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Jian Y, Han Y, Fu Z, Xia M, Jiang G, Lu D, Wu J, Liu Z. The role of conformational dynamics on the activity of polymer-conjugated CalB in organic solvents. Phys Chem Chem Phys 2022; 24:22028-22037. [DOI: 10.1039/d2cp02208g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A perennial interest in enzyme catalysis has been expanding its applicability from aqueous phase where enzymes are naturally evolved to organic solvents in which the majority of industrial chemical synthesis...
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2
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Chambers JM, Miller W, Quichocho G, Upadhye V, Matteo DA, Bobkov AA, Sohl CD, Schiffer JM. Water Networks and Correlated Motions in Mutant Isocitrate Dehydrogenase 1 (IDH1) Are Critical for Allosteric Inhibitor Binding and Activity. Biochemistry 2020; 59:479-490. [PMID: 31869219 DOI: 10.1021/acs.biochem.9b01023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Point mutations in human isocitrate dehydrogenase 1 (IDH1) can drive malignancies, including lower-grade gliomas and secondary glioblastomas, chondrosarcomas, and acute myeloid leukemias. These mutations, which usually affect residue R132, ablate the normal activity of catalyzing the NADP+-dependent oxidation of isocitrate to α-ketoglutarate (αKG) while also acquiring a neomorphic activity of reducing αKG to d-2-hydroxyglutarate (D2HG). Mutant IDH1 can be selectively therapeutically targeted due to structural differences that occur in the wild type (WT) versus mutant form of the enzyme, though the full mechanisms of this selectivity are still under investigation. Here we probe the mechanistic features of the neomorphic activity and selective small molecule inhibition through a new lens, employing WaterMap and molecular dynamics simulations. These tools identified a high-energy path of water molecules connecting the inhibitor binding site with the αKG and NADP+ binding sites in mutant IDH1. This water path aligns spatially with the α10 helix from WT IDH1 crystal structures. Mutating residues at the termini of this water path specifically disrupted inhibitor binding and/or D2HG production, revealing additional key residues to consider in optimizing druglike molecules against mutant IDH1. Taken together, our findings from molecular simulations and mutant enzyme kinetic assays provide insight into how disrupting water paths through enzyme active sites can impact not only inhibitor potency but also substrate recognition and activity.
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Affiliation(s)
- Jennifer M Chambers
- Schrödinger , 120 West 45th Street , New York , New York 10036 , United States
| | - Wade Miller
- Schrödinger , 222 Third Street, Suite 2230 , Cambridge , Massachusetts 02142 , United States
| | - Giovanni Quichocho
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Viraj Upadhye
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Diego Avellaneda Matteo
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute , La Jolla , California 92037 , United States
| | - Christal D Sohl
- Department of Chemistry and Biochemistry , San Diego State University , San Diego , California 92182 , United States
| | - Jamie M Schiffer
- Janssen Research and Development , 3210 Merryfield Row , San Diego , California 92121 , United States
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3
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Dahanayake JN, Shahryari E, Roberts KM, Heikes ME, Kasireddy C, Mitchell-Koch KR. Protein Solvent Shell Structure Provides Rapid Analysis of Hydration Dynamics. J Chem Inf Model 2019; 59:2407-2422. [PMID: 30865440 DOI: 10.1021/acs.jcim.9b00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structure of the solvation layer around different regions of the enzyme Candida antarctica lipase B, wherein the radial distribution function (RDF) was used to calculate the pairwise entropy, providing a link between dynamics (diffusion) and thermodynamics (excess entropy) known as Rosenfeld scaling. Regions with higher RDF values/peaks in the hydration layer (the first peak, within 6 Å of the protein surface) have faster diffusion in the hydration layer. The finding thus hinted at a handle for rapid evaluation of hydration dynamics at different regions on the protein surface in molecular dynamics simulations. Such an approach may move the analysis of hydration dynamics from a specialized venture to routine analysis, enabling an informatics approach to evaluate the role of hydration dynamics in biomolecular function. This paper first confirms that the correlation between regional diffusive dynamics and hydration layer structure (via water center of mass around protein side-chain atom RDF) is observed as a general relationship across a set of proteins. Second, it seeks to devise an approach for rapid analysis of hydration dynamics, determining the minimum amount of information and computational effort required to get a reliable value of hydration dynamics from structural data in MD simulations based on the protein-water RDF. A linear regression model using the integral of the hydration layer in the water-protein RDF was found to provide statistically equivalent apparent diffusion coefficients at the 95% confidence level for a set of 92 regions within five different proteins. In summary, RDF analysis of 10 ns of data after simulation convergence is sufficient to accurately map regions of fast and slow hydration dynamics around a protein surface. Additionally, it is anticipated that a quick look at protein-water RDFs, comparing peak heights, will be useful to provide a qualitative ranking of regions of faster and slower hydration dynamics at the protein surface for rapid analysis when investigating the role of solvent dynamics in protein function.
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Affiliation(s)
- Jayangika N Dahanayake
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Elaheh Shahryari
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Kirsten M Roberts
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Micah E Heikes
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Chandana Kasireddy
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
| | - Katie R Mitchell-Koch
- Department of Chemistry , Wichita State University , 1845 Fairmount Street , Wichita , Kansas 67260-0051 , United States
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4
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Brotzakis ZF, Voets IK, Bakker HJ, Bolhuis PG. Water structure and dynamics in the hydration layer of a type III anti-freeze protein. Phys Chem Chem Phys 2018; 20:6996-7006. [PMID: 29468240 DOI: 10.1039/c8cp00170g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a molecular dynamics study on the relation between the structure and the orientational (and hydrogen bond) dynamics of hydration water around the ocean pout AFP III anti-freeze protein. We find evidence for an increasing tetrahedral structure from the area opposite to the ice binding site (IBS) towards the protein IBS, with the strongest signal of tetrahedral structure around the THR-18 residue of the IBS. The tetrahedral structural parameter mostly positively correlates with increased reorientation decay times. Interestingly, for several key (polar) residues that are not part of the IBS but are in its vicinity, we observe a decrease of the reorientation time with increasing tetrahedral structure. A similar anti-correlation is observed for the hydrogen-bonded water molecules. These effects are enhanced at a lower temperature. We interpret these results in terms of the structure-making and structure-breaking residues. Moreover, we investigate the tetrahedral structure and dynamics of waters at a partially dehydrated IBS, and for the protein adsorbed at the air-water interface. We find that the mutation changes the preferred protein orientation upon adsorption at an air-water interface. These results are in agreement with the water-air Vibration Sum Frequency Generation spectroscopic experiments showing a strongly reduced tetrahedral signal upon mutation at the IBS.
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Affiliation(s)
- Z Faidon Brotzakis
- Van't Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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5
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Low temperature dependence of protein-water interactions on barstar surface: A nano-scale modelling. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.10.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Dahanayake JN, Mitchell-Koch KR. How Does Solvation Layer Mobility Affect Protein Structural Dynamics? Front Mol Biosci 2018; 5:65. [PMID: 30057902 PMCID: PMC6053501 DOI: 10.3389/fmolb.2018.00065] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/20/2018] [Indexed: 11/18/2022] Open
Abstract
Solvation is critical for protein structural dynamics. Spectroscopic studies have indicated relationships between protein and solvent dynamics, and rates of gas binding to heme proteins in aqueous solution were previously observed to depend inversely on solution viscosity. In this work, the solvent-compatible enzyme Candida antarctica lipase B, which functions in aqueous and organic solvents, was modeled using molecular dynamics simulations. Data was obtained for the enzyme in acetonitrile, cyclohexane, n-butanol, and tert-butanol, in addition to water. Protein dynamics and solvation shell dynamics are characterized regionally: for each α-helix, β-sheet, and loop or connector region. Correlations are seen between solvent mobility and protein flexibility. So, does local viscosity explain the relationship between protein structural dynamics and solvation layer dynamics? Halle and Davidovic presented a cogent analysis of data describing the global hydrodynamics of a protein (tumbling in solution) that fits a model in which the protein's interfacial viscosity is higher than that of bulk water's, due to retarded water dynamics in the hydration layer (measured in NMR τ2 reorientation times). Numerous experiments have shown coupling between protein and solvation layer dynamics in site-specific measurements. Our data provides spatially-resolved characterization of solvent shell dynamics, showing correlations between regional solvation layer dynamics and protein dynamics in both aqueous and organic solvents. Correlations between protein flexibility and inverse solvent viscosity (1/η) are considered across several protein regions and for a rather disparate collection of solvents. It is seen that the correlation is consistently higher when local solvent shell dynamics are considered, rather than bulk viscosity. Protein flexibility is seen to correlate best with either the local interfacial viscosity or the ratio of the mobility of an organic solvent in a regional solvation layer relative to hydration dynamics around the same region. Results provide insight into the function of aqueous proteins, while also suggesting a framework for interpreting and predicting enzyme structural dynamics in non-aqueous solvents, based on the mobility of solvents within the solvation layer. We suggest that Kramers' theory may be used in future work to model protein conformational transitions in different solvents by incorporating local viscosity effects.
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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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Duboué-Dijon E, Pluhařová E, Domin D, Sen K, Fogarty AC, Chéron N, Laage D. Coupled Valence-Bond State Molecular Dynamics Description of an Enzyme-Catalyzed Reaction in a Non-Aqueous Organic Solvent. J Phys Chem B 2017; 121:7027-7041. [PMID: 28675789 DOI: 10.1021/acs.jpcb.7b03102] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are widely used in nonaqueous solvents to catalyze non-natural reactions. While experimental measurements showed that the solvent nature has a strong effect on the reaction kinetics, the molecular details of the catalytic mechanism in nonaqueous solvents have remained largely elusive. Here we study the transesterification reaction catalyzed by the paradigm subtilisin Carlsberg serine protease in an organic apolar solvent. The rate-limiting acylation step involves a proton transfer between active-site residues and the nucleophilic attack of the substrate to form a tetrahedral intermediate. We design the first coupled valence-bond state model that simultaneously describes both reactions in the enzymatic active site. We develop a new systematic procedure to parametrize this model on high-level ab initio QM/MM free energy calculations that account for the molecular details of the active site and for both substrate and protein conformational fluctuations. Our calculations show that the reaction energy barrier changes dramatically with the solvent and protein conformational fluctuations. We find that the mechanism of the tetrahedral intermediate formation during the acylation step is similar to that determined under aqueous conditions, and that the proton transfer and nucleophilic attack reactions occur concertedly. We identify the reaction coordinate to be mostly due to the rearrangement of some residual water molecules close to the active site.
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Affiliation(s)
- Elise Duboué-Dijon
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Eva Pluhařová
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Dominik Domin
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Kakali Sen
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Aoife C Fogarty
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Nicolas Chéron
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Damien Laage
- École Normale Supérieure - PSL Research University , Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
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9
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Brotzakis ZF, Groot CCM, Brandeburgo WH, Bakker HJ, Bolhuis PG. Dynamics of Hydration Water around Native and Misfolded α-Lactalbumin. J Phys Chem B 2016; 120:4756-66. [DOI: 10.1021/acs.jpcb.6b02592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Z. F. Brotzakis
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | - C. C. M. Groot
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - W. H. Brandeburgo
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
| | - H. J. Bakker
- FOM Institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
| | - P. G. Bolhuis
- Van’t
Hoff Institute for Molecular Sciences, Universiteit van Amsterdam, Science
Park 904, 1098 XH Amsterdam, The Netherlands
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10
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Balcão VM, Vila MMDC. Structural and functional stabilization of protein entities: state-of-the-art. Adv Drug Deliv Rev 2015; 93:25-41. [PMID: 25312675 DOI: 10.1016/j.addr.2014.10.005] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 08/03/2014] [Accepted: 10/01/2014] [Indexed: 12/13/2022]
Abstract
Within the context of biomedicine and pharmaceutical sciences, the issue of (therapeutic) protein stabilization assumes particular relevance. Stabilization of protein and protein-like molecules translates into preservation of both structure and functionality during storage and/or targeting, and such stabilization is mostly attained through establishment of a thermodynamic equilibrium with the (micro)environment. The basic thermodynamic principles that govern protein structural transitions and the interactions of the protein molecule with its (micro)environment are, therefore, tackled in a systematic fashion. Highlights are given to the major classes of (bio)therapeutic molecules, viz. enzymes, recombinant proteins, (macro)peptides, (monoclonal) antibodies and bacteriophages. Modification of the microenvironment of the biomolecule via multipoint covalent attachment onto a solid surface followed by hydrophilic polymer co-immobilization, or physical containment within nanocarriers, are some of the (latest) strategies discussed aiming at full structural and functional stabilization of said biomolecules.
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Affiliation(s)
- Victor M Balcão
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil; CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
| | - Marta M D C Vila
- LaBNUS - Biomaterials and Nanotechnology Laboratory, i(bs)(2) - intelligent biosensing and biomolecule stabilization research group, University of Sorocaba, Sorocaba, SP, Brazil
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11
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Stepankova V, Bidmanova S, Koudelakova T, Prokop Z, Chaloupkova R, Damborsky J. Strategies for Stabilization of Enzymes in Organic Solvents. ACS Catal 2013. [DOI: 10.1021/cs400684x] [Citation(s) in RCA: 415] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Veronika Stepankova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
| | - Sarka Bidmanova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tana Koudelakova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and Research Centre
for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- International
Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
- Enantis,
Ltd., Palackeho trida
1802/129, 612 00 Brno, Czech Republic
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12
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Stirnemann G, Wernersson E, Jungwirth P, Laage D. Mechanisms of acceleration and retardation of water dynamics by ions. J Am Chem Soc 2013; 135:11824-31. [PMID: 23865559 DOI: 10.1021/ja405201s] [Citation(s) in RCA: 173] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
There are fundamental and not yet fully resolved questions concerning the impact of solutes, ions in particular, on the structure and dynamics of water, which can be formulated as follows: Are the effects of ions local or long-ranged? Is the action of cations and anions on water cooperative or not? Here, we investigate how the reorientation and hydrogen-bond dynamics of water are affected by ions in dilute and concentrated aqueous salt solutions. By combining simulations and analytic modeling, we first show that ions have a short-ranged influence on the reorientation of individual water molecules and that depending on their interaction strength with water, they may accelerate or slow down water dynamics. A simple additive picture combining the effects of the cations and anions is found to provide a good description in dilute solutions. In concentrated solutions, we show that the average water reorientation time ceases to scale linearly with salt concentration due to overlapping hydration shells and structural rearrangements which reduce the translational displacements induced by hydrogen-bond switches and increase the solution viscosity. This effect is not ion-specific and explains why all concentrated salt solutions slow down water dynamics. Our picture, which is demonstrated to be robust vis-a-vis a change in the force-field, reconciles the seemingly contradictory experimental results obtained by ultrafast infrared and NMR spectroscopies, and suggests that there are no long-ranged cooperative ion effects on the dynamics of individual water molecules in dilute solutions.
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Affiliation(s)
- Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond, 75005 Paris, France
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13
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Meng Y, Yuan Y, Zhu Y, Guo Y, Li M, Wang Z, Pu X, Jiang L. Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media. J Mol Model 2013; 19:3749-66. [DOI: 10.1007/s00894-013-1900-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 05/27/2013] [Indexed: 11/29/2022]
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14
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JIN Q, JIA G, WANG X, LI C. Comparison of the salt-induced activation of Pseudomonas cepacia lipase in organic media by phosphate buffer and sodium sulfate. CHINESE JOURNAL OF CATALYSIS 2013. [DOI: 10.1016/s1872-2067(12)60558-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J. Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. Chembiochem 2013; 14:890-7. [DOI: 10.1002/cbic.201200733] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Indexed: 11/11/2022]
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16
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Xu J, Zhuang Y, Wu B, Su L, He B. Calcium-ion-induced stabilization of the protease from Bacillus cereus WQ9-2 in aqueous hydrophilic solvents: effect of calcium ion binding on the hydration shell and intramolecular interactions. J Biol Inorg Chem 2013; 18:211-221. [PMID: 23322168 DOI: 10.1007/s00775-012-0966-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/24/2012] [Indexed: 01/12/2023]
Abstract
The neutral protease WQ from Bacillus cereus is stable in various aqueous organic mixtures, with the exception of those containing acetonitrile (ACN) and dimethylformamide (DMF). The stability of the enzyme in aqueous hydrophilic solvents was dramatically enhanced with the addition of calcium ions, with the degree of improvement in the half-life relative to different solutions ranging from fourfold to more than 70-fold. Studies of the kinetic constants showed that calcium ions induced slight conformational changes in the active site of the enzyme in aqueous ACN. We investigated the molecular mechanisms underlying this stabilizing effect by employing a combination of biophysical techniques and molecular dynamics simulation. In aqueous ACN, the intrinsic fluorescence and circular dichroism analysis demonstrated that the addition of calcium ions induced a relatively compact conformation and maintained both the native-like microenvironment near the tryptophan residues and the secondary structure. Alternatively, homology modeling confirmed the location of four calcium-ion-binding sites in the enzyme, and molecular dynamics simulation revealed that three other calcium ions were bound to the surface of the enzyme. Calcium ions, known as a type of kosmotrope, can strongly bond with water molecules, thus aiding in the formation of the regional hydration shell required for the maintenance of enzyme activity. In addition, the introduction of calcium ions resulted in the formation of additional ionic interactions, providing propitious means for protein stabilization. Thus, the stronger intramolecular interactions were also expected to contribute partially to the enhanced stability of the enzyme in an aqueous organic solvent.
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Affiliation(s)
- Jiaxing Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Yu Zhuang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Long Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China
| | - Bingfang He
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, 30 Puzhunan Road, Nanjing, 211816, Jiangsu, China.
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17
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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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18
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Liszka MJ, Clark ME, Schneider E, Clark DS. Nature Versus Nurture: Developing Enzymes That Function Under Extreme Conditions. Annu Rev Chem Biomol Eng 2012; 3:77-102. [DOI: 10.1146/annurev-chembioeng-061010-114239] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Elizabeth Schneider
- Department of Chemical and Biomolecular Engineering,
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720; , , ,
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19
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Illanes A, Cauerhff A, Wilson L, Castro GR. Recent trends in biocatalysis engineering. BIORESOURCE TECHNOLOGY 2012; 115:48-57. [PMID: 22424920 DOI: 10.1016/j.biortech.2011.12.050] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 12/08/2011] [Accepted: 12/10/2011] [Indexed: 05/31/2023]
Abstract
During the last 30 years the scope of biocatalysis has been expanding due to the advances in several technological fields. Diverse techniques as structural enzyme improvement (e.g. protein engineering, direct evolution), engineering approaches (e.g. ionic liquids, supercritical fluids) and physical stabilization (e.g. immobilization, CLEAS) have been developed, which in combination are powerful tools to improve biotransformation and to synthesize new products. In the present work, recent advances in biocatalysis are reviewed.
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Affiliation(s)
- Andrés Illanes
- Escuela de Ingeniería Bioquímica, Universidad Católica de Valparaíso, Valparaíso, Chile.
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20
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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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21
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Zhu L, Yang W, Meng YY, Xiao X, Guo Y, Pu X, Li M. Effects of Organic Solvent and Crystal Water on γ-Chymotrypsin in Acetonitrile Media: Observations from Molecular Dynamics Simulation and DFT Calculation. J Phys Chem B 2012; 116:3292-304. [DOI: 10.1021/jp3002405] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lijuan Zhu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Wei Yang
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Yan Yan Meng
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Xiuchan Xiao
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu 610064, People’s Republic of China
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22
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Sterpone F, Stirnemann G, Laage D. Magnitude and Molecular Origin of Water Slowdown Next to a Protein. J Am Chem Soc 2012; 134:4116-9. [DOI: 10.1021/ja3007897] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
| | - Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond,
75005 Paris, France
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23
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Hedstrom L. The dynamic determinants of reaction specificity in the IMPDH/GMPR family of (β/α)(8) barrel enzymes. Crit Rev Biochem Mol Biol 2012; 47:250-63. [PMID: 22332716 DOI: 10.3109/10409238.2012.656843] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The inosine monophosphate dehydrogenase (IMPDH)/guanosine monophosphate reductase (GMPR) family of (β/α)(8) enzymes presents an excellent opportunity to investigate how subtle changes in enzyme structure change reaction specificity. IMPDH and GMPR bind the same ligands with similar affinities and share a common set of catalytic residues. Both enzymes catalyze a hydride transfer reaction involving a nicotinamide cofactor hydride, and both reactions proceed via the same covalent intermediate. In the case of IMPDH, this intermediate reacts with water, while in GMPR it reacts with ammonia. In both cases, the two chemical transformations are separated by a conformational change. In IMPDH, the conformational change involves a mobile protein flap while in GMPR, the cofactor moves. Thus reaction specificity is controlled by differences in dynamics, which in turn are controlled by residues outside the active site. These findings have some intriguing implications for the evolution of the IMPDH/GMPR family.
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Affiliation(s)
- Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA 02454, USA.
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24
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Riera TV, Zheng L, Josephine HR, Min D, Yang W, Hedstrom L. Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase. Biochemistry 2011; 50:8508-18. [PMID: 21870820 PMCID: PMC3186055 DOI: 10.1021/bi200785s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allosteric activators are generally believed to shift the equilibrium distribution of enzyme conformations to favor a catalytically productive structure; the kinetics of conformational exchange is seldom addressed. Several observations suggested that the usual allosteric mechanism might not apply to the activation of IMP dehydrogenase (IMPDH) by monovalent cations. Therefore, we investigated the mechanism of K(+) activation in IMPDH by delineating the kinetic mechanism in the absence of monovalent cations. Surprisingly, the K(+) dependence of k(cat) derives from the rate of flap closure, which increases by ≥65-fold in the presence of K(+). We performed both alchemical free energy simulations and potential of mean force calculations using the orthogonal space random walk strategy to computationally analyze how K(+) accelerates this conformational change. The simulations recapitulate the preference of IMPDH for K(+), validating the computational models. When K(+) is replaced with a dummy ion, the residues of the K(+) binding site relax into ordered secondary structure, creating a barrier to conformational exchange. K(+) mobilizes these residues by providing alternate interactions for the main chain carbonyls. Potential of mean force calculations indicate that K(+) changes the shape of the energy well, shrinking the reaction coordinate by shifting the closed conformation toward the open state. This work suggests that allosteric regulation can be under kinetic as well as thermodynamic control.
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Affiliation(s)
- Thomas V. Riera
- Graduate Program in Biochemistry, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
| | - Lianqing Zheng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
| | - Helen R. Josephine
- Department of Biology, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
| | - Donghong Min
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
| | - Wei Yang
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306 USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306 USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
- Department of Chemistry, Brandeis University, 415 South St., MS 009, Waltham, MA 02454 USA
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25
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Silvestre-Ryan J, Lin Y, Chu JW. "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution. PLoS Comput Biol 2011; 7:e1002023. [PMID: 21455286 PMCID: PMC3063751 DOI: 10.1371/journal.pcbi.1002023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 02/13/2011] [Indexed: 11/21/2022] Open
Abstract
The mechanism of intra-protein communication and allosteric coupling is key to understanding the structure-property relationship of protein function. For subtilisin Carlsberg, the Ca2+-binding loop is distal to substrate-binding and active sites, yet the serine protease function depends on Ca2+ binding. The atomic molecular dynamics (MD) simulations of apo and Ca2+-bound subtilisin show similar structures and there is no direct evidence that subtilisin has alternative conformations. To model the intra-protein communication due to Ca2+ binding, we transform the sequential segments of an atomic MD trajectory into separate elastic network models to represent anharmonicity and nonlinearity effectively as the temporal and spatial variation of the mechanical coupling network. In analogy to the spectrogram of sound waves, this transformation is termed the “fluctuogram” of protein dynamics. We illustrate that the Ca2+-bound and apo states of subtilisin have different fluctuograms and that intra-protein communication proceeds intermittently both in space and in time. We found that residues with large mechanical coupling variation due to Ca2+ binding correlate with the reported mutation sites selected by directed evolution for improving the stability of subtilisin and its activity in a non-aqueous environment. Furthermore, we utilize the fluctuograms calculated from MD to capture the highly correlated residues in a multiple sequence alignment. We show that in addition to the magnitude, the variance of coupling strength is also an indicative property for the sequence correlation observed in a statistical coupling analysis. The results of this work illustrate that the mechanical coupling networks calculated from atomic details can be used to correlate with functionally important mutation sites and co-evolution. A hallmark of protein molecules is their machine-like behaviors while carrying out biological functions. At the molecular level, molecular signals such as binding a metal ion at an action site can cause long-range effects and alter protein function. Such phenomena are often referred to as intra-protein communication or allosteric coupling. Elucidating the underlying mechanisms could lead to novel discovery of molecular modulators to regulate protein function in a more specific and effective manner. A long-standing puzzle is the roles of the anharmonicity and nonlinearity in protein dynamics. To incorporate these characters in modeling intra-protein communication, we devise a “fluctuogram” analysis to record the choreography of allosteric coupling in an atomic molecular dynamics simulation. We show that fluctuogram analysis can bridge the results of physics-based simulation and sequence alignment in bioinformatics by capturing the residues that exhibit high correlation in a multiple sequence alignment. We also show that the fluctuograms calculated from atomic details have the potential to be applied as a tool to select mutation sites for modulating protein function.
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Affiliation(s)
- Jordi Silvestre-Ryan
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Yuchun Lin
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America
| | - Jhih-Wei Chu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
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26
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Brokaw JB, Chu JW. On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase. Biophys J 2011; 99:3420-9. [PMID: 21081091 DOI: 10.1016/j.bpj.2010.09.040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Revised: 09/09/2010] [Accepted: 09/21/2010] [Indexed: 11/28/2022] Open
Abstract
We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro(177) on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro(177) hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.
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Affiliation(s)
- Jason B Brokaw
- Department of Chemistry, University of California, Berkeley, CA, USA
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27
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Egusa S, Kitaoka T, Igarashi K, Samejima M, Goto M, Wariishi H. Preparation and enzymatic behavior of surfactant-enveloped enzymes for glycosynthesis in nonaqueous aprotic media. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Castillo B, Delgado Y, Barletta G, Griebenow K. Enantioselective Transesterification Catalysis by Nanosized Serine Protease Subtilisin Carlsberg Particles in Tetrahydrofuran. Tetrahedron 2010; 66:2175-2180. [PMID: 20661313 DOI: 10.1016/j.tet.2010.01.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Enzyme catalysis in organic solvents is a powerful tool for stereo-selective synthesis but the enantioselectivity is still hard to predict. To overcome this obstacle, we employed a nanoparticulate formulation of subtilisin Carlsberg (SC) and designed a series of 14 structurally related racemic alcohols. They were employed in the model transesterification reaction with vinyl butyrate and the enantioselectivities were determined. In general, short alcohol side chains led to low enantioselectivties, while larger and bulky side chains caused better discrimination of the enantiomers by the enzyme. With several bulky substrates high enantioselectivities with E>100 were obtained. Computational modeling highlighted that key to high enantioselectivity is the discrimination of the R and S substrates by the sole hydrophobic binding pocket based on their size and bulkiness. While bulky S enantiomer side chains could be accommodated within the binding pocket, bulky R enantiomer side chains could not. However, when also the S enantiomer side chain becomes too large and does not fit into the binding pocket anymore, enantioselectivity accordingly drops.
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Affiliation(s)
- Betzaida Castillo
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, P.O. Box 23346, San Juan, Puerto Rico 00931-3346
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29
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Cianci M, Tomaszewski B, Helliwell JR, Halling PJ. Crystallographic Analysis of Counterion Effects on Subtilisin Enzymatic Action in Acetonitrile. J Am Chem Soc 2010; 132:2293-300. [DOI: 10.1021/ja908703c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Cianci
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Bartlomiej Tomaszewski
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - John R. Helliwell
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Peter J. Halling
- European Molecular Biology Laboratory, Hamburg Outstation, c/o DESY, Building 25a, Notkestrasse 85, 22603 Hamburg, Germany, WestCHEM, Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, United Kingdom, and Department of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
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30
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Haas K, Chu JW. Decomposition of energy and free energy changes by following the flow of work along reaction path. J Chem Phys 2009; 131:144105. [DOI: 10.1063/1.3243080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Affiliation(s)
- Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South Street, Waltham, Massachusetts 02454, USA.
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32
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Adamczak M, Bornscheuer UT. Improving ascorbyl oleate synthesis catalyzed by Candida antarctica lipase B in ionic liquids and water activity control by salt hydrates. Process Biochem 2009. [DOI: 10.1016/j.procbio.2008.10.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions. Proc Natl Acad Sci U S A 2008; 105:15672-7. [PMID: 18840689 DOI: 10.1073/pnas.0804566105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies exploring the relationship between enzymatic catalysis and protein dynamics in the aqueous phase have yielded evidence that dynamics and enzyme activity are strongly correlated. Given that protein dynamics are significantly attenuated in organic solvents and that proteins exhibit a wide range of motions depending on the specific solvent environment, the nonaqueous milieu provides a unique opportunity to examine the role of protein dynamics in enzyme activity. Variable-temperature kinetic measurements, X-band electron spin resonance spectroscopy, (1)H NMR relaxation, and (19)F NMR spectroscopy experiments were performed on subtilisin Carlsberg colyophilized with several inorganic salts and suspended in organic solvents. The results indicate that salt activation induces a greater degree of transition-state flexibility, reflected by a more positive DeltaDeltaS(dagger), for the more active biocatalyst preparations in organic solvents. In contrast, DeltaDeltaH(dagger) was negligible regardless of salt type or salt content. Electron spin resonance spectroscopy and (1)H NMR relaxation measurements, including spin-lattice relaxation, spin-lattice relaxation in the rotating frame, and longitudinal magnetization exchange, revealed that the enzyme's turnover number (k(cat)) was strongly correlated with protein motions in the centisecond time regime, weakly correlated with protein motions in the millisecond regime, and uncorrelated with protein motions on the piconanosecond timescale. In addition, (19)F chemical shift measurements and hyperfine tensor measurements of biocatalyst formulations inhibited with 4-fluorobenzenesulfonyl fluoride and 4-ethoxyfluorophosphinyl-oxy-TEMPO, respectively, suggest that enzyme activation was only weakly affected by changes in active-site polarity.
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34
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35
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Bilaničová D, Salis A, Ninham BW, Monduzzi M. Specific Anion Effects on Enzymatic Activity in Nonaqueous Media. J Phys Chem B 2008; 112:12066-72. [DOI: 10.1021/jp805451w] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dagmar Bilaničová
- Department of Chemical Sciences, University of Cagliari−CSGI Cittadella Monserrato, S.S. 554 Bivio Sestu, 09042 Monserrato, Italy, Department of Applied Mathematics, Australian National University, Canberra, Australia, and Department of Food Technology and Biotechnology, Slovak Technical University, Bratislava, Slovak Republic
| | - Andrea Salis
- Department of Chemical Sciences, University of Cagliari−CSGI Cittadella Monserrato, S.S. 554 Bivio Sestu, 09042 Monserrato, Italy, Department of Applied Mathematics, Australian National University, Canberra, Australia, and Department of Food Technology and Biotechnology, Slovak Technical University, Bratislava, Slovak Republic
| | - Barry W. Ninham
- Department of Chemical Sciences, University of Cagliari−CSGI Cittadella Monserrato, S.S. 554 Bivio Sestu, 09042 Monserrato, Italy, Department of Applied Mathematics, Australian National University, Canberra, Australia, and Department of Food Technology and Biotechnology, Slovak Technical University, Bratislava, Slovak Republic
| | - Maura Monduzzi
- Department of Chemical Sciences, University of Cagliari−CSGI Cittadella Monserrato, S.S. 554 Bivio Sestu, 09042 Monserrato, Italy, Department of Applied Mathematics, Australian National University, Canberra, Australia, and Department of Food Technology and Biotechnology, Slovak Technical University, Bratislava, Slovak Republic
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36
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Serdakowski AL, Dordick JS. Enzyme activation for organic solvents made easy. Trends Biotechnol 2008; 26:48-54. [DOI: 10.1016/j.tibtech.2007.10.007] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 10/17/2007] [Accepted: 10/18/2007] [Indexed: 11/16/2022]
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37
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Shaw AK, Pal SK. Activity of Subtilisin Carlsberg in macromolecular crowding. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2007; 86:199-206. [PMID: 17110125 DOI: 10.1016/j.jphotobiol.2006.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 10/06/2006] [Accepted: 10/10/2006] [Indexed: 11/17/2022]
Abstract
Enzymatic activity of a proteolytic enzyme Subtilisin Carlsberg (SC) in anionic sodium dodecyl sulfate (SDS) micellar medium has been explored and found to be retarded compared to that in bulk buffer. Circular dichroism (CD) study reveals that SDS, which is a potential protein denaturant, has an insignificant denaturation effect on SC. The structural integrity of the protein offers an opportunity to study the functionality of the enzyme SC in a macromolecular crowding of micelles. Dynamic light scattering (DLS) data indicates no sandwich-like micelle-SC complex formation ruling out the possibility of interaction of the enzyme with the hydrophobic core of the micelle. However, steady state and time resolved emission studies on specific and nonspecific fluorescent probes indicate the proximity effect at the surface of the enzyme due to macromolecular crowding of the micelles. The agreement of retarded enzymatic activity in the micellar crowd with a theoretical model ascribed to the facts that substrates are compartmentalized in the micelles and enzyme interacts with the micelle through stern layer.
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Affiliation(s)
- Ajay Kumar Shaw
- Unit for Nano Science and Technology, Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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38
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Polizzi KM, Bommarius AS, Broering JM, Chaparro-Riggers JF. Stability of biocatalysts. Curr Opin Chem Biol 2007; 11:220-5. [PMID: 17307381 DOI: 10.1016/j.cbpa.2007.01.685] [Citation(s) in RCA: 290] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 01/17/2007] [Indexed: 11/15/2022]
Abstract
Despite their many favorable qualities, the marginal stability of biocatalysts in many types of reaction media often has prevented or delayed their implementation for industrial-scale synthesis of fine chemicals and pharmaceuticals. Consequently, there is great interest in understanding effects of solution conditions on protein stability, as well as in developing strategies to improve protein stability in desired reaction media. Recent methods include novel chemical modifications of protein, lyophilization in the presence of additives, and physical immobilization on novel supports. Rational and combinatorial protein engineering techniques have been used to yield unmodified proteins with exceptionally improved stability. Both have been aided by the development of computational tools and structure-guided heuristics aimed at reducing library sizes that must be generated and screened to identify improved mutants. The number of parameters used to indicate protein stability can complicate discussions and investigations, and care should be taken to identify whether thermodynamic or kinetic stability limits the observed stability of proteins. Although the useful lifetime of a biocatalyst is dictated by its kinetic stability, only 6% of protein stability studies use kinetic stability measures. Clearly, more effort is needed to study how solution conditions impact protein kinetic stability.
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Affiliation(s)
- Karen M Polizzi
- School of Chemical & Biomolecular Engineering, Parker H Petit Institute of Bioengineering and Bioscience, USA
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39
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Shemella P, Pereira B, Zhang Y, Van Roey P, Belfort G, Garde S, Nayak SK. Mechanism for intein C-terminal cleavage: a proposal from quantum mechanical calculations. Biophys J 2006; 92:847-53. [PMID: 17085503 PMCID: PMC1779973 DOI: 10.1529/biophysj.106.092049] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inteins are autocatalytic protein cleavage and splicing elements. A cysteine to alanine mutation at the N-terminal of inteins inhibits splicing and isolates the C-terminal cleavage reaction. Experiments indicate an enhanced C-terminal cleavage reaction rate upon decreasing the solution pH for the cleavage mutant, which cannot be explained by the existing mechanistic framework. We use intein crystal structure data and the information about conserved amino acids to perform semiempirical PM3 calculations followed by high-level density functional theory calculations in both gas phase and implicit solvent environments. Based on these calculations, we propose a detailed "low pH" mechanism for intein C-terminal cleavage. Water plays an important role in the proposed reaction mechanism, acting as an acid as well as a base. The protonation of the scissile peptide bond nitrogen by a hydronium ion is an important first step in the reaction. That step is followed by the attack of the C-terminal asparagine side chain on its carbonyl carbon, causing succinimide formation and simultaneous peptide bond cleavage. The computed reaction energy barrier in the gas phase is approximately 33 kcal/mol and reduces to approximately 25 kcal/mol in solution, close to the 21 kcal/mol experimentally observed at pH 6.0. This mechanism is consistent with the observed increase in C-terminal cleavage activity at low pH for the cleavage mutant of the Mycobacterium tuberculosis RecA mini-intein.
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Affiliation(s)
- Philip Shemella
- Department of Physics, Applied Physics and Astronomy, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
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