1
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Hallier DC, Smales GJ, Seitz H, Hahn MB. Bio-SAXS of single-stranded DNA-binding proteins: radiation protection by the compatible solute ectoine. Phys Chem Chem Phys 2023; 25:5372-5382. [PMID: 36637121 DOI: 10.1039/d2cp05053f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL-1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies.
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Affiliation(s)
- Dorothea C Hallier
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), 14476 Potsdam, Germany.,Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
| | - Glen J Smales
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
| | - Harald Seitz
- Universität Potsdam, Institut für Biochemie und Biologie, 14476 Potsdam, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Branch Bioanalytics and Bioprocesses (IZI-BB), 14476 Potsdam, Germany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und -prüfung (BAM), 12205 Berlin, Germany.
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2
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Koopmann IK, Kramer A, Labes A. Development and validation of reliable astaxanthin quantification from natural sources. PLoS One 2022; 17:e0278504. [PMID: 36459522 PMCID: PMC9718415 DOI: 10.1371/journal.pone.0278504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 11/09/2022] [Indexed: 12/04/2022] Open
Abstract
Astaxanthin derived from natural sources occurs in the form of various esters and stereomers, which complicates its quantitative and qualitative analysis. To simplify and standardize astaxanthin measurement with high precision, an enzymolysis-based astaxanthin quantification method was developed to hydrolyze astaxanthin esters and determine free astaxanthin in all its diastereomeric forms. Astaxanthin standards and differently processed Haematococcus pluvialis biomass were investigated. Linear correlation of standards of all-E-astaxanthin was observed in a measurement range between extract concentrations of 1.0 μg/mL and 11.2 μg/mL with a coefficient of variation below 5%. The diastereomers 9Z-, and 13Z-astaxanthin, and two di-Z-forms were detected. In contrast to the measurement of standards, the observed measurement range was extended to 30 μg/mL in extracts from H. pluvialis. The nature of the sample had to be taken into account for measurement, as cell, respectively, sample composition altered the optimal concentration for astaxanthin determination. The measurement precision of all-E-astaxanthin quantification in dried H. pluvialis biomass (1.2-1.8 mg dried biomass per sample) was calculated with a coefficient of variation of maximum 1.1%, whereas it was below 10% regarding the diastereomers. Complete enzymolysis was performed with 1.0 to 2.0 units of cholesterol esterase in the presence of various solvents with up to 2.0 mg biomass (dry weight). The method was compared with other astaxanthin determination approaches in which astaxanthin is converted to acetone in a further step before measurement. The developed method resulted in a higher total astaxanthin recovery but lower selectivity of the diastereomers. The reliability of photometric astaxanthin estimations was assessed by comparing them with the developed chromatographic method. At later stages in the cell cycle of H. pluvialis, all methods yielded similar results (down to 0.1% deviation), but photometry lost precision at earlier stages (up to 31.5% deviation). To optimize sample storage, the shelf life of astaxanthin-containing samples was investigated. Temperatures below -20°C, excluding oxygen, and storing intact H. pluvialis cells instead of dried or disrupted biomass reduced astaxanthin degradation.
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Affiliation(s)
- Inga K. Koopmann
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
| | - Annemarie Kramer
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
| | - Antje Labes
- ZAiT, Center for Analytics in Technology Transfer of Bio and Food Technology Innovations, Flensburg University of Applied Sciences, Flensburg, Schleswig-Holstein, Germany
- * E-mail:
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3
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Camino JD, Gracia P, Chen SW, Sot J, de la Arada I, Sebastián V, Arrondo JLR, Goñi FM, Dobson CM, Cremades N. The extent of protein hydration dictates the preference for heterogeneous or homogeneous nucleation generating either parallel or antiparallel β-sheet α-synuclein aggregates. Chem Sci 2020; 11:11902-11914. [PMID: 33520152 PMCID: PMC7816767 DOI: 10.1039/d0sc05297c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/09/2020] [Indexed: 11/21/2022] Open
Abstract
α-Synuclein amyloid self-assembly is the hallmark of a number of neurodegenerative disorders, including Parkinson's disease, although there is still very limited understanding about the factors and mechanisms that trigger this process. Primary nucleation has been observed to be initiated in vitro at hydrophobic/hydrophilic interfaces by heterogeneous nucleation generating parallel β-sheet aggregates, although no such interfaces have yet been identified in vivo. In this work, we have discovered that α-synuclein can self-assemble into amyloid aggregates by homogeneous nucleation, without the need of an active surface, and with a preference for an antiparallel β-sheet arrangement. This particular structure has been previously proposed to be distinctive of stable toxic oligomers and we here demonstrate that it indeed represents the most stable structure of the preferred amyloid pathway triggered by homogeneous nucleation under limited hydration conditions, including those encountered inside α-synuclein droplets generated by liquid-liquid phase separation. In addition, our results highlight the key role that water plays not only in modulating the transition free energy of amyloid nucleation, and thus governing the initiation of the process, but also in dictating the type of preferred primary nucleation and the type of amyloid polymorph generated depending on the extent of protein hydration. These findings are particularly relevant in the context of in vivo α-synuclein aggregation where the protein can encounter a variety of hydration conditions in different cellular microenvironments, including the vicinity of lipid membranes or the interior of membraneless compartments, which could lead to the formation of remarkably different amyloid polymorphs by either heterogeneous or homogeneous nucleation.
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Affiliation(s)
- José D Camino
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC) , University of Zaragoza , 50018 Zaragoza , Spain .
| | - Pablo Gracia
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC) , University of Zaragoza , 50018 Zaragoza , Spain .
| | - Serene W Chen
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , UK
| | - Jesús Sot
- Biofisika Institute (CSIC, UPV/EHU) , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
| | - Igor de la Arada
- Biofisika Institute (CSIC, UPV/EHU) , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
| | - Víctor Sebastián
- Instituto de Nanociencia y Materiales de Aragon (INMA) , CSIC-Universidad de Zaragoza , 50009 Zaragoza , Spain
- Department of Chemical and Enviromental Engineering , Aragon Health Research Institute (IIS Aragon) , University of Zaragoza , 50018 Zaragoza , Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine , CIBER-BBN , 28029 Madrid , Spain
| | - José L R Arrondo
- Biofisika Institute (CSIC, UPV/EHU) , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
- Department of Biochemistry and Molecular Biology , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
| | - Félix M Goñi
- Biofisika Institute (CSIC, UPV/EHU) , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
- Department of Biochemistry and Molecular Biology , University of the Basque Country , Campus Universitario, B. Sarriena , 48940 Leioa , Spain
| | - Christopher M Dobson
- Centre for Misfolding Diseases , Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , UK
| | - Nunilo Cremades
- Biocomputation and Complex Systems Physics Institute (BIFI)-Joint Unit BIFI-IQFR (CSIC) , University of Zaragoza , 50018 Zaragoza , Spain .
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4
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Romodin LA, Vladimirov YA, Shangin SV, Vladimirov GK, Lysenko NP, Demikhov EI. Isoquinoline Coumarin Derivatives as Chemiluminescence Activators in Reactions of Lipid Peroxidation. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920040181] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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5
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Abstract
The aggregation of amyloid fibrils can lead to various diseases including Alzheimer's, Parkinson's disease, and transmissible spongiform encephalopathy. Amyloid fibrils can develop from a variety of proteins in the body as they misfold into a primarily β-sheet structure and aggregate. Human lysozyme has been shown to have far reaching effects in the human health-a homologous enzyme, hen egg-white lysozyme, has been shown to denature to a primarily β-sheet structure at low pH and high alcohol content solution. We have studied these systems in atomic-level detail with a combination of constant pH and microsecond long molecular dynamics simulation in explicit solvent, which cumulatively total over 10 μs of simulation time. These studies have allowed us to determine two potential unfolding pathways depending on the protonation state of a key glutamic acid residue as well as the effect of solution dynamics and pH on the unfolding process.
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Affiliation(s)
- Alice R. Walker
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Nikhil Baddam
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
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6
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Nandi S, Parui S, Halder R, Jana B, Bhattacharyya K. Interaction of proteins with ionic liquid, alcohol and DMSO and in situ generation of gold nano-clusters in a cell. Biophys Rev 2018; 10:757-768. [PMID: 29147940 PMCID: PMC5988615 DOI: 10.1007/s12551-017-0331-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 10/23/2017] [Indexed: 12/27/2022] Open
Abstract
In this review, we give a brief overview on how the interaction of proteins with ionic liquids, alcohols and dimethyl sulfoxide (DMSO) influences the stability, conformational dynamics and function of proteins/enzymes. We present experimental results obtained from fluorescence correlation spectroscopy on the effect of ionic liquid or alcohol or DMSO on the size (more precisely, the diffusion constant) and conformational dynamics of lysozyme, cytochrome c and human serum albumin in aqueous solution. The interaction of ionic liquid with biomolecules (e.g. protein, DNA etc.) has emerged as a current frontier. We demonstrate that ionic liquids are excellent stabilizers of protein and DNA and, in some cases, cause refolding of a protein already denatured by chemical denaturing agents. We show that in ethanol-water binary mixture, proteins undergo non-monotonic changes in size and dynamics with increasing ethanol content. We also discuss the effect of water-DMSO mixture on the stability of proteins. We demonstrate how large-scale molecular dynamics simulations have revealed the molecular origin of this observed phenomenon and provide a microscopic picture of the immediate environment of the biomolecules. Finally, we describe how favorable interactions of ionic liquids may be utilized for in situ generation of fluorescent gold nano-clusters for imaging a live cell.
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Affiliation(s)
- Somen Nandi
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Sridip Parui
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
| | - Kankan Bhattacharyya
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India.
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462 066, India.
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7
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Rueda AJV, Monzon AM, Ardanaz SM, Iglesias LE, Parisi G. Large scale analysis of protein conformational transitions from aqueous to non-aqueous media. BMC Bioinformatics 2018; 19:27. [PMID: 29382320 PMCID: PMC5791380 DOI: 10.1186/s12859-018-2044-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical arrangements when compared to their aqueous forms. However, it is well established that the catalytic activity of proteins in organic solvents is much lower than in water. In order to explain this diminished activity and to further characterize the behaviour of proteins in non-aqueous environments, we performed a large-scale analysis (1737 proteins) of the conformational diversity of proteins crystallized in aqueous and co-crystallized or soaked in non-aqueous media. Results Using proteins’ experimentally determined conformational diversity taken from CoDNaS database, we found that proteins in non-aqueous media display much lower conformational diversity when compared to the corresponding conformers obtained in water. When conformational diversity is compared between conformers obtained in different non-aqueous media, their structural differences are larger and mostly independent of the presence of cognate ligands. We also found that conformers corresponding to non-aqueous media have larger but less flexible cavities, lower number of disordered regions and lower active-site residue mobility. Conclusions Our results show that non-aqueous media conformers have specific structural features and that they do not adopt extreme conformations found in aqueous media. This makes them clearly different from their corresponding aqueous conformers. Electronic supplementary material The online version of this article (10.1186/s12859-018-2044-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Julia Velez Rueda
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Alexander Miguel Monzon
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Sebastián M Ardanaz
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Luis E Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, CONICET, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Provincia de Buenos Aires, Argentina.
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8
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Tokunaga H, Maeda J, Arakawa T, Tokunaga M. Reversible Activation of Halophilic β-lactamase from Methanol-Induced Inactive Form: Contrast to Irreversible Inactivation of Non-Halophilic Counterpart. Protein J 2017; 36:228-237. [DOI: 10.1007/s10930-017-9715-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Nonmonotonic Hydration Behavior of Bovine Serum Albumin in Alcohol/Water Binary Mixtures: A Terahertz Spectroscopic Investigation. Chemphyschem 2017; 18:749-754. [DOI: 10.1002/cphc.201601217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Indexed: 11/07/2022]
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10
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Vorontsova MA, Chan HY, Lubchenko V, Vekilov PG. Lack of Dependence of the Sizes of the Mesoscopic Protein Clusters on Electrostatics. Biophys J 2015; 109:1959-68. [PMID: 26536272 PMCID: PMC4643268 DOI: 10.1016/j.bpj.2015.09.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 12/21/2022] Open
Abstract
Protein-rich clusters of steady submicron size and narrow size distribution exist in protein solutions in apparent violation of the classical laws of phase equilibrium. Even though they contain a minor fraction of the total protein, evidence suggests that they may serve as essential precursors for the nucleation of ordered solids such as crystals, sickle-cell hemoglobin polymers, and amyloid fibrils. The cluster formation mechanism remains elusive. We use the highly basic protein lysozyme at nearly neutral and lower pH as a model and explore the response of the cluster population to the electrostatic forces, which govern numerous biophysical phenomena, including crystallization and fibrillization. We tune the strength of intermolecular electrostatic forces by varying the solution ionic strength I and pH and find that despite the weaker repulsion at higher I and pH, the cluster size remains constant. Cluster responses to the presence of urea and ethanol demonstrate that cluster formation is controlled by hydrophobic interactions between the peptide backbones, exposed to the solvent after partial protein unfolding that may lead to transient protein oligomers. These findings reveal that the mechanism of the mesoscopic clusters is fundamentally different from those underlying the two main classes of ordered protein solid phases, crystals and amyloid fibrils, and partial unfolding of the protein chain may play a significant role.
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Affiliation(s)
- Maria A Vorontsova
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas
| | - Ho Yin Chan
- Department of Physics, University of Houston, Houston, Texas
| | - Vassiliy Lubchenko
- Department of Physics, University of Houston, Houston, Texas; Department of Chemistry, University of Houston, Houston, Texas
| | - Peter G Vekilov
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas; Department of Chemistry, University of Houston, Houston, Texas.
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11
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Lotti M, Pleiss J, Valero F, Ferrer P. Effects of methanol on lipases: molecular, kinetic and process issues in the production of biodiesel. Biotechnol J 2014; 10:22-30. [PMID: 25046365 DOI: 10.1002/biot.201400158] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 04/05/2014] [Accepted: 06/11/2014] [Indexed: 01/05/2023]
Abstract
The biotechnological production of biodiesel is based on transesterification/esterification reactions between a source of fatty acids and a short-chain alcohol, usually methanol, catalysed by enzymes belonging to the class known as lipases. Several lipases used in industrial processes, although stable in the presence of other organic solvents, are inactivated by methanol at or below the concentration optimal for biodiesel production, making it necessary to use stepwise methanol feeding or pre-treatment of the enzyme. In this review article we focus on what is currently know about methanol inactivation of lipases, a phenomenon which is not common to all lipase enzymes, with the goal of improving the biocatalytic process. We suggest that different mechanisms can lead to inactivation of different lipases, in particular substrate inhibition and protein unfolding. Attempts to improve the performances of methanol sensitive lipases by mutagenesis as well as process engineering approaches are also summarized.
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Affiliation(s)
- Marina Lotti
- Department of Biotechnology and Biosciences, State University of Milano Bicocca, Milano, Italy.
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12
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Alvarez-Garcia D, Barril X. Relationship between Protein Flexibility and Binding: Lessons for Structure-Based Drug Design. J Chem Theory Comput 2014; 10:2608-14. [DOI: 10.1021/ct500182z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Alvarez-Garcia
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Xavier Barril
- Departament
de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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13
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Diffusion Properties of the Ternary System Human Serum Albumin–Sodium Cholate–Water. J SOLUTION CHEM 2014. [DOI: 10.1007/s10953-014-0179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Chattoraj S, Mandal AK, Bhattacharyya K. Effect of ethanol-water mixture on the structure and dynamics of lysozyme: A fluorescence correlation spectroscopy study. J Chem Phys 2014; 140:115105. [DOI: 10.1063/1.4868642] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Lexa KW, Carlson HA. Improving protocols for protein mapping through proper comparison to crystallography data. J Chem Inf Model 2013; 53:391-402. [PMID: 23327200 DOI: 10.1021/ci300430v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective-or even erroneous-atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. On the basis of comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future multiple solvent crystallographic structures.
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Affiliation(s)
- Katrina W Lexa
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109-1065, USA
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16
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Lousa D, Cianci M, Helliwell JR, Halling PJ, Baptista AM, Soares CM. Interaction of Counterions with Subtilisin in Acetonitrile: Insights from Molecular Dynamics Simulations. J Phys Chem B 2012; 116:5838-48. [DOI: 10.1021/jp303008g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Diana Lousa
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Michele Cianci
- European Molecular
Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestraße 85, 22603 Hamburg, Germany
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Manchester M13 9PL, United
Kingdom
| | - Peter J. Halling
- WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
| | - Cláudio M. Soares
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras,
Portugal
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17
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Idris A, Bukhari A. Immobilized Candida antarctica lipase B: Hydration, stripping off and application in ring opening polyester synthesis. Biotechnol Adv 2011; 30:550-63. [PMID: 22041165 DOI: 10.1016/j.biotechadv.2011.10.002] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Revised: 09/09/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
Abstract
This work reviews the stripping off, role of water molecules in activity, and flexibility of immobilized Candida antarctica lipase B (CALB). Employment of CALB in ring opening polyester synthesis emphasizing on a polylactide is discussed in detail. Execution of enzymes in place of inorganic catalysts is the most green alternative for sustainable and environment friendly synthesis of products on an industrial scale. Robust immobilization and consequently performance of enzyme is the essential objective of enzyme application in industry. Water bound to the surface of an enzyme (contact class of water molecules) is inevitable for enzyme performance; it controls enzyme dynamics via flexibility changes and has intensive influence on enzyme activity. The value of pH during immobilization of CALB plays a critical role in fixing the active conformation of an enzyme. Comprehensive selection of support and protocol can develop a robust immobilized enzyme thus enhancing its performance. Organic solvents with a log P value higher than four are more suitable for enzymatic catalysis as these solvents tend to strip away very little of the enzyme surface bound water molecules. Alternatively ionic liquid can work as a more promising reaction media. Covalent immobilization is an exclusively reliable technique to circumvent the leaching of enzymes and to enhance stability. Activated polystyrene nanoparticles can prove to be a practical and economical support for chemical immobilization of CALB. In order to reduce the E-factor for the synthesis of biodegradable polymers; enzymatic ring opening polyester synthesis (eROPS) of cyclic monomers is a more sensible route for polyester synthesis. Synergies obtained from ionic liquids and immobilized enzyme can be much effective eROPS.
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Affiliation(s)
- Ani Idris
- Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310 UTM Skudai, Johor, Malaysia.
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Nabati F, Habibi-Rezaei M, Amanlou M, Moosavi-Movahedi A. Dioxane enhanced immobilization of urease on alkyl modified nano-porous silica using reversible denaturation approach. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2011.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Yang CY, Wang S. Hydrophobic Binding Hot Spots of Bcl-xL Protein-Protein Interfaces by Cosolvent Molecular Dynamics Simulation. ACS Med Chem Lett 2011; 2:280-4. [PMID: 24900309 PMCID: PMC4018050 DOI: 10.1021/ml100276b] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 01/05/2011] [Indexed: 12/31/2022] Open
Abstract
Identifying binding hot spots in protein-protein interfaces is important for understanding the binding specificity and for the design of nonpeptide, small molecule inhibitors. Molecular dynamics simulation in the isopropanol/water cosolvent environment and in water was employed to investigate Bcl-xL protein, which has a highly flexible, large, and primarily hydrophobic binding site. Simulations of either the apo- or holocrystal structures of the Bcl-xL in pure water fail to generate conformations found in the cocrystal structures of Bcl-xL in complex with its binding partners due to hydrophobic collapse. In contrast, simulations in cosolvent starting either from the apo- or holocrystal structure of the Bcl-xL yield binding-site conformations similar to that found in the cocrystal structures of Bcl-xL. Hydrophobic binding hot spots identified using the conformations from the cosolvent simulations are in excellent agreement with experimental structural data of known inhibitors. Importantly, cosolvent simulations revealed the highly dynamic nature of the hydrophobic binding pockets in Bcl-xL and yielded new structural insights for the design of novel Bcl-xL small-molecule inhibitors.
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Affiliation(s)
- Chao-Yie Yang
- Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States
| | - Shaomeng Wang
- Comprehensive Cancer Center, Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States
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Capuano F, Paduano L, D'Errico G, Mangiapia G, Sartorio R. Diffusion in ternary aqueous systems containing human serum albumin and precipitants of different classes. Phys Chem Chem Phys 2011; 13:3319-27. [DOI: 10.1039/c0cp00761g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Xiong K, Asher SA. Circular dichroism and UV resonance raman study of the impact of alcohols on the Gibbs free energy landscape of an alpha-helical peptide. Biochemistry 2010; 49:3336-42. [PMID: 20225890 DOI: 10.1021/bi100176a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We used CD and UV resonance Raman spectroscopy to study the impact of alcohols on the conformational equilibria and relative Gibbs free energy landscapes along the Ramachandran Psi-coordinate of a mainly poly-Ala peptide, AP with an AAAAA(AAARA)(3)A sequence. 2,2,2-Trifluoroethanol (TFE) most stabilizes the alpha-helix-like conformations, followed by ethanol, methanol, and pure water. The pi-bulge conformation is stabilized more than the alpha-helix, while the 3(10)-helix is destabilized due to the alcohol-increased hydrophobicity. Turns are also stabilized by alcohols. We also found that while TFE induces more alpha-helices, it favors multiple, shorter helix segments.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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Kaczka P, Polkowska-Nowakowska A, Bolewska K, Zhukov I, Poznański J, Wierzchowski KL. Backbone dynamics of TFE-induced native-like fold of region 4 of Escherichia coli RNA polymerase sigma70 subunit. Proteins 2010; 78:754-68. [PMID: 19847776 DOI: 10.1002/prot.22607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Folding of a recombinant protein rECsigma(70) (4) comprising domain 4 of E. coli RNA polymerase sigma(70) subunit, upon addition of 2,2,2-trifluoroethanol (TFE) to its aqueous solution, was monitored by heteronuclear NMR spectroscopy. The TFE-induced migration of resonance signals in a series of (15)N-HSQC spectra displayed sequence-dependent heterogeneity. A common trend of uniform upfield shift in both (1)H and (15)N dimensions, indicative of generation of helical structures, breaks down for some residues almost cooperatively at 10-15% TFE (v/v), pointing to the buildup of non-helical regions separating the initially induced helices. The preferences of residues to assume either helical or non-helical conformation are correlated with the location in the sequence rather than with their type. CSI descriptors and (15)N relaxation data obtained for the protein at 10% TFE allowed characterization of the stability of the pre-folded state of rECsigma(70) (4). By all the criteria applied, three highly populated alpha-helical regions separated by much more flexible residues forming a loop and a turn in the DNA-binding HLHTH motif were identified. The location of the secondary structure elements along the protein sequence coincides with those found in homologous proteins, and with the helix nucleation regions determined in unfolded rECsigma(70) (4) at low pH. The bimodal distribution of the (15)N relaxation parameters enabled identification of residues forming a framework of the folded protein strictly corresponding to the HLHTH motif, bracketed by unfolded terminal regions. Thus, in respect to rECsigma(70) (4) in aqueous solution TFE acts not only as a strong helix inducer, but also as a folding agent.
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Affiliation(s)
- Piotr Kaczka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warszawa, Poland
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Meersman F, Bowron D, Soper AK, Koch MHJ. Counteraction of urea by trimethylamine N-oxide is due to direct interaction. Biophys J 2009; 97:2559-66. [PMID: 19883599 PMCID: PMC2770612 DOI: 10.1016/j.bpj.2009.08.017] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 08/12/2009] [Accepted: 08/13/2009] [Indexed: 10/20/2022] Open
Abstract
Trimethylamine N-oxide (TMAO) is a naturally occurring osmolyte that stabilizes proteins, induces folding, and counteracts the denaturing effects of urea, pressure, and ice. To establish the mechanism behind these effects, isotopic substitution neutron-scattering measurements were performed on aqueous solutions of TMAO and 1:1 TMAO-urea at a solute mole fraction of 0.05. The partial pair distribution functions were extracted using the empirical potential structure refinement method. The results were compared with previous results obtained with isosteric tert-butanol, as well as the available data from spectroscopy and molecular-dynamics simulations. In solution, the oxygen atom of TMAO is strongly hydrogen-bonded to, on average, between two and three water molecules, and the hydrogen-bond network is tighter in water than in pure water. In TMAO-urea solutions, the oxygen atom in TMAO preferentially forms hydrogen bonds with urea. This explains why the counteraction is completed at a 2:1 urea/TMAO concentration ratio, independently of urea concentration. These results strongly support models for the effect of TMAO on the stability of proteins based on a modification of the simultaneous equilibria that control hydrogen bonding between the peptide backbone and water or intramolecular sites, without any need for direct interaction between TMAO and the protein.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium.
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Influence of alcohols and osmolytes on thermal stability and catalytic activity of myoglobin: Co-solvent clustering effects. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Michaux C, Pouyez J, Wouters J, Privé GG. Protecting role of cosolvents in protein denaturation by SDS: a structural study. BMC STRUCTURAL BIOLOGY 2008; 8:29. [PMID: 18522744 PMCID: PMC2429906 DOI: 10.1186/1472-6807-8-29] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 06/03/2008] [Indexed: 11/12/2022]
Abstract
Background Recently, we reported a unique approach to preserve the activity of some proteins in the presence of the denaturing agent, Sodium Dodecyl Sulfate (SDS). This was made possible by addition of the amphipathic solvent 2,4-Methyl-2-PentaneDiol (MPD), used as protecting but also as refolding agent for these proteins. Although the persistence of the protein activity in the SDS/MPD mixture was clearly established, preservation of their structure was only speculative until now. Results In this paper, a detailed X-ray study addresses the pending question. Crystals of hen egg-white lysozyme were grown for the first time in the presence of MPD and denaturing concentrations of SDS. Depending on crystallization conditions, tetragonal crystals in complex with either SDS or MPD were collected. The conformation of both structures was very similar to the native lysozyme and the obtained complexes of SDS-lysozyme and MPD-lysozyme give some insights in the interplay of protein-SDS and protein-MPD interactions. Conclusion This study clearly established the preservation of the enzyme structure in a SDS/MPD mixture. It is hypothesized that high concentrations of MPD would change the properties of SDS and lower or avoid interactions between the denaturant and the protein. These structural data therefore support the hypothesis that MPD avoids disruption of the enzyme structure by SDS and can protect proteins from SDS denaturation.
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Affiliation(s)
- Catherine Michaux
- Chemistry department, CBS lab, CPTS group, 61 rue de Bruxelles, B-5000 Namur, Belgium.
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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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Murugan R, Mazumdar S. Effect of alcohols on binding of camphor to cytochrome P450cam: Spectroscopic and stopped flow transient kinetic studies. Arch Biochem Biophys 2006; 455:154-62. [PMID: 17049478 DOI: 10.1016/j.abb.2006.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 09/10/2006] [Accepted: 09/11/2006] [Indexed: 10/24/2022]
Abstract
Addition of alcohols to cytochrome P450cam (CYP101) was shown to release the substrate camphor from the heme pocket of the enzyme. The release of the substrate was found to be caused both due to increased solubility of the substrate in solution in presence of alcohol and due to change in the tertiary structure of the active site of the enzyme. The far-UV CD and near-UV CD spectra reveal that addition of alcohols to cytochrome P450cam cause a small change in the secondary structural elements but a significant change in the tertiary structural organization of this enzyme. The CD spectra at the heme region at various concentrations of alcohols indicate a substantial change in the tertiary structural organization around the heme moiety too. The equilibrium constant associated with the binding of camphor to Cyt P450cam is strongly dependent on the concentration of alcohols and the corresponding free energy associated with the binding is found to scale linearly with the concentration of alcohols. Kinetic experiments on binding of camphor to Cyt P450cam show that both k(on) and k(off) rate constants are strongly affected by addition of alcohols suggesting that alcohol expel camphor out of the heme cavity of Cyt P450cam by affecting tertiary structure of Cyt P450cam as well as by modifying the solubility properties of camphor in aqueous medium.
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Affiliation(s)
- R Murugan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
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