) mixtures within the temperature range from (274.15 to 333.15) K at atmospheric pressure. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113105] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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6
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Liu X, Cheng K, Jia G. Investigation of nonlinear dielectric response of DMSO-methanol mixture by molecular dynamics simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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Taha M, Nassar HF. Molecular design of mass-separating agents for separation of cyclic ethers and acetonitrile from water. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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8
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Rani A, Taha M, Venkatesu P, Lee MJ. Coherent Experimental and Simulation Approach To Explore the Underlying Mechanism of Denaturation of Stem Bromelain in Osmolytes. J Phys Chem B 2017; 121:6456-6470. [DOI: 10.1021/acs.jpcb.7b01776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anjeeta Rani
- Department
of Chemistry, University of Delhi, Delhi 110 007, India
| | - Mohamed Taha
- Department
of Chemistry, College of Science, Sultan Qaboos University, PO Box 36, PC 123 Muscat, Oman
| | | | - Ming- Jer Lee
- Department of Chemical Engineering, National Taiwan University of Science & Technology, Taipei 10607, Taiwan
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Separation of 1,3-dioxolane, 1,4-dioxane, acetonitrile and tert -butanol from their aqueous solutions by using Good's buffer HEPES-Na as an auxiliary agent. J Taiwan Inst Chem Eng 2016. [DOI: 10.1016/j.jtice.2016.06.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Taha M, Coutinho JA. Organic-phase biological buffers for biochemical and biological research in organic media. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.05.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Cao Z, Voth GA. The multiscale coarse-graining method. XI. Accurate interactions based on the centers of charge of coarse-grained sites. J Chem Phys 2016; 143:243116. [PMID: 26723601 DOI: 10.1063/1.4933249] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and accurately reproduce key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operator are found to better reproduce the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.
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Affiliation(s)
- Zhen Cao
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, 5735 S Ellis Ave., Chicago, Illinois 60637, USA
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Souza RL, Lima RA, Coutinho JA, Soares CM, Lima ÁS. Aqueous two-phase systems based on cholinium salts and tetrahydrofuran and their use for lipase purification. Sep Purif Technol 2015. [DOI: 10.1016/j.seppur.2015.05.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Novel aqueous two-phase systems based on tetrahydrofuran and potassium phosphate buffer for purification of lipase. Process Biochem 2015. [DOI: 10.1016/j.procbio.2015.05.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gupta BS, Taha M, Lee MJ. Buffers more than buffering agent: introducing a new class of stabilizers for the protein BSA. Phys Chem Chem Phys 2015; 17:1114-33. [DOI: 10.1039/c4cp04663c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we have analyzed the influence of four biological buffers on the thermal stability of bovine serum albumin (BSA) using dynamic light scattering (DLS).
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Affiliation(s)
- Bhupender S. Gupta
- Department of Chemical Engineering
- National Taiwan University of Science and Technology
- Taipei 106-07
- Taiwan
| | - Mohamed Taha
- CICECO
- Departamento de Química
- Universidade de Aveiro
- Portugal
| | - Ming-Jer Lee
- Department of Chemical Engineering
- National Taiwan University of Science and Technology
- Taipei 106-07
- Taiwan
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Taha M, e Silva FA, Quental MV, Ventura SPM, Freire MG, Coutinho JAP. Good's buffers as a basis for developing self-buffering and biocompatible ionic liquids for biological research. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2014; 16:3149-3159. [PMID: 25729325 PMCID: PMC4340528 DOI: 10.1039/c4gc00328d] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
This work reports a promising approach to the development of novel self-buffering and biocompatible ionic liquids for biological research in which the anions are derived from biological buffers (Good's buffers, GB). Five Good's buffers (Tricine, TES, CHES, HEPES, and MES) were neutralized with four suitable hydroxide bases (1-ethyl-3-methylimidazolium, tetramethylammonium, tetraethylammonium, and tetrabutylammonium) producing 20 Good's buffer ionic liquids (GB-ILs). The presence of the buffering action of the synthesized GB-ILs was ascertained by measuring their pH-profiles in water. Moreover, a series of mixed GB-ILs with wide buffering ranges were formulated as universal buffers. The impact of GB-ILs on bovine serum albumin (BSA), here used as a model protein, is discussed and compared with more conventional ILs using spectroscopic techniques, such as infrared and dynamic light scattering. They appear to display, in general, a greater stabilizing effect on the protein secondary structure than conventional ILs. A molecular docking study was also carried out to investigate on the binding sites of GB-IL ions to BSA. We further used the QSAR-human serum albumin binding model, log K(HSA), to calculate the binding affinity of some conventional ILs/GB-ILs to HSA. The toxicity of the GB and GB-ILs was additionally evaluated revealing that they are non-toxic against Vitro fischeri. Finally, the GB-ILs were also shown to be able to form aqueous biphasic systems when combined with aqueous solutions of inorganic or organic salts, and we tested their extraction capability for BSA. These systems were able to extract BSA with an outstanding extraction efficiency of 100% in a single step for the GB-IL-rich phase, and, as a result, the use of GB-IL-based ABS for the separation and extraction of other added-value biomolecules is highly encouraging and worthy of further investigation.
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Taha M, Lee MJ. TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: phase diagrams and molecular dynamic simulations. J Chem Phys 2014; 138:244501. [PMID: 23822250 DOI: 10.1063/1.4809995] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol∕acetonitrile∕acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials.
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Affiliation(s)
- Mohamed Taha
- Department of Chemical Engineering, National Taiwan University of Science and Technology, 43 Keelung Road, Section 4, Taipei 106-07, Taiwan
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