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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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2
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Klinger A, Lindorfer D, Müh F, Renger T. Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer. J Chem Phys 2020; 153:215103. [PMID: 33291900 DOI: 10.1063/5.0027994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intermolecular contribution to the spectral density of the exciton-vibrational coupling of the homotrimeric Fenna-Matthews-Olson (FMO) light-harvesting protein of green sulfur bacteria P. aestuarii is analyzed by combining a normal mode analysis of the protein with the charge density coupling method for the calculation of local transition energies of the pigments. Correlations in site energy fluctuations across the whole FMO trimer are found at low vibrational frequencies. Including, additionally, the high-frequency intrapigment part of the spectral density, extracted from line-narrowing spectra, we study intra- and intermonomer exciton transfer. Whereas the intrapigment part of the spectral density is important for fast intramonomer exciton relaxation, the intermolecular contributions (due to pigment-environment coupling) determine the intermonomer exciton transfer. Neither the variations of the local Huang-Rhys factors nor the correlations in site energy fluctuations have a critical influence on energy transfer. At room temperature, the intermonomer transfer in the FMO protein occurs on a 10 ps time scale, whereas intramonomer exciton equilibration is roughly two orders of magnitude faster. At cryogenic temperatures, intermonomer transfer limits the lifetimes of the lowest exciton band. The lifetimes are found to increase between 20 ps in the center of this band up to 100 ps toward lower energies, which is in very good agreement with the estimates from hole burning data. Interestingly, exciton delocalization in the FMO monomers is found to slow down intermonomer energy transfer, at both physiological and cryogenic temperatures.
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Affiliation(s)
- Alexander Klinger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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3
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Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2017; 8:2350-2356. [PMID: 28485971 DOI: 10.1021/acs.jpclett.7b00669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation of excitonic quantum beats in photosynthetic antennae has prompted wide debate regarding the function of excitonic coherence in pigment-protein complexes. Much of this work focuses on the interactions of excitons with the femto-to-picosecond dynamical fluctuations of their environment. However, in experiments these effects can be masked by static disorder of the excited-state energies across ensembles, whose microscopic origins are challenging to predict. Here the excited-state properties of ∼2000 atom clusters of the Fenna-Matthews-Olson complex are simulated using a unique combination of linear-scaling density functional theory and constrained geometric dynamics. While slow, large amplitude protein motion leads to large variations in the Qy transitions of two pigments, we identify pigment-protein correlations that greatly reduce variations in the energy gap across the ensemble, which is consistent with experimental observations of suppressed inhomogeneous dephasing of quantum beats.
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Affiliation(s)
- Alexander S Fokas
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- School of Chemistry, Newcastle University , Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick , Coventry CV4 7AL, United Kingdom
| | - Stephen A Wells
- Department of Chemistry, University of Bath , Claverton Down BA2 7AY, United Kingdom
| | - Michael C Payne
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alex W Chin
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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4
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Hermans SM, Pfleger C, Nutschel C, Hanke CA, Gohlke H. Rigidity theory for biomolecules: concepts, software, and applications. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1311] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susanne M.A. Hermans
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christina Nutschel
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Christian A. Hanke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry; Heinrich Heine University Düsseldorf; Düsseldorf Germany
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5
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Aghtar M, Kleinekathöfer U, Curutchet C, Mennucci B. Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545. J Phys Chem B 2017; 121:1330-1339. [DOI: 10.1021/acs.jpcb.6b10772] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mortaza Aghtar
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department
of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carles Curutchet
- Departament
de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica
and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Benedetta Mennucci
- Dipartimento
di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi
13, I-56124 Pisa, Italy
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6
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Morgan SE, Cole DJ, Chin AW. Nonlinear network model analysis of vibrational energy transfer and localisation in the Fenna-Matthews-Olson complex. Sci Rep 2016; 6:36703. [PMID: 27827409 PMCID: PMC5101523 DOI: 10.1038/srep36703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/19/2016] [Indexed: 11/10/2022] Open
Abstract
Collective protein modes are expected to be important for facilitating energy transfer in the Fenna-Matthews-Olson (FMO) complex of photosynthetic green sulphur bacteria, however to date little work has focussed on the microscopic details of these vibrations. The nonlinear network model (NNM) provides a computationally inexpensive approach to studying vibrational modes at the microscopic level in large protein structures, whilst incorporating anharmonicity in the inter-residue interactions which can influence protein dynamics. We apply the NNM to the entire trimeric FMO complex and find evidence for the existence of nonlinear discrete breather modes. These modes tend to transfer energy to the highly connected core pigments, potentially opening up alternative excitation energy transfer routes through their influence on pigment properties. Incorporating localised modes based on these discrete breathers in the optical spectra calculations for FMO using ab initio site energies and excitonic couplings can substantially improve their agreement with experimental results.
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Affiliation(s)
- Sarah E Morgan
- Theory of Condensed Matter Group, Physics Department, University of Cambridge, CB3 0HE, United Kingdom
| | - Daniel J Cole
- Theory of Condensed Matter Group, Physics Department, University of Cambridge, CB3 0HE, United Kingdom.,School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alex W Chin
- Theory of Condensed Matter Group, Physics Department, University of Cambridge, CB3 0HE, United Kingdom
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7
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Cole DJ, Hine NDM. Applications of large-scale density functional theory in biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:393001. [PMID: 27494095 DOI: 10.1088/0953-8984/28/39/393001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
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Affiliation(s)
- Daniel J Cole
- Theory of Condensed Matter group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK. School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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8
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Fokas AS, Cole DJ, Ahnert SE, Chin AW. Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis. Sci Rep 2016; 6:33213. [PMID: 27623708 PMCID: PMC5021933 DOI: 10.1038/srep33213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/12/2016] [Indexed: 01/23/2023] Open
Abstract
Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.
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Affiliation(s)
- Alexander S. Fokas
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Daniel J. Cole
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Sebastian E. Ahnert
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
| | - Alex W. Chin
- Theory of Condensed Matter Group, Cavendish Laboratory, 19 JJ Thomson Avenue, CB3 0HE, Cambridge, U.K
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9
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Wilkins DM, Dattani NS. Why Quantum Coherence Is Not Important in the Fenna–Matthews–Olsen Complex. J Chem Theory Comput 2015; 11:3411-9. [DOI: 10.1021/ct501066k] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- David M. Wilkins
- Physical and Theoretical
Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Nikesh S. Dattani
- Quantum
Chemistry Laboratory,
Department of Chemistry, Kyoto University, 606-8502, Kyoto, Japan
- School of Materials Science
and Engineering, Nanyang Technological University, Block N4.1, Nanyang Avenue, Singapore 639798
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10
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Jeske J, Ing DJ, Plenio MB, Huelga SF, Cole JH. Bloch-Redfield equations for modeling light-harvesting complexes. J Chem Phys 2015; 142:064104. [DOI: 10.1063/1.4907370] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jan Jeske
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - David J. Ing
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
| | - Martin B. Plenio
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm, Germany
| | - Susana F. Huelga
- Institut für Theoretische Physik, Albert-Einstein-Allee 11, Universität Ulm, D-89069 Ulm, Germany
| | - Jared H. Cole
- Chemical and Quantum Physics, School of Applied Sciences, RMIT University, Melbourne 3001, Australia
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