1
|
Zheng H, Zheng YC, Cui Y, Zhu JJ, Zhong JY. Study on effects of co-solvents on the structure of DhaA by molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:5999-6007. [PMID: 32696722 DOI: 10.1080/07391102.2020.1796801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
With the increasing application of enzymes in various research fields, the choices of co-solvents in enzymatic preparations which directly related to the catalytic activity have been attracted attention. Thus, researching on the stabilization or destabilization behaviors of enzymes in different solvents is extremely essential. In this study, the structural changes of DhaA in two typical aprotic co-solvents (acetonitrile and tetrahydrofuran) were firstly investigated by molecular dynamics (MD) simulation. The simulation results revealed the strong van der Waals force between co-solvents and DhaA which could induce the structural change of enzyme. Interestingly, the differences of molecular size and the electrostatic force with enzyme of two co-solvents led to quite different influences on DhaA. As for acetonitrile, solvent molecules could penetrate into the catalytic site of DhaA which promoted by the electrostatic interaction. On the contrary, tetrahydrofuran molecules were mainly distributed around the catalytic site due to the relative weak electrostatic interaction and steric resistance effect. It can be concluded that different co-solvent can affect the key domains, substrate pathway and catalytic pocket of DhaA.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- He Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Yong-Chao Zheng
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Yan Cui
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Jian-Jun Zhu
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Jin-Yi Zhong
- State Key Laboratory of NBC Protection for Civilian, Beijing, China
| |
Collapse
|
2
|
Ostermeier L, Oliva R, Winter R. The multifaceted effects of DMSO and high hydrostatic pressure on the kinetic constants of hydrolysis reactions catalyzed by α-chymotrypsin. Phys Chem Chem Phys 2020; 22:16325-16333. [DOI: 10.1039/d0cp03062g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cosolvent DMSO and high pressure have antagonistic effects on the kinetic constants of α-chymotrypsin-catalyzed hydrolysis reactions.
Collapse
Affiliation(s)
- Lena Ostermeier
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Rosario Oliva
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- TU Dortmund University
- D-44227 Dortmund
- Germany
| |
Collapse
|
3
|
Tomohara K, Adachi I, Horino Y, Kesamaru H, Abe H, Suyama K, Nose T. DMSO-Perturbing Assay for Identifying Promiscuous Enzyme Inhibitors. ACS Med Chem Lett 2019; 10:923-928. [PMID: 31223449 DOI: 10.1021/acsmedchemlett.9b00093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/10/2019] [Indexed: 01/09/2023] Open
Abstract
In search for enzyme inhibitors, we often encounter "promiscuous" enzyme inhibitors exhibiting nonspecific binding property toward enzyme active site. Therefore, inhibitory candidates should be mechanistically characterized as early as possible in discovery processes. However, there remains a lack of highly reliable and readily available methodology to evaluate specificity of initial hits inhibitors. The present study developed and established a novel DMSO-perturbing assay to identify promiscuous enzyme inhibitors. The assay successfully identified nonspecific binding inhibitors with a broad scope, typically by the attenuation of inhibitory activity by the influence of DMSO-addition. This attenuation would be attributed to the nonspecific binding property of inhibitors toward both productive and nonproductive (nondenatured) states of enzymes in perturbation solution. This working hypothesis was supported by spectroscopic analyses of enzyme conformations and analyses of solvent effects on perturbation. Overall, these results provided a novel concept of the DMSO-perturbing assay.
Collapse
Affiliation(s)
- Keisuke Tomohara
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Isao Adachi
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Yoshikazu Horino
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Hitoshi Kesamaru
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hitoshi Abe
- Graduate School of Science and Engineering, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
4
|
Farhadian S, Shareghi B, Momeni L, Abou-Zied OK, Sirotkin VA, Tachiya M, Saboury AA. Insights into the molecular interaction between sucrose and α-chymotrypsin. Int J Biol Macromol 2018; 114:950-960. [DOI: 10.1016/j.ijbiomac.2018.03.143] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 12/12/2022]
|
5
|
Jaworek MW, Schuabb V, Winter R. The effects of glycine, TMAO and osmolyte mixtures on the pressure dependent enzymatic activity of α-chymotrypsin. Phys Chem Chem Phys 2018; 20:1347-1354. [DOI: 10.1039/c7cp06042d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different natural osmolytes modulate the pressure dependent enzyme kinetics in different ways.
Collapse
Affiliation(s)
- Michel W. Jaworek
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Vitor Schuabb
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry
- Faculty of Chemistry and Chemical Biology
- Technical University Dortmund
- 44227 Dortmund
- Germany
| |
Collapse
|
6
|
Wangler A, Canales R, Held C, Luong TQ, Winter R, Zaitsau DH, Verevkin SP, Sadowski G. Co-solvent effects on reaction rate and reaction equilibrium of an enzymatic peptide hydrolysis. Phys Chem Chem Phys 2018; 20:11317-11326. [DOI: 10.1039/c7cp07346a] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This work presents an approach that expresses the Michaelis constant KaM and the equilibrium constant Kth of an enzymatic peptide hydrolysis based on thermodynamic activities instead of concentrations.
Collapse
Affiliation(s)
- A. Wangler
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - R. Canales
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
- Departamento de Ingeniería Química y Bioprocesos
| | - C. Held
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - T. Q. Luong
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - R. Winter
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - D. H. Zaitsau
- Department of Physical Chemistry
- Institute of Chemistry
- University of Rostock
- 18059 Rostock
- Germany
| | - S. P. Verevkin
- Department of Physical Chemistry
- Institute of Chemistry
- University of Rostock
- 18059 Rostock
- Germany
| | - G. Sadowski
- Department BCI, Laboratory of Thermodynamics
- TU Dortmund University
- 44227 Dortmund
- Germany
| |
Collapse
|
7
|
Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| |
Collapse
|
8
|
Sirotkin VA, Kuchierskaya AA. α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration. Proteins 2017; 85:1808-1819. [PMID: 28612358 DOI: 10.1002/prot.25334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 11/10/2022]
Abstract
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems.
Collapse
Affiliation(s)
- Vladimir A Sirotkin
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
| | - Alexandra A Kuchierskaya
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
| |
Collapse
|
9
|
Srivastava KR, Goyal B, Kumar A, Durani S. Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide. RSC Adv 2017. [DOI: 10.1039/c7ra02137b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.
Collapse
Affiliation(s)
| | - Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| |
Collapse
|
10
|
Dolidze TD, Shushanyan M, Khoshtariya DE. Electron transfer with myoglobin in free and strongly confined regimes: disclosing diverse mechanistic role of the Fe-coordinated water by temperature- and pressure-assisted voltammetric studies. J COORD CHEM 2015. [DOI: 10.1080/00958972.2015.1068937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Tinatin D. Dolidze
- Department of Biophysics, I. Beritashvili Center for Experimental Biomedicine, Tbilisi, Georgia
- Department of Physics, Institute for Biophysics and Bionanosciences, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia
- Department of Chemistry and Pharmacy, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Mikhael Shushanyan
- Department of Biophysics, I. Beritashvili Center for Experimental Biomedicine, Tbilisi, Georgia
- Department of Physics, Institute for Biophysics and Bionanosciences, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Dimitri E. Khoshtariya
- Department of Biophysics, I. Beritashvili Center for Experimental Biomedicine, Tbilisi, Georgia
- Department of Physics, Institute for Biophysics and Bionanosciences, I. Javakhishvili Tbilisi State University, Tbilisi, Georgia
- Department of Chemistry and Pharmacy, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| |
Collapse
|
11
|
Luong TQ, Winter R. Combined pressure and cosolvent effects on enzyme activity – a high-pressure stopped-flow kinetic study on α-chymotrypsin. Phys Chem Chem Phys 2015; 17:23273-8. [DOI: 10.1039/c5cp03529e] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pressure enhances the hydrolysis of peptides catalysed by α-CT, which is efficiently and differently modulated by chaotropic and kosmotropic cosolvents.
Collapse
Affiliation(s)
- Trung Quan Luong
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
| | - Roland Winter
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- D-44221 Dortmund
- Germany
| |
Collapse
|
12
|
Roy S, Bagchi B. Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting. J Phys Chem B 2014; 118:5691-7. [DOI: 10.1021/jp5037348] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Susmita Roy
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Biman Bagchi
- Solid State
and Structural
Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| |
Collapse
|
13
|
Khoshtariya DE, Dolidze TD, Shushanyan M, van Eldik R. Long-range electron transfer with myoglobin immobilized at Au/mixed-SAM junctions: mechanistic impact of the strong protein confinement. J Phys Chem B 2014; 118:692-706. [PMID: 24369906 DOI: 10.1021/jp4101569] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horse muscle myoglobin (Mb) was tightly immobilized at Au-deposited ~15-Å-thick mixed-type (1:1) alkanethiol SAMs, HS-(CH₂)₁₁-COOH/HS-(CH₂)₁₁-OH, and placed in contact with buffered H₂O or D₂O solutions. Fast-scan cyclic voltammetry (CV) and a Marcus-equation-based analysis were applied to determine unimolecular standard rate constants and reorganization free energies for electron transfer (ET), under variable-temperature (15-55 °C) and -pressure (0.01-150 MPa) conditions. The CV signal was surprisingly stable and reproducible even after multiple temperature and pressure cycles. The data analysis revealed the following values: standard rate constant, 33 s⁻¹ (25 °C, 0.01 MPa, H₂O); reorganization free energy, 0.5 ± 0.1 eV (throughout); activation enthalpy, 12 ± 3 kJ mol⁻¹; activation volume, -3.1 ± 0.2 cm³ mol⁻¹; and pH-dependent solvent kinetic isotope effect (k(H)⁰/k(D)⁰), 0.7-1.4. Furthermore, the values for the rate constant and reorganization free energy are very similar to those previously found for cytochrome c electrostatically immobilized at the monocomponent Au/HS-(CH₂)₁₁-COOH junction. In vivo, Mb apparently forms a natural electrostatic complex with cytochrome b₅ (cyt-b₅) through the "dynamic" (loose) docking pattern, allowing for a slow ET that is intrinsically coupled to the water's removal from the "defective" heme iron (altogether shaping the biological repair mechanism for Mb's "met" form). In contrary, our experiments rather mimic the case of a "simple" (tight) docking of the redesigned (mutant) Mb with cyt-b₅ (Nocek et al. J. Am. Chem. Soc. 2010, 132, 6165-6175). According to our analysis, in this configuration, Mb's distal pocket (linked to the "ligand channel") seems to be arrested within the restricted configuration, allowing the rate-determining reversible ET process to be coupled only to the inner-sphere reorganization (minimal elongation/shortening of an Fe-OH₂ bond) rather than the pronounced detachment (rebinding) of water and, hence, to be much faster.
Collapse
Affiliation(s)
- Dimitri E Khoshtariya
- Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg , 91058 Erlangen, Germany
| | | | | | | |
Collapse
|
14
|
Notable Stabilization of α-Chymotrypsin by the Protic Ionic Additive, [ch][dhp]: Calorimetric Evidence for a Fine Enthalpy/Entropy Balance. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:834189. [PMID: 27437474 PMCID: PMC4897175 DOI: 10.1155/2014/834189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 06/23/2014] [Indexed: 01/21/2023]
Abstract
An impact of 0.5 to 3 M choline dihydrogen phosphate, [ch][dhp], the biotechnologically relevant ionic substance, on the thermal stability of a model globular protein, α-chymotrypsin (α-CT), has been studied exploiting the highly sensitive differential scanning calorimetry (DSC) technique. The notable overall stabilizing effect of 11 ± 2 K regarding the thermal transition (melting) temperature, T m , has been detected. For this kind of series, for the first time, the calorimetric melting enthalpy (ΔH cal) and transition entropy (ΔS m ) parameters have been determined simultaneously throughout. The first analysis indicated a two-phase impact implying (a) the initial, dramatic drop in both ΔH cal and ΔS m , obviously connected to specific, direct interaction between the [ch][dhp] components and α-CT's charged groups (within 0 to 1 mol/L [ch][dhp]), leading to the essential rearrangement of the interfacial hydrogen-bonded (HB) network; and (b) the follow-up (within 1 to 3.0 mol/L [ch][dhp]), modest changes in ΔH cal and lack of changes in ΔS m , seemingly connected with a subsequent steady strengthening of already reformed HB network, respectively. These changes, presumably, are primarily facilitated by Coulombic interactions between the [dhp] anions and solvent-exposed positively charged amino groups of α-CT.
Collapse
|
15
|
Khoshtariya DE, Dolidze TD, Tretyakova T, Waldeck DH, van Eldik R. Electron transfer with azurin at Au–SAM junctions in contact with a protic ionic melt: impact of glassy dynamics. Phys Chem Chem Phys 2013; 15:16515-26. [DOI: 10.1039/c3cp51896e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|