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Reaction mechanism of metalloenzymes studied by theoretical methods

Dong, Geng LU (2018)
Abstract (Swedish)
Metalloenzymes are proteins that contain one or more metal ions bound to protein. They constitute about one-third of all enzymes known so far and they often perform hard chemical reactions involving small substrates, like H2 and N2. In our research, we focus on those metal ions that are located in the active sites and perform redox reactions, i.e. involving electron transfer.
Why enzymes? As we know, human benefit from enzymes. For example, more than 700 types of enzymes exist in our body, and O2, which is necessary to people, is generated by enzymes. However, the enzymes are complicated and very difficult to understand. In this thesis, theoretical methods were used to investigate enzymes.
Why theoretical methods?... (More)
Metalloenzymes are proteins that contain one or more metal ions bound to protein. They constitute about one-third of all enzymes known so far and they often perform hard chemical reactions involving small substrates, like H2 and N2. In our research, we focus on those metal ions that are located in the active sites and perform redox reactions, i.e. involving electron transfer.
Why enzymes? As we know, human benefit from enzymes. For example, more than 700 types of enzymes exist in our body, and O2, which is necessary to people, is generated by enzymes. However, the enzymes are complicated and very difficult to understand. In this thesis, theoretical methods were used to investigate enzymes.
Why theoretical methods? Enzymatic reactions are generally fast, so the details of the reaction are hard to study experimentally. Theoretical methods, using computers and software, have become more and more important in the study of enzyme catalytic mechanisms. With theoretical methods, we can construct models to mimic the reaction, so that we can understand the reaction in atomistic details, e.g. electron and proton transfer, bond cleavage and formation, etc. These findings from theoretical studies can then be used in the experimental studies. Here, we study three metalloenzymes, viz. [NiFe] hydrogenase, dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase.
[NiFe] hydrogenases catalyse the reversible formation of hydrogen molecules from protons and electrons. This very simple reaction has attracted much interest because H2 may be used as clean and renewable energy carrier. In DMSOR, the reduced enzyme reacts with dimethyl sulfoxide (DMSO) to generate dimethyl sulfide (DMS). This enzyme is interesting because the molybdenum (Mo) is the only known second-row transition metal that employed by proteins, and Mo enzymes exist in almost all organisms and they are involved in the metabolism of many biological systems. Finally, the formate dehydrogenases (FDHs) can react with formate to generate carbon dioxide reversibly. This reaction is a key part of biological transformations of carbon dioxide (CO2) in the global carbon cycle.
These enzymes are very interesting and play important roles in nature. However, the reaction mechanisms are still not fully understood. In this thesis, we explored the details of the reaction mechanism for the three enzymes with theoretical methods.
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Abstract
Metalloenzymes catalyse a wide variety of reactions in nature. In the thesis, I have studied the reaction mechanism of three metalloenzymes, viz. [NiFe] hydrogenase (H2ase), dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase (FDH), by theoretical methods, namely quantum mechanics (QM), combined quantum mechanical and molecular mechanics (QM/MM), as well as QM/MM thermodynamic cycle perturbation (QTCP).

For H2ase, we have studied the protonation states of the four cysteine residues in the active site at four intermediate states, the H2 binding site and the full reaction mechanism. Our results demonstrate that the Cys546 residue is most easily protonated by 14−51 kJ/mol, H2 binding to Ni ion in singlet state is most... (More)
Metalloenzymes catalyse a wide variety of reactions in nature. In the thesis, I have studied the reaction mechanism of three metalloenzymes, viz. [NiFe] hydrogenase (H2ase), dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase (FDH), by theoretical methods, namely quantum mechanics (QM), combined quantum mechanical and molecular mechanics (QM/MM), as well as QM/MM thermodynamic cycle perturbation (QTCP).

For H2ase, we have studied the protonation states of the four cysteine residues in the active site at four intermediate states, the H2 binding site and the full reaction mechanism. Our results demonstrate that the Cys546 residue is most easily protonated by 14−51 kJ/mol, H2 binding to Ni ion in singlet state is most favourable by at least 47 kJ/mol, and the Ni-L state is not involved in the reaction mechanism. For the H2 binding, we have calibrated density-functional methods with advanced QM methods, like CCSD(T), DMRG-CASPT2 and CAS-srDFT.

For DMSOR, we have studied the effect of the protein ligand in reaction mechanism. Our results indicate that enzymes with ligand with a single negative charge (serine, cysteine, selenocysteine, SH– and OH–) are predicted to have two-step reaction mechanisms, giving an activation energy of 69−85 kJ/mol. However, the O2– and S2– ligands gave much higher activation energies of 212 and 168 kJ/mol.

For FDH, we have studied the reaction mechanism. Our results indicate that the substrate formate does not coordinate directly to Mo ion when it enters the oxidised active site of FDH, but instead resides in the second coordination sphere. The sulfido ligand abstracts a hydride from substrate, giving a Mo(IV)−SH state. Finally, the CO2 will be released when the active site is oxidised by two electrons.
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Please use this url to cite or link to this publication:
author
supervisor
opponent
  • Prof. Ramos, Maria João, Computational Biochemistry, University of Porto, Portugal
organization
publishing date
type
Thesis
publication status
published
subject
keywords
Metalloenzymes, Reaction mechanism, QM/MM, DFT, DMRG, CAS-srDFT, Big-QM, QTCP
pages
116 pages
publisher
Lund University, Faculty of Science, Department of Chemistry, Division of Theoretical Chemistry
defense location
Lecture hall B, Center for chemistry and chemical engineering, Naturvetarvägen 14, Lund
defense date
2018-05-31 10:15
ISBN
978-91-7422-585-3
978-91-7422-584-6
language
English
LU publication?
yes
id
ac98f894-73df-4664-85b6-3910599332d3
date added to LUP
2018-05-04 16:09:12
date last changed
2018-05-29 11:31:50
@phdthesis{ac98f894-73df-4664-85b6-3910599332d3,
  abstract     = {Metalloenzymes catalyse a wide variety of reactions in nature. In the thesis, I have studied the reaction mechanism of three metalloenzymes, viz. [NiFe] hydrogenase (H2ase), dimethyl sulfoxide reductase (DMSOR) and formate dehydrogenase (FDH), by theoretical methods, namely quantum mechanics (QM), combined quantum mechanical and molecular mechanics (QM/MM), as well as QM/MM thermodynamic cycle perturbation (QTCP). <br/><br/>For H2ase, we have studied the protonation states of the four cysteine residues in the active site at four intermediate states, the H2 binding site and the full reaction mechanism. Our results demonstrate that the Cys546 residue is most easily protonated by 14−51 kJ/mol, H2 binding to Ni ion in singlet state is most favourable by at least 47 kJ/mol, and the Ni-L state is not involved in the reaction mechanism. For the H2 binding, we have calibrated density-functional methods with advanced QM methods, like CCSD(T), DMRG-CASPT2 and CAS-srDFT.<br/><br/>For DMSOR, we have studied the effect of the protein ligand in reaction mechanism. Our results indicate that enzymes with ligand with a single negative charge (serine, cysteine, selenocysteine, SH– and OH–) are predicted to have two-step reaction mechanisms, giving an activation energy of 69−85 kJ/mol. However, the O2– and S2– ligands gave much higher activation energies of 212 and 168 kJ/mol. <br/><br/>For FDH, we have studied the reaction mechanism. Our results indicate that the substrate formate does not coordinate directly to Mo ion when it enters the oxidised active site of FDH, but instead resides in the second coordination sphere. The sulfido ligand abstracts a hydride from substrate, giving a Mo(IV)−SH state. Finally, the CO2 will be released when the active site is oxidised by two electrons.<br/>},
  author       = {Dong, Geng},
  isbn         = {978-91-7422-585-3},
  keyword      = {Metalloenzymes,Reaction mechanism,QM/MM,DFT,DMRG,CAS-srDFT,Big-QM,QTCP},
  language     = {eng},
  pages        = {116},
  publisher    = {Lund University, Faculty of Science, Department of Chemistry, Division of Theoretical Chemistry},
  school       = {Lund University},
  title        = {Reaction mechanism of metalloenzymes studied by theoretical methods},
  year         = {2018},
}