Computation of electron transfer properties for heme-containing oxidoreductases
Lead Research Organisation:
University of Cambridge
Department Name: Chemistry
Abstract
Atomistic computer simulations are proposed to advance aquantitative understanding of long-range electron transfer (ET) reactionsin electron transport proteins. This work is carried out to aid and complementexperimental work in this field. Existing computer simulation techniques areextended to compute key parameters that govern the rate of biologicalET reactions. These parameters are often unknown and usually ratherdifficult to measure. Using numerical methods we aim at providingquantitative estimates that can be used in electron tunneling simulations ofbiological electron carriers. Moreover, exploiting the microscopic information ofmolecular simulations, the contributions of single amino acid residues andthe surrounding solvent to the ET rate are analyzed and used to interpret effects ofprotein mutations that could guide the design of efficient biomimetics. In the short term the simulation methods are validated on simple and experimentally well characterized electron transport proteins (specific aim I). In the medium to long term redox and ET reactions in the more complex heme catalases are investigated (specific aim II). Research programme (specific aim I): Reliable experimental ET parameters areavailable for only very few biological ET reactions where donor and acceptor havea well defined structure. Among these systems are ruthenium modified cytochrome (cyt) proteins such as cyt c, myoglobin, cyt b5 and cyt b562. A wealth of structural, thermodynamic and kinetic data available for these proteins, which makes them possibly the best benchmark systems for assessment of the accuracy ofcomputer simulations. First objective is the computation of ET parametersfor ET from the heme group located inside the proteinto the ruthenium complex located at the surface of the protein. The simulationsof the proteins are carried out for models with increasing degree of complexity. Depending on the deviation with experimental data, new ideas for improvement of the simulation methodology are explored. The finite temperature motion of the different cytochromes are analyzed and used to investigate the influence of the different protein folds and heme groups on the ET parameters. Thereafter the focus of research will shift to the more complicated heme catalases described below.Research programme (specific aim II):Heme catalases prevent cells from oxidative damage by catalyzing the decomposition of hydrogen peroxide in oxygen and water. The catalytic activity is drasticallyreduced or even lost under certain conditions, if reaction intermediatecompound I undergoes one-electron reduction to compound II.Recent crystallographic and computational studies have given evidencethat the oxidized form of heme b containing catalase of H. pylori (HPC) formsthe catalytically less active compound II whereas the heme d containing catalase of P. vitale remains in theactive compound I form. Naturally, the question arises whether this difference is related to the different heme groups or to the different protein structure of the two catalases. Using the methods validated on simple cytochrome proteins (see above), we propose to calculate ET parameters for HPC and PVC and to determine the corresponding contributions of cofactor, protein and solvent.In the next step ionizable groups in the vicinity of the heme groups are identified and the ET parameters computed for ET from the ionizable group to the oxidized heme center. We hope that on the basis of these calculations one can explain the different tendencies of HPC and PVC to form the catalytically less active compound II.
People |
ORCID iD |
| Jochen Blumberger (Principal Investigator) |
Publications
Alfonso-Prieto M
(2011)
Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase.
in Journal of the American Chemical Society
Blumberger J
(2015)
Recent Advances in the Theory and Molecular Simulation of Biological Electron Transfer Reactions.
in Chemical reviews
Blumberger J
(2008)
Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment.
in Physical chemistry chemical physics : PCCP
Oberhofer H
(2010)
Insight into the mechanism of the Ru2+-Ru3+ electron self-exchange reaction from quantitative rate calculations.
in Angewandte Chemie (International ed. in English)
Oberhofer H
(2012)
Revisiting electronic couplings and incoherent hopping models for electron transport in crystalline C60 at ambient temperatures.
in Physical chemistry chemical physics : PCCP
Oberhofer H
(2009)
Charge constrained density functional molecular dynamics for simulation of condensed phase electron transfer reactions.
in The Journal of chemical physics
Oberhofer H
(2010)
Electronic coupling matrix elements from charge constrained density functional theory calculations using a plane wave basis set.
in The Journal of chemical physics
Tipmanee V
(2010)
Prediction of reorganization free energies for biological electron transfer: a comparative study of Ru-modified cytochromes and a 4-helix bundle protein.
in Journal of the American Chemical Society
| Description | The aim of the project was to develop and apply ab-initio and classical molecular dynamics methods for the calculation of electron transfer parameter in redox proteins. The results for each specific aim described in the proposal are summarized below. 1.) Specific aim I. Atomistic simulation methods for computation of reorganization free energy and driving force (redox potential) for intraprotein ET are investigated and validated on Ru-modified cytochrome c (cyt c), myoglobin, cyt b_5 and cyt b_562. The contributions of single amino acid residues and of the surrounding protein matrix is determined to investigate the relationship between protein fold, redox potential and reorganization free energy. At first we investigated a number of quantum mechanical/molecular mechanical (QM/MM) approaches for the calculation of biological electron transfer free energies with emphasis on reorganization free energy. The latter determines the free energy barrier for ET. We have used the well characterized Ru-modified cytochrome c protein as model system. It turned out that the non-polarizable force fields typically adopted in QM/MM schemes are not sufficiently accurate for calculation of reorganization free energy. The use of an electronically polarizable force field was necessary in order to obtain good agreement with experiment. After the initial testing of simulation protocols, applications to four heme containing proteins followed. Here we have made a slightly different choice of the proteins simulated than originally proposed. Instead of myoglobin, we have simulated a second cytochrome c protein, now modified with a more hydrophilic Ru-label, and instead of cyt b_562 we have simulated a designed 4-helix bundle binding two heme-cofactors. The Ru-modified cytochrome b5 was simulated as originally proposed. Our revised choice allowed us to probe the influence of the different protein fold and of the different hydrophilicity of the electron accepting group on the reorganization free energy. Rather surprisingly the reorganization free energy of all proteins except the 4-helix bundle fell within a narrow range. In the latter, both redox active cofactors are inside the protein scaffold and protected from the solvent, which gives rise to a significantly lower reorganization energy. We also found that in three out of the four proteins studied reorganization free energy is a collective effect including many residues, each contributing a small fraction. The results obtained have important implications for the design of artificial electron transport proteins. They suggest that reorganization free energy may in general not be effectively controlled by point mutations, but to a large degree by the solvent exposure of the redox active groups. The results have been published in a `Perspective article' in (Phys. Chem. Chem. Phys. 2008, inside cover article), and in a top Chemistry Journal, (J. Am. Chem. Soc. 2010). 2.) Work towards specific aim II has been carried out in collaboration with C. Rovira's group (Barcelona). Specific aim II. Heme catalases prevent cells from oxidative damage by catalyzing the decomposition of hydrogen peroxide in oxygen and water. The catalytic activity is drastically reduced or even lost under certain conditions, if reaction intermediate compound I (Fe(IV)(O)Por+) undergoes one-electron reduction to compound II (Fe(IV)(O)Por). By choosing two different heme catalases, one which is suspected to form compound II (from H. pylori) and one that is suspected not to form compound II (from P. vitale), we want to identify the factors that lead to formation of this catalytically less active intermediate. The most obvious difference between P. vitale catalase (PVC) and H. pylori catalase (HPC) is that the former binds heme d, whereas the latter binds a heme b cofactor. The different heme cofactors could exhibit different reduction potentials that in turn could give rise to the different tendency for formation of the catalytically less active Cpd II form. We have investigated this hypothesis by calculating the relevant reduction potentials of the two catalases using the QM/MM method devised in `Specific aim I' (we note that computation is the only alternative here since experimental measurements were unsuccessful). We found that -within the statistical uncertainty of our simulations- the reduction potentials of the two catalases were the same, implying that another reaction step causes the different behaviour. Carrying out elaborate QM/MM metadynamics simulations, we found that it is the proton transfer from a distal histidine residue to the vertically reduced Cpd I that exhibits very different energetics in the two catalases. While in HPC this reaction step drives the formation of Cpd II, in PVC the free energy released by proton transfer is not sufficient for formation of Cpd II. Our results suggest that the proton transfer following vertical reduction of Cpd I is a key factor regulating radical migration in catalase and possibly also in hydroperoxidases. A paper on these results has been published in J. Am. Chem. Soc. 2011. 3) During the grant period we have also implemented a special density functional method (constrained density functional theory) for the calculation of electronic coupling matrix elements. The latter is the third electron transfer parameter that, together with reorganization free energy and driving force, determines the rate for electron transfer reactions. The method was applied to ET reactions of simpler systems, such as ET between two transition metal ions in aqueous solution and intramolecular ET in an organic molecule. |
| Exploitation Route | Methodology for calculation of electron transfer parameters in redox proteins published and already adopted by the scientific community in the field. Constrained DFT implemented in freely available CPMD program package. |
| Sectors | Chemicals,Other |
| URL | http://www.cmmp.ucl.ac.uk/~jb/research/research.html |
| Description | A key advance during the grant period was the implementation of constrained density functional theory in the CPMD program package (2010). This software has about 5000 users world-wide in academia and industry, who have benefited from the software development. The project has resulted in 7 peer-reviewed publications. Two publications were featured on Journal cover pages and 3 papers were published in the top 2 Chemistry Journals. The results were also presented at international conferences, at the fall meetings of the American Chemical Society in Philadelphia (2008), Washington (2009) and Boston (2010), at the IUPAC conference in Glasgow (2009), at the Computational Molecular Science conference in Cirencester UK (2008, 2010), and at smaller meetings and workshops in Trieste (2008) and Konstanz (2008). The work was key to the award of a PRACE computing grant in June 2010. The grant facilitated our collaboration with the group of C. Rovira in Barcelona and made our activities visible to UK and overseas researchers. The project has contributed to the personal development of the PDRA (H. Oberhofer) and the successful outcome put him in a strong position for a permanent academic job. Immediately after finishing his EPSRC-sponsored post he was successful in obtaining a prestigious Humboldt-Research fellowship (2011) to carry on work on the subject at one of the top German Universities (TU Munich). He is currently a sub-group leader within the Chair of Theoretical Chemistry in this institution, and will soon finish his habilitation which will place him in a strong position for more senior independent group-leader positions. This research project was also the basis for the start of a number of collaborations, both with academics and researchers in US-national laboratories funded by the US-Department of Energy (e.g. Pacific Northwest National Laboratory, 2010-current). This has resulted in a number of studentships and long-term research collaborations as well as in a recent successful EPSRC grant application on electron transport in bacterial nanowire proteins (EP/M001946/1, 2014-17). This grant has also helped to disseminate and advertise the research of my group to a wider audience. As a result I was invited to give 36 invited talks since 2008 and to join the Editorial Board of the Journal J R Soc Interface in 2012. In my role as board member I have helped commission a series of Headline reviews on computer simulation of electron and proton transfer in biological systems, which should increase the visibility and recognition of this still rather young scientific journal at the interface between the life and natural sciences. |
| First Year Of Impact | 2010 |
| Sector | Other |
| Impact Types | Cultural |
| Description | EPSRC Responsive Mode Grant |
| Amount | £793,197 (GBP) |
| Funding ID | EP/M001946/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2014 |
| End | 10/2017 |
| Title | Constrained density functional theory implementation in the CPMD program package |
| Description | An improved method for calcualation of electron transfer parameters and rates. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2009 |
| Provided To Others? | Yes |
| Impact | A number of research publications. |
| URL | http://www.cpmd.org/downloadable-files/no-authentication/manual_v3_17_1.pdf |
| Description | Calculation of electron transfer properties in molecules relevant for organic semiconductors |
| Organisation | Technical University of Munich |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Application of the constrained DFT and FODFT routine implemented in the CPMD package during the grant period. |
| Collaborator Contribution | partner at TU Munich: H. Oberhofer: code maintenance/small extensions and assistance with the calculations |
| Impact | F. Gajdos, H. Oberhofer, M. Dupuis, J. Blumberger "On the inapplicability of electron hopping models for the organic semiconductor Phenyl-C61-butyric Acid Methyl Ester (PCBM)" , J. Phys. Chem. Lett. 4, 1012 (2013). A. Kubas, F. Hoffmann, A. Heck, H. Oberhofer, M. Elstner, J. Blumberger "Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations", J. Chem. Phys. 140, 104105 (2014). A. Kubas, F. Gajdos, A. Heck, H. Oberhofer, M. Elstner, J. Blumberger "Electronic couplings for molecular charge transfer: benchmarking CDFT, FODFT and FODFTB against high-level ab initio calculations. II.", submitted to Phys. Chem. Chem. Phys. (2014). |
| Start Year | 2011 |
| Description | Calculation of electron transfer properties in oxide materials |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Application of the constrained DFT method implemented during the grant period to electron transfer between F-center defects in oxide materials, specifically MgO. |
| Collaborator Contribution | Suggestion of project, preparation of unit cells, development of finite size corrections and part of the calculations (Keith McKenna) |
| Impact | K. P. McKenna, J. Blumberger "Crossover from Incoherent to Coherent Electron Tunneling between Defects in MgO", Phys. Rev. B 86, 245110 (2012). J. Blumberger, K. P. McKenna "Constrained Density Functional Theory Applied to Electron Tunnelling between Defects in MgO", Phys. Chem. Chem. Phys. 15, 2184 (2013). |
| Start Year | 2011 |