1
|
Pu Z, Cao J, Wu W, Song Z, Yang L, Wu J, Yu H. Reconstructing dynamics correlation network to simultaneously improve activity and stability of 2,3-butanediol dehydrogenase by design of distal interchain disulfide bonds. Int J Biol Macromol 2024; 267:131415. [PMID: 38582485 DOI: 10.1016/j.ijbiomac.2024.131415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/08/2024]
Abstract
The complete enzyme catalytic cycle includes substrate binding, chemical reaction and product release, in which different dynamic conformations are adopted. Due to the complex relationship among enzyme activity, stability and dynamics, the directed evolution of enzymes for improved activity or stability commonly leads to a trade-off in stability or activity. It hence remains a challenge to engineer an enzyme to have both enhanced activity and stability. Here, we have attempted to reconstruct the dynamics correlation network involved with active center to improve both activity and stability of a 2,3-butanediol dehydrogenase (2,3-BDH) by introducing inter-chain disulfide bonds. A computational strategy was first applied to evaluate the effect of introducing inter-chain disulfide bond on activity and stability of three 2,3-BDHs, and the N258C mutation of 2,3-BDH from Corynebacterium glutamicum (CgBDH) was proved to be effective in improving both activity and stability. In the results, CgBDH-N258C showed a different unfolding curve from the wild type, with two melting temperatures (Tm) of 68.3 °C and 50.8 °C, 19.7 °C and 2 °C higher than 48.6 °C of the wild type. Its half-life was also improved by 14.8-fold compared to the wild type. Catalytic efficiency (kcat/Km) of the mutant was increased by 7.9-fold toward native substrate diacetyl and 8.8-fold toward non-native substrate 2,5-hexanedione compared to the wild type. Molecular dynamics simulations revealed that an interaction network formed by Cys258, Arg162, Ala144 and the catalytic residues was reconstructed in the mutant and the dynamics change caused by the disulfide bond could be propagated through the interactions network. This improved the enzyme stability and activity by decreasing the flexibility and locking more "reactive" pose, respectively. Further construction of mutations including A144G showing a 44-fold improvement in catalytic efficiency toward meso-2,3-BD confirmed the role of modifying dynamics correlation network in tunning enzyme activity and selectivity. This study provided important insights into the relationship among dynamics, enzyme catalysis and stability, and will be useful in the designing new enzymes with co-evolution of stability, activity and selectivity.
Collapse
Affiliation(s)
- Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Jiawen Cao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Wenhui Wu
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou 310015, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, Zhejiang 311200, China.
| |
Collapse
|
2
|
Cicek E, Monard G, Sungur FA. Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations. Biochemistry 2022; 61:1286-1297. [PMID: 35737372 PMCID: PMC9260958 DOI: 10.1021/acs.biochem.2c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylarginine deiminase 2 (PAD2) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. This kind of structural modification in histone molecules may affect gene regulation, leading to effects that may trigger several diseases, including breast cancer, which makes PAD2 an attractive target for anticancer drug development. To design new effective inhibitors to control activation of PAD2, improving our understanding of the molecular mechanisms of PAD2 using up-to-date computational techniques is essential. We have designed five different PAD2-substrate complex systems based on varying protonation states of the active site residues. To search the conformational space broadly, multiple independent molecular dynamics simulations of the complexes have been performed. In total, 50 replica simulations have been performed, each of 1 μs, yielding a total simulation time of 50 μs. Our findings identify that the protonation states of Cys647, Asp473, and His471 are critical for the binding and localization of the N-α-benzoyl-l-arginine ethyl ester substrate within the active site. A novel mechanism for enzyme activation is proposed according to near attack conformers. This represents an important step in understanding the mechanism of citrullination and developing PAD2-inhibiting drugs for the treatment of breast cancer.
Collapse
Affiliation(s)
- Erdem Cicek
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Fethiye Aylin Sungur
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
| |
Collapse
|
3
|
Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review. Catalysts 2020. [DOI: 10.3390/catal10060691] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts.
Collapse
|
4
|
Srinivasan B, Kantae V, Robinson J. Resurrecting the phoenix: When an assay fails. Med Res Rev 2020; 40:1776-1793. [DOI: 10.1002/med.21670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 02/18/2020] [Accepted: 03/27/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Vasudev Kantae
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - James Robinson
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| |
Collapse
|
5
|
Prejanò M, Medina FE, Ramos MJ, Russo N, Fernandes PA, Marino T. How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase. ACS Catal 2020; 10:2872-2881. [PMID: 33828899 PMCID: PMC8016368 DOI: 10.1021/acscatal.9b04690] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/04/2020] [Indexed: 12/16/2022]
Abstract
![]()
Atomic
resolution X-ray crystallography has shown that an intermediate
(the X5P-ThDP adduct) of the catalytic cycle of transketolase (TK)
displays a significant, putatively highly energetic, out-of-plane
distortion in a sp2 carbon
adjacent to a lytic bond, suggested to lower the barrier of the subsequent
step, and thus was postulated to embody a clear-cut demonstration
of the intermediate destabilization effect. The lytic
bond of the subsequent rate-limiting step was very elongated in the
X-ray structure (1.61 Å), which was proposed to be a consequence
of the out-of-plane distortion. Here we use high-level QM and QM/MM
calculations to study the intermediate destabilization effect. We show that the intrinsic energy penalty for the observed
distortion is small (0.2 kcal·mol–1) and that
the establishment of a favorable hydrogen bond within X5P-ThDP, instead
of enzyme steric strain, was found to be the main cause for the distortion.
As the net energetic effect of the distortion is small, the establishment
of the internal hydrogen bond (−0.6 kcal·mol–1) offsets the associated penalty. This makes the distorted structure
more stable than the nondistorted one. Even though the energy contributions
determined here are close to the accuracy of the computational methods
in estimating penalties for geometric distortions, our data show that
the intermediate destabilization effect provides
a small contribution to the observed reaction rate and does not represent
a catalytic effect that justifies the many orders of magnitude which
enzymes accelerate reaction rates. The results help to understand
the intrinsic enzymatic machinery behind enzyme’s amazing proficiency.
Collapse
Affiliation(s)
- Mario Prejanò
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - Fabiola E. Medina
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Quı́mica e Bioquı́mica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Arcavacata di Rende (CS), Italy
| |
Collapse
|
6
|
Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| |
Collapse
|
7
|
Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| |
Collapse
|
8
|
Santos-Martins D, Calixto AR, Fernandes PA, Ramos MJ. A Buried Water Molecule Influences Reactivity in α-Amylase on a Subnanosecond Time Scale. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04400] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Diogo Santos-Martins
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Ana R. Calixto
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
9
|
Barrera Valderrama DI, Doerr M, Daza Espinosa MC. Función de los confórmeros de ataque cercano en la acilación enantioselectiva del (R,S)-propranolol catalizada por lipasa B de Candida antarctica. REVISTA COLOMBIANA DE BIOTECNOLOGÍA 2018. [DOI: 10.15446/rev.colomb.biote.v20n1.73652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
La lipasa B de Candida antarctica (CalB) se ha utilizado en la acilación quimio- y enantioselectiva del racemato (R,S)-propranolol. CalB tiene enantioselectividad moderada (E=63) por el R-propranolol. La enantioselectividad, se origina en la reacción de transferencia del grupo acilo desde la serina catalítica, acilada, al propranolol. La fase inicial de esta reacción involucra la formación de complejos de Michaelis y posteriormente conformaciones de ataque cercano. El análisis de las conformaciones de ataque cercano ha permitido en varios casos explicar el origen de la catálisis o reproducir el efecto catalítico. En este trabajo se profundiza en la comprensión la función de las conformaciones de ataque cercano en la enantioselectividad de la acilación del (R,S)-propranolol catalizada por CalB. Para lo anterior se realizó un estudio detallado de los complejos de Michaelis y de las conformaciones de ataque cercano del paso enantioselectivo de la reacción de acilación del (R,S)-propranolol utilizando un protocolo de dinámica molecular QM/MM (SCCDFTB/CHARMM) utilizando 6 distribuciones de velocidades iniciales y simulaciones de 2,5 ns. Se estudiaron 7 complejos CalB-propranolol. Los enlaces de hidrógeno del sitio activo de CalB acilada relevantes para la actividad catalítica fueron estables en todas las simulaciones. Las poblaciones de los complejos de Michaelis y de las conformaciones de ataque cercano son dependientes de la distribución de las velocidades iniciales de la dinámica molecular. La enantioselectividad moderada de CalB acilada, encontrada experimentalmente, puede ser parcialmente atribuida a la alta población de conformaciones de ataque cercano observada para el S-propranolol.
Collapse
|
10
|
Vöhringer-Martinez E, Dörner C. Conformational Substrate Selection Contributes to the Enzymatic Catalytic Reaction Mechanism of Pin1. J Phys Chem B 2016; 120:12444-12453. [DOI: 10.1021/acs.jpcb.6b09187] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Esteban Vöhringer-Martinez
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
| | - Ciro Dörner
- Departamento de Físico-Química,
Facultad de Ciencias Químicas, Universidad de Concepción, 4030000 Concepción, Chile
| |
Collapse
|
11
|
Vasilevskaya T, Thiel W. Periodic Boundary Conditions in QM/MM Calculations: Implementation and Tests. J Chem Theory Comput 2016; 12:3561-70. [DOI: 10.1021/acs.jctc.6b00269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Walter Thiel
- Max-Planck-Institut
für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
12
|
Enzyme promiscuity in earthworm serine protease: substrate versatility and therapeutic potential. Amino Acids 2016; 48:941-948. [PMID: 26739820 DOI: 10.1007/s00726-015-2162-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
Abstract
Enzymes are the most versatile molecules in the biological world. These amazing molecules play an integral role in the regulation of various metabolic pathways and physiology subsequently. Promiscuity of an enzyme is the capacity to catalyze additional biochemical reactions besides their native one. Catalytic promiscuity has shown great impact in enzyme engineering for commercial enzyme and therapeutics with natural or engineered catalytic promiscuity. The earthworm serine protease (ESP) is a classic example of enzyme promiscuity and studied for its therapeutic potential over the last few decades. The ESP was reported for several therapeutic properties and fibrinolytic activity has been much explored. ESP, a complex enzyme exists as several isoforms of molecular weight ranging from 14 to 33 kDa. The fibrinolytic capacity of the enzyme has been studied in different species of earthworm and molecular mechanism is quite different from conventional thrombolytics. Cytotoxic and anti-tumor activities of ESP were evaluated using several cancer cell lines. Enzyme had shown tremendous scope in fighting against plant viruses and microbes. ESP is also reported for anti-inflammatory activity and anti-oxidant property. Apart from these, recently, ESP is reported for DNase activity. The daunting challenge for researchers is to understand the molecular mechanism for such diverse properties and possibility of enzyme promiscuity. This review emphasizes molecular mechanism of ESP governing various biochemical reactions. Further, the concept of enzyme promiscuity in ESP towards development of novel enzyme based drugs has been reviewed in this study.
Collapse
|
13
|
Sousa SF, Ramos MJ, Lim C, Fernandes PA. Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Pedro A. Fernandes
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| |
Collapse
|
14
|
Zapata-Torres G, Fierro A, Barriga-González G, Salgado JC, Celis-Barros C. Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach. J Chem Inf Model 2015; 55:1349-60. [PMID: 26091526 DOI: 10.1021/acs.jcim.5b00140] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.
Collapse
Affiliation(s)
- Gerald Zapata-Torres
- †Molecular Graphics Suite, Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Angélica Fierro
- ‡Facultad de Química, Departamento de Química Orgánica, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - German Barriga-González
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
| | - J Cristian Salgado
- ∥Laboratory of Process Modeling and Distributed Computing, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Cristian Celis-Barros
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
| |
Collapse
|
15
|
Faleev NG, Zakomirdina LN, Vorob'ev MM, Tsvetikova MA, Gogoleva OI, Demidkina TV, Phillips RS. A straightforward kinetic evidence for coexistence of "induced fit" and "selected fit" in the reaction mechanism of a mutant tryptophan indole lyase Y72F from Proteus vulgaris. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1844:1860-7. [PMID: 25084024 DOI: 10.1016/j.bbapap.2014.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/30/2014] [Accepted: 07/21/2014] [Indexed: 11/25/2022]
Abstract
The interaction of the mutant tryptophan indole-lyase (TIL) from Proteus vulgaris Y72F with the transition state analogue, oxindolyl-l-alanine (OIA), with the natural substrate, l-tryptophan, and with a substrate S-ethyl-l-cysteine was examined. In the case of wild-type enzyme these reactions are described by the same kinetic scheme where binding of holoenzyme with an amino acid, leading to reversible formation of an external aldimine, proceeds very fast, while following transformations, leading finally to reversible formation of a quinonoid intermediate proceed with measureable rates. Principally the same scheme ("induced fit") is realized in the case of mutant Y72F enzyme reaction with OIA. For the reaction of mutant enzyme with l-Trp at lower concentrations of the latter a principally different kinetic scheme is observed. This scheme suggests that binding of the substrate and formation of the quinonoid intermediate are at fast equilibrium, while preceding conformational changes of the holoenzyme proceed with measureable rates ("selected fit"). For the reaction with S-ethyl-l-cysteine the observed concentration dependence of kobs agrees with the realization of both kinetic schemes, the "selected fit" becoming predominant at lower concentrations of substrate, the "induced fit"- at higher ones. In the reaction with S-ethyl-l-cysteine the formation of the quinonoid intermediate proceeds slower than does catalytic α,β-elimination of ethylthiol from S-ethyl-l-cysteine, and consequently does not play a considerable role in the catalysis, which may be effected by a concerted E2 mechanism.
Collapse
Affiliation(s)
- Nicolai G Faleev
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia.
| | - Lyudmila N Zakomirdina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Mikhail M Vorob'ev
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Marina A Tsvetikova
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Olga I Gogoleva
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow 119991, Russia
| | - Tatyana V Demidkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Robert S Phillips
- Department of Chemistry, University of Georgia, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| |
Collapse
|
16
|
Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K. Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2013; 135:17432-43. [PMID: 24151964 PMCID: PMC3949427 DOI: 10.1021/ja408197k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the ΔΔG(⧧) value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.
Collapse
Affiliation(s)
- Masahiro Fujihashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toyokazu Ishida
- Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Shingo Kuroda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Lakshmi P. Kotra
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- Departments of Pharmaceutical Sciences and Chemistry, McLaughlin Center for Molecular Medicine, University of Toronto, Canada M5S 3M2
| | - Emil F. Pai
- Center for Molecular Design and Preformulations and Division of Cell & Molecular Biology, Toronto General Research Institute/University Health Network, Toronto, ON, Canada M5G 1L7
- The Campbell Family Cancer Research Institute, Ontario Cancer Institute/University Health Network & Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G 1L7
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| |
Collapse
|
17
|
In Silico Strategies Toward Enzyme Function and Dynamics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012. [DOI: 10.1016/b978-0-12-398312-1.00009-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|
18
|
Fedorova OS, Kuznetsov NA, Koval VV, Knorre DG. Conformational dynamics and pre-steady-state kinetics of DNA glycosylases. BIOCHEMISTRY (MOSCOW) 2011; 75:1225-39. [PMID: 21166640 DOI: 10.1134/s0006297910100044] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Results of investigations of E. coli DNA glycosylases using pre-steady-state kinetics are considered. Special attention is given to the connection of conformational changes in the interacting biomolecules with kinetic mechanisms of the enzymatic processes.
Collapse
Affiliation(s)
- O S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
| | | | | | | |
Collapse
|
19
|
Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
Collapse
Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
| | | |
Collapse
|
20
|
|
21
|
Roca M, De Maria L, Wodak SJ, Moliner V, Tuñón I, Giraldo J. Coupling of the guanosine glycosidic bond conformation and the ribonucleotide cleavage reaction: implications for barnase catalysis. Proteins 2008; 70:415-28. [PMID: 17680698 DOI: 10.1002/prot.21573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gchi) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2 '. Similar energetic profiles featuring two minima corresponding to the anti and syn Gchi regions were obtained for both ionic forms. For both forms the anti conformation was more stable than the syn, and barriers of approximately 4 kcal/mol were obtained for the anti --> syn transition. Structural analysis showed a remarkable sensitivity of the phosphate moiety to the conformation of the Gchi angle, suggesting a possible connection between this conformation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2 '--P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2'. The simulations revealed that the O2 ' attack along the syn Gchi was more favorable than that along the anti Gchi: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O--P bond formation; structurally, a lesser O2 '--P initial distance, and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the catalytically competent conformation of barnase-ribonucleotide complex, which requires a guanine syn conformation of the substrate to enable abstraction of the ribose H2 ' proton by the general base Glu73, thereby suggesting a coupling between the reactive substrate conformation and enzyme structure and mechanism.
Collapse
Affiliation(s)
- Maite Roca
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
| | | | | | | | | | | |
Collapse
|
22
|
van der Kamp MW, Mulholland AJ. Computational enzymology: insight into biological catalysts from modelling. Nat Prod Rep 2008; 25:1001-14. [DOI: 10.1039/b600517a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) methods are making rapid progress both methodologically and with respect to their range of application. Mechanistic studies on enzymes, including contributions towards the understanding of enzyme catalysis, continue to be a major target. They are joined by calculations of pK(a) values, redox properties, ground- and excited-state spectroscopic parameters, and excited-state dynamics. Methodological advances include improved QM/MM schemes, in particular new approaches for an effective treatment of the QM-MM electrostatic interactions, and the incorporation of new efficient and accurate QM methods in QM/MM schemes.
Collapse
Affiliation(s)
- Hans Martin Senn
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
| | | |
Collapse
|