Perspective on Integrative Simulations of Bioenergetic Domains

Pirnia, Adam; Maqdisi, Ranel; Mittal, Sumit; Sener, Melih; Singharoy, Abhishek

doi:10.1021/acs.jpcb.3c07335

Title: Perspective on Integrative Simulations of Bioenergetic Domains

Journal Article · 02 April 2024 · Journal of Physical Chemistry. B

DOI: https://doi.org/10.1021/acs.jpcb.3c07335 · OSTI ID:2339485

^[1]; Maqdisi, Ranel ^[2];

^[3];

^[4];

^[2]

Arizona State Univ., Tempe, AZ (United States); Arizona State University
Arizona State Univ., Tempe, AZ (United States)
VIT Bhopal University (India)
Arizona State Univ., Tempe, AZ (United States); Univ. of Illinois at Urbana-Champaign, IL (United States)

Bioenergetic processes in cells, such as photosynthesis or respiration, integrate many time and length scales, which makes the simulation of energy conversion with a mere single level of theory impossible. Just like the myriad of experimental techniques required to examine each level of organization, an array of overlapping computational techniques is necessary to model energy conversion. Here, in this work, a perspective is presented on recent efforts for modeling bioenergetic phenomena with a focus on molecular dynamics simulations and its variants as a primary method. An overview of the various classical, quantum mechanical, enhanced sampling, coarse-grained, Brownian dynamics, and Monte Carlo methods is presented. Example applications discussed include multiscale simulations of membrane-wide electron transport, rate kinetics of ATP turnover from electrochemical gradients, and finally, integrative modeling of the chromatophore, a photosynthetic pseudo-organelle.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Arizona State Univ., Tempe, AZ (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division (CSGB)

Grant/Contract Number:: SC0010575; SC0022956

OSTI ID:: 2339485

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 14 Vol. 128; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (240)

ATP Synthesis by Rotary Catalysis (Nobel lecture) Walker, John E. Angewandte Chemie International Edition, Vol. 37, Issue 17 https://doi.org/10.1002/(SICI)1521-3773(19980918)37:17<2308::AID-ANIE2308>3.0.CO;2-W	journal	September 1998
Time-Dependent Density Functional Theory Huix-Rotllant, Miquel; Ferré, Nicolas; Barbatti, Mario Quantum Chemistry and Dynamics of Excited States: Methods and Applications https://doi.org/10.1002/9781119417774.ch2	book	November 2020
Photosynthesis Drives the Motion of Bio‐nanomotors Mathesh, Motilal; Wilson, Daniela Apreutesei Advanced Intelligent Systems, Vol. 2, Issue 5 https://doi.org/10.1002/aisy.202000028	journal	April 2020
Multiple Charge‐Separation Pathways in Photosystem II: Modeling of Transient Absorption Kinetics Novoderezhkin, Vladimir I.; Romero, Elisabet; Dekker, Jan P. ChemPhysChem, Vol. 12, Issue 3 https://doi.org/10.1002/cphc.201000830	journal	February 2011
Förster Energy Transfer Theory as Reflected in the Structures of Photosynthetic Light‐Harvesting Systems Şener, Melih; Strümpfer, Johan; Hsin, Jen ChemPhysChem, Vol. 12, Issue 3 https://doi.org/10.1002/cphc.201000944	journal	February 2011
Multireference Methods are Realistic and Useful Tools for Modeling Catalysis Vitillo, Jenny G.; Cramer, Christopher J.; Gagliardi, Laura Israel Journal of Chemistry, Vol. 62, Issue 1-2 https://doi.org/10.1002/ijch.202100136	journal	February 2022
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Accelerating molecular modeling applications with graphics processors Stone, John E.; Phillips, James C.; Freddolino, Peter L. Journal of Computational Chemistry, Vol. 28, Issue 16 https://doi.org/10.1002/jcc.20829	journal	January 2007
MCCE2: Improving protein p K _a calculations with extensive side chain rotamer sampling Song, Yifan; Mao, Junjun; Gunner, M. R. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21222	journal	January 2009
On the effect of a variation of the force field, spatial boundary condition and size of the QM region in QM/MM MD simulations Meier, Katharina; Thiel, Walter; van Gunsteren, Wilfred F. Journal of Computational Chemistry, Vol. 33, Issue 4 https://doi.org/10.1002/jcc.21962	journal	December 2011
Force field development for cofactors in the photosystem II Zhang, Lu; Silva, Daniel-Adriano; Yan, YiJing Journal of Computational Chemistry, Vol. 33, Issue 25 https://doi.org/10.1002/jcc.23016	journal	June 2012
Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond Scemama, Anthony; Caffarel, Michel; Oseret, Emmanuel Journal of Computational Chemistry, Vol. 34, Issue 11 https://doi.org/10.1002/jcc.23216	journal	January 2013
Revised CHARMM force field parameters for iron-containing cofactors of photosystem II Adam, Suliman; Knapp-Mohammady, Michaela; Yi, Jun Journal of Computational Chemistry, Vol. 39, Issue 1 https://doi.org/10.1002/jcc.24918	journal	August 2017
New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems Jung, Jaewoon; Kobayashi, Chigusa; Kasahara, Kento Journal of Computational Chemistry, Vol. 42, Issue 4 https://doi.org/10.1002/jcc.26450	journal	November 2020
pH replica-exchange method based on discrete protonation states Itoh, Satoru G.; Damjanović, Ana; Brooks, Bernard R. Proteins: Structure, Function, and Bioinformatics, Vol. 79, Issue 12 https://doi.org/10.1002/prot.23176	journal	October 2011
Monte Carlo replica-exchange based ensemble docking of protein conformations Zhang, Zhe; Ehmann, Uwe; Zacharias, Martin Proteins: Structure, Function, and Bioinformatics, Vol. 85, Issue 5 https://doi.org/10.1002/prot.25262	journal	February 2017
The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3 https://doi.org/10.1002/wcms.1169	journal	August 2013
Classical molecular dynamics on graphics processing unit architectures Jász, Ádám; Rák, Ádám; Ladjánszki, István WIREs Computational Molecular Science, Vol. 10, Issue 2 https://doi.org/10.1002/wcms.1444	journal	August 2019
Metadynamics: Metadynamics Barducci, Alessandro; Bonomi, Massimiliano; Parrinello, Michele Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 5 https://doi.org/10.1002/wcms.31	journal	February 2011
Quantum Monte Carlo methods: Quantum Monte Carlo methods Lüchow, Arne Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 3 https://doi.org/10.1002/wcms.40	journal	April 2011
Umbrella sampling: Umbrella sampling Kästner, Johannes Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6 https://doi.org/10.1002/wcms.66	journal	May 2011
Metabolism in cancer metastasis: bioenergetics, biosynthesis, and beyond Teoh, Shao Thing; Lunt, Sophia Y. WIREs Systems Biology and Medicine, Vol. 10, Issue 2 https://doi.org/10.1002/wsbm.1406	journal	October 2017
Protein-protein association: investigation of factors influencing association rates by Brownian dynamics simulations Gabdoulline, Razif R.; Wade, Rebecca C. Journal of Molecular Biology, Vol. 306, Issue 5 https://doi.org/10.1006/jmbi.2000.4404	journal	March 2001
Molecular Dynamics Methods for Bioelectronic Systems in Photosynthesis Kosztin, Ioan; Schulten, Klaus Biophysical Techniques in Photosynthesis https://doi.org/10.1007/978-1-4020-8250-4_22	book	January 2008
Functional Coupling Between Reaction Centers and Cytochrome bc ₁ Complexes Lavergne, Jérôme; Verméglio, André; Joliot, Pierre The Purple Phototrophic Bacteria https://doi.org/10.1007/978-1-4020-8815-5_26	book	January 2009
Transition Path Sampling and Other Advanced Simulation Techniques for Rare Events Dellago, Christoph; Bolhuis, Peter G. Advanced Computer Simulation Approaches for Soft Matter Sciences III https://doi.org/10.1007/978-3-540-87706-6_3	book	January 2009
Dissipation in bioenergetic electron transfer chains Lavergne, J�r�me; Joliot, Pierre Photosynthesis Research, Vol. 48, Issue 1-2 https://doi.org/10.1007/BF00041003	journal	May 1996
Brownian dynamics simulation of protein association Northrup, Scott H.; Luton, J. Alan; Boles, Jeffrey O. Journal of Computer-Aided Molecular Design, Vol. 1, Issue 4 https://doi.org/10.1007/BF01677278	journal	January 1988
The study of conformational changes in photosystem II during a charge separation Kulik, Natalia; Kutý, Michal; Řeha, David Journal of Molecular Modeling, Vol. 26, Issue 4 https://doi.org/10.1007/s00894-020-4332-9	journal	March 2020
Relationship of proton motive force and the F0F1-ATPase with bio-hydrogen production activity of Rhodobacter sphaeroides: effects of diphenylene iodonium, hydrogenase inhibitor, and its solvent dimethylsulphoxide Hakobyan, Lilit; Gabrielyan, Lilit; Trchounian, Armen Journal of Bioenergetics and Biomembranes, Vol. 44, Issue 4 https://doi.org/10.1007/s10863-012-9450-3	journal	June 2012
Membrane development in purple photosynthetic bacteria in response to alterations in light intensity and oxygen tension Niederman, Robert A. Photosynthesis Research, Vol. 116, Issue 2-3 https://doi.org/10.1007/s11120-013-9851-0	journal	May 2013
The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function Mukherjee, Shayantani; Warshel, Arieh Photosynthesis Research, Vol. 134, Issue 1 https://doi.org/10.1007/s11120-017-0411-x	journal	July 2017
Molecular dynamics simulations in photosynthesis Liguori, Nicoletta; Croce, Roberta; Marrink, Siewert J. Photosynthesis Research, Vol. 144, Issue 2 https://doi.org/10.1007/s11120-020-00741-y	journal	April 2020
Return on investment from industrial energy efficiency: evidence from developing countries Alcorta, Ludovico; Bazilian, Morgan; De Simone, Giuseppe Energy Efficiency, Vol. 7, Issue 1 https://doi.org/10.1007/s12053-013-9198-6	journal	March 2013
Linear dichroism and fluorescence emission of antenna complexes during photosynthetic unit assembly in Rhodopseudomonas sphaeroides Hunter, C. N.; Kramer, H. J. M.; van Grondelle, R. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 807, Issue 1 https://doi.org/10.1016/0005-2728(85)90051-9	journal	April 1985
Effect of β-carotene on structural and dynamic properties of model phosphatidylcholine membranes. I. An EPR spin label study Strzałka, Kazimierz; Gruszecki, Wiesław I. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1194, Issue 1 https://doi.org/10.1016/0005-2736(94)90212-7	journal	August 1994
Effect of β-carotene on structural and dynamic properties of model phosphatidylcholine membranes. II. A 31P-NMR and 13C-NMR study Jeżowska, Iwona; Wolak, Adam; Gruszecki, Wiesław I. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1194, Issue 1 https://doi.org/10.1016/0005-2736(94)90213-5	journal	August 1994
Molecular rectifiers Aviram, Arieh; Ratner, Mark A. Chemical Physics Letters, Vol. 29, Issue 2 https://doi.org/10.1016/0009-2614(74)85031-1	journal	November 1974
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme Warshel, A.; Levitt, M. Journal of Molecular Biology, Vol. 103, Issue 2 https://doi.org/10.1016/0022-2836(76)90311-9	journal	May 1976
A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations Merchant, Bonnie A.; Madura, Jeffry D. Annual Reports in Computational Chemistry https://doi.org/10.1016/B978-0-444-53835-2.00003-1	book	October 2011
Photobioreactors – Models of Photosynthesis and Related Effects Merchuk, J. C.; Garcia-Camacho, F.; Molina-Grima, E. Comprehensive Biotechnology https://doi.org/10.1016/B978-0-444-64046-8.00081-1	book	July 2019
Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase Aksimentiev, Aleksij; Balabin, Ilya A.; Fillingame, Robert H. Biophysical Journal, Vol. 86, Issue 3 https://doi.org/10.1016/S0006-3495(04)74205-8	journal	March 2004
Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations Olkhova, Elena; Hutter, Michael C.; Lill, Markus A. Biophysical Journal, Vol. 86, Issue 4 https://doi.org/10.1016/S0006-3495(04)74254-X	journal	April 2004
Bound water in the proton translocation mechanism of the haem‐copper oxidases FEBS Letters, Vol. 414, Issue 2, p. 275-280 https://doi.org/10.1016/S0014-5793(97)01003-X	journal	September 1997
The Structure and Thermal Motion of the B800–850 LH2 Complex from Rps.acidophila at 2.0Å Resolution and 100K: New Structural Features and Functionally Relevant Motions Papiz, Miroslav Z.; Prince, Steve M.; Howard, Tina Journal of Molecular Biology, Vol. 326, Issue 5 https://doi.org/10.1016/S0022-2836(03)00024-X	journal	March 2003
The crystal structure of the light-harvesting complex II (B800–850) from Rhodospirillum molischianum Koepke, Juergen; Hu, Xiche; Muenke, Cornelia Structure, Vol. 4, Issue 5 https://doi.org/10.1016/S0969-2126(96)00063-9	journal	May 1996
Quantum Monte Carlo methods for the solution of the Schrödinger equation for molecular systems Aspuru-Guzik, Alán; Lester, William A. Handbook of Numerical Analysis https://doi.org/10.1016/S1570-8659(03)10007-5	book	January 2003
Methods for Monte Carlo Simulations of Biomacromolecules Vitalis, Andreas; Pappu, Rohit V. Annual Reports in Computational Chemistry, p. 49-76 https://doi.org/10.1016/S1574-1400(09)00503-9	book	January 2009
Dependence of plastoquinol diffusion on the shape, size, and density of integral thylakoid proteins Tremmel, I. G.; Kirchhoff, H.; Weis, E. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1607, Issue 2-3 https://doi.org/10.1016/j.bbabio.2003.09.004	journal	December 2003
Disruption of a specific molecular interaction with a bound lipid affects the thermal stability of the purple bacterial reaction centre Fyfe, Paul K.; Isaacs, Neil W.; Cogdell, Richard J. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1608, Issue 1 https://doi.org/10.1016/j.bbabio.2003.09.014	journal	January 2004
Role of Ca2+ in structure and function of Complex I from Escherichia coli Verkhovskaya, Marina; Knuuti, Juho; Wikström, Mårten Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 1 https://doi.org/10.1016/j.bbabio.2010.09.002	journal	January 2011
The Q cycle of cytochrome bc complexes: A structure perspective Cramer, William A.; Hasan, S. Saif; Yamashita, Eiki Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1807, Issue 7 https://doi.org/10.1016/j.bbabio.2011.02.006	journal	July 2011
High-light vs. low-light: Effect of light acclimation on photosystem II composition and organization in Arabidopsis thaliana Kouřil, Roman; Wientjes, Emilie; Bultema, Jelle B. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 3 https://doi.org/10.1016/j.bbabio.2012.12.003	journal	March 2013
Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides Cartron, Michaël L.; Olsen, John D.; Sener, Melih Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837 https://doi.org/10.1016/j.bbabio.2014.05.314	journal	July 2014
Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations Oliveira, A. Sofia F.; Campos, Sara R. R.; Baptista, António M. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1857, Issue 6 https://doi.org/10.1016/j.bbabio.2016.03.024	journal	June 2016
Enhanced sampling techniques in molecular dynamics simulations of biological systems Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1850, Issue 5 https://doi.org/10.1016/j.bbagen.2014.10.019	journal	May 2015
Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations van Eerden, Floris J.; de Jong, Djurre H.; de Vries, Alex H. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1848, Issue 6 https://doi.org/10.1016/j.bbamem.2015.02.025	journal	June 2015
Photosynthetic Vesicle Architecture and Constraints on Efficient Energy Harvesting Şener, Melih; Strümpfer, Johan; Timney, John A. Biophysical Journal, Vol. 99, Issue 1 https://doi.org/10.1016/j.bpj.2010.04.013	journal	July 2010
The Binding Interface of Cytochrome c and Cytochrome c1 in the bc1 Complex: Rationalizing the Role of Key Residues Kokhan, Oleksandr; Wraight, Colin A.; Tajkhorshid, Emad Biophysical Journal, Vol. 99, Issue 8 https://doi.org/10.1016/j.bpj.2010.08.042	journal	October 2010
Coexistence of Fluid and Crystalline Phases of Proteins in Photosynthetic Membranes Schneider, Anna R.; Geissler, Phillip L. Biophysical Journal, Vol. 105, Issue 5 https://doi.org/10.1016/j.bpj.2013.06.052	journal	September 2013
The BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms Fernandez Solano, Carlos J. Biophysical Journal, Vol. 110, Issue 3 https://doi.org/10.1016/j.bpj.2015.11.1765	journal	February 2016
Prediction of Thylakoid Lipid Binding Sites on Photosystem II Van Eerden, Floris J.; Melo, Manuel N.; Frederix, Pim W. J. M. Biophysical Journal, Vol. 113, Issue 12 https://doi.org/10.1016/j.bpj.2017.09.039	journal	December 2017
Lipid Fingerprints and Cofactor Dynamics of Light-Harvesting Complex II in Different Membranes Thallmair, Sebastian; Vainikka, Petteri A.; Marrink, Siewert J. Biophysical Journal, Vol. 116, Issue 8 https://doi.org/10.1016/j.bpj.2019.03.009	journal	April 2019
Modeling the Role of LHCII-LHCII, PSII-LHCII, and PSI-LHCII Interactions in State Transitions Wood, William H. J.; Johnson, Matthew P. Biophysical Journal, Vol. 119, Issue 2 https://doi.org/10.1016/j.bpj.2020.05.034	journal	July 2020
Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism Singharoy, Abhishek; Maffeo, Christopher; Delgado-Magnero, Karelia H. Cell, Vol. 179, Issue 5 https://doi.org/10.1016/j.cell.2019.10.021	journal	November 2019
Structural model and excitonic properties of the dimeric RC–LH1–PufX complex from Rhodobacter sphaeroides Şener, Melih; Hsin, Jen; Trabuco, Leonardo G. Chemical Physics, Vol. 357, Issue 1-3 https://doi.org/10.1016/j.chemphys.2009.01.003	journal	February 2009
Environmental effects on the dynamics in the light-harvesting complexes LH2 and LH3 based on molecular simulations Mallus, Maria Ilaria; Shakya, Yashoj; Prajapati, Jigneshkumar Dahyabhai Chemical Physics, Vol. 515 https://doi.org/10.1016/j.chemphys.2018.08.013	journal	November 2018
The behaviour of β-carotene in the phosphatidylcholine bilayer as revealed by a molecular simulation study Jemioła-Rzemińska, Małgorzata; Pasenkiewicz-Gierula, Marta; Strzałka, Kazimierz Chemistry and Physics of Lipids, Vol. 135, Issue 1 https://doi.org/10.1016/j.chemphyslip.2005.01.006	journal	May 2005
Artificial light-harvesting systems and their applications in photocatalysis and cell labeling Wang, Ying; Han, Ning; Li, Xinglong ChemPhysMater, Vol. 1, Issue 4 https://doi.org/10.1016/j.chphma.2022.05.002	journal	October 2022
Single-molecule biophysics experiments in silico: Toward a physical model of a replisome Maffeo, Christopher; Chou, Han-Yi; Aksimentiev, Aleksei iScience, Vol. 25, Issue 5 https://doi.org/10.1016/j.isci.2022.104264	journal	May 2022
A conserved arginine residue is critical for stabilizing the N2 FeS cluster in mitochondrial complex I Hameedi, Mikhail A.; Grba, Daniel N.; Richardson, Katherine H. Journal of Biological Chemistry, Vol. 296 https://doi.org/10.1016/j.jbc.2021.100474	journal	January 2021
The 8.5Å Projection Structure of the Core RC–LH1–PufX Dimer of Rhodobacter sphaeroides Qian, Pu; Neil Hunter, C.; Bullough, Per A. Journal of Molecular Biology, Vol. 349, Issue 5 https://doi.org/10.1016/j.jmb.2005.04.032	journal	June 2005
CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps Shekhar, Mrinal; Terashi, Genki; Gupta, Chitrak Matter, Vol. 4, Issue 10 https://doi.org/10.1016/j.matt.2021.09.004	journal	October 2021
The power of life—Cytochrome c oxidase takes center stage in metabolic control, cell signalling and survival Arnold, Susanne Mitochondrion, Vol. 12, Issue 1 https://doi.org/10.1016/j.mito.2011.05.003	journal	January 2012
Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing Stone, John E.; Sener, Melih; Vandivort, Kirby L. Parallel Computing, Vol. 55 https://doi.org/10.1016/j.parco.2015.10.015	journal	July 2016
Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales Sener, Melih; Levy, Stuart; Stone, John E. Parallel Computing, Vol. 102 https://doi.org/10.1016/j.parco.2020.102698	journal	May 2021
Molecular dynamics simulations of proteins in lipid bilayers Gumbart, J.; Wang, Y.; Aksimentiev, A. Current Opinion in Structural Biology, Vol. 15, Issue 4 https://doi.org/10.1016/j.sbi.2005.07.007	journal	August 2005
Coarse-grained molecular simulations of large biomolecules Takada, Shoji Current Opinion in Structural Biology, Vol. 22, Issue 2 https://doi.org/10.1016/j.sbi.2012.01.010	journal	April 2012
Constant pH molecular dynamics simulations: Current status and recent applications Martins de Oliveira, Vinicius; Liu, Ruibin; Shen, Jana Current Opinion in Structural Biology, Vol. 77 https://doi.org/10.1016/j.sbi.2022.102498	journal	December 2022
The Warburg Effect: How Does it Benefit Cancer Cells? Liberti, Maria V.; Locasale, Jason W. Trends in Biochemical Sciences, Vol. 41, Issue 3 https://doi.org/10.1016/j.tibs.2015.12.001	journal	March 2016
Brownian Dynamics Simulations of Biological Molecules Huber, Gary A.; McCammon, J. Andrew Trends in Chemistry, Vol. 1, Issue 8 https://doi.org/10.1016/j.trechm.2019.07.008	journal	November 2019
Ab Initio Molecular Dynamics Marx, Dominik; Hutter, Jurg https://doi.org/10.1017/CBO9780511609633	book	January 2009
Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications Christensen, Anders S.; Kubař, Tomáš; Cui, Qiang Chemical Reviews, Vol. 116, Issue 9 https://doi.org/10.1021/acs.chemrev.5b00584	journal	April 2016
Multireference Approaches for Excited States of Molecules Lischka, Hans; Nachtigallová, Dana; Aquino, Adélia J. A. Chemical Reviews, Vol. 118, Issue 15 https://doi.org/10.1021/acs.chemrev.8b00244	journal	April 2018
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules Jones, Derek; Allen, Jonathan E.; Yang, Yue Journal of Chemical Theory and Computation, Vol. 18, Issue 7 https://doi.org/10.1021/acs.jctc.1c01214	journal	June 2022
Best Practices in Constant pH MD Simulations: Accuracy and Sampling Buslaev, Pavel; Aho, Noora; Jansen, Anton Journal of Chemical Theory and Computation, Vol. 18, Issue 10 https://doi.org/10.1021/acs.jctc.2c00517	journal	September 2022
Fast Calculation of Protein–Protein Binding Free Energies Using Umbrella Sampling with a Coarse-Grained Model Patel, Jagdish Suresh; Ytreberg, F. Marty Journal of Chemical Theory and Computation, Vol. 14, Issue 2 https://doi.org/10.1021/acs.jctc.7b00660	journal	January 2018
Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding Cabeza de Vaca, Israel; Qian, Yue; Vilseck, Jonah Z. Journal of Chemical Theory and Computation, Vol. 14, Issue 6 https://doi.org/10.1021/acs.jctc.8b00031	journal	April 2018
Brownian Dynamics Approach Including Explicit Atoms for Studying Ion Permeation and Substrate Translocation across Nanopores Solano, Carlos J. F.; Prajapati, Jigneshkumar D.; Pothula, Karunakar R. Journal of Chemical Theory and Computation, Vol. 14, Issue 12 https://doi.org/10.1021/acs.jctc.8b00917	journal	November 2018
Characterizing Protein Protonation Microstates Using Monte Carlo Sampling Khaniya, Umesh; Mao, Junjun; Wei, Rongmei Judy The Journal of Physical Chemistry B, Vol. 126, Issue 13 https://doi.org/10.1021/acs.jpcb.2c00139	journal	March 2022
Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex de Jong, Djurre H.; Liguori, Nicoletta; van den Berg, Tom The Journal of Physical Chemistry B, Vol. 119, Issue 25 https://doi.org/10.1021/acs.jpcb.5b00809	journal	June 2015
Molecular Motors: Power Strokes Outperform Brownian Ratchets Wagoner, Jason A.; Dill, Ken A. The Journal of Physical Chemistry B, Vol. 120, Issue 26 https://doi.org/10.1021/acs.jpcb.6b02776	journal	May 2016
Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane van Eerden, Floris J.; van den Berg, Tom; Frederix, Pim W. J. M. The Journal of Physical Chemistry B, Vol. 121, Issue 15 https://doi.org/10.1021/acs.jpcb.6b06865	journal	September 2016
Mechanism of the Primary Charge Transfer Reaction in the Cytochrome bc ₁ Complex Barragan, Angela M.; Schulten, Klaus; Solov’yov, Ilia A. The Journal of Physical Chemistry B, Vol. 120, Issue 44 https://doi.org/10.1021/acs.jpcb.6b07394	journal	October 2016
Methodology for the Simulation of Molecular Motors at Different Scales Singharoy, Abhishek; Chipot, Christophe The Journal of Physical Chemistry B, Vol. 121, Issue 15 https://doi.org/10.1021/acs.jpcb.6b09350	journal	November 2016
Determination of Cell Doubling Times from the Return-on-Investment Time of Photosynthetic Vesicles Based on Atomic Detail Structural Models Hitchcock, Andrew; Hunter, C. Neil; Sener, Melih The Journal of Physical Chemistry B, Vol. 121, Issue 15 https://doi.org/10.1021/acs.jpcb.6b12335	journal	January 2017
Molecular Anatomy of Plant Photoprotective Switches: The Sensitivity of PsbS to the Environment, Residue by Residue Liguori, Nicoletta; Campos, Sara R. R.; Baptista, António M. The Journal of Physical Chemistry Letters, Vol. 10, Issue 8 https://doi.org/10.1021/acs.jpclett.9b00437	journal	March 2019
Magnetic Propulsion of Microswimmers with DNA-Based Flagellar Bundles Maier, Alexander M.; Weig, Cornelius; Oswald, Peter Nano Letters, Vol. 16, Issue 2 https://doi.org/10.1021/acs.nanolett.5b03716	journal	January 2016
Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations Shekhar, Mrinal; Gupta, Chitrak; Suzuki, Kano ACS Central Science, Vol. 8, Issue 7 https://doi.org/10.1021/acscentsci.1c01599	journal	June 2022
Mutation of histidine residues in CP47 leads to destabilization of the photosystem II complex and to impairment of light energy transfer Shen, Gaozhong; Eaton-Rye, Julian J.; Vermaas, Wim F. J. Biochemistry, Vol. 32, Issue 19 https://doi.org/10.1021/bi00070a019	journal	May 1993
Modeling Binding Kinetics at the Q _A Site in Bacterial Reaction Centers ^† Madeo, Jennifer; Gunner, M. R. Biochemistry, Vol. 44, Issue 33 https://doi.org/10.1021/bi050544j	journal	August 2005
ENDOR Spectroscopy Reveals Light Induced Movement of the H-Bond from Ser-L223 upon Forming the Semiquinone (Q _B ^- ^• ) in Reaction Centers from Rhodobacter sphaeroide s Paddock, M. L.; Flores, M.; Isaacson, R. Biochemistry, Vol. 46, Issue 28 https://doi.org/10.1021/bi7005256	journal	June 2007
Low-Light-Induced Formation of Semicrystalline Photosystem II Arrays in Higher Plant Chloroplasts ^† Kirchhoff, Helmut; Haase, Winfried; Wegner, Sandra Biochemistry, Vol. 46, Issue 39 https://doi.org/10.1021/bi700748y	journal	October 2007
Single-Reference ab Initio Methods for the Calculation of Excited States of Large Molecules Dreuw, Andreas; Head-Gordon, Martin Chemical Reviews, Vol. 105, Issue 11 https://doi.org/10.1021/cr0505627	journal	November 2005
Quantum Monte Carlo and Related Approaches Austin, Brian M.; Zubarev, Dmitry Yu.; Lester, William A. Chemical Reviews, Vol. 112, Issue 1 https://doi.org/10.1021/cr2001564	journal	December 2011
Classical Electrostatics for Biomolecular Simulations Cisneros, G. Andrés; Karttunen, Mikko; Ren, Pengyu Chemical Reviews, Vol. 114, Issue 1 https://doi.org/10.1021/cr300461d	journal	August 2013
Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States Brunk, Elizabeth; Rothlisberger, Ursula Chemical Reviews, Vol. 115, Issue 12 https://doi.org/10.1021/cr500628b	journal	April 2015
Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y Ozer, Gungor; Valeev, Edward F.; Quirk, Stephen Journal of Chemical Theory and Computation, Vol. 6, Issue 10 https://doi.org/10.1021/ct100320g	journal	September 2010
Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering Cole, Daniel J.; Tirado-Rives, Julian; Jorgensen, William L. Journal of Chemical Theory and Computation, Vol. 10, Issue 2 https://doi.org/10.1021/ct400989x	journal	January 2014
Use of Broken-Symmetry Density Functional Theory To Characterize the IspH Oxidized State: Implications for IspH Mechanism and Inhibition Blachly, Patrick G.; Sandala, Gregory M.; Giammona, Debra Ann Journal of Chemical Theory and Computation, Vol. 10, Issue 9 https://doi.org/10.1021/ct5005214	journal	August 2014
Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model Meng, Yilin; Roitberg, Adrian E. Journal of Chemical Theory and Computation, Vol. 6, Issue 4 https://doi.org/10.1021/ct900676b	journal	March 2010
Electrostatic effects in the Brownian dynamics of association and orientation of heme proteins Northrup, Scott H.; Boles, Jeffrey O.; Reynolds, John C. L. The Journal of Physical Chemistry, Vol. 91, Issue 23 https://doi.org/10.1021/j100307a036	journal	November 1987
Catalytic Nanomotors: Autonomous Movement of Striped Nanorods Paxton, Walter F.; Kistler, Kevin C.; Olmeda, Christine C. Journal of the American Chemical Society, Vol. 126, Issue 41 https://doi.org/10.1021/ja047697z	journal	October 2004
Slow Dissociation of a Charged Ligand: Analysis of the Primary Quinone Q_ASite of Photosynthetic Bacterial Reaction Centers Madeo, Jennifer; Mihajlovic, Maja; Lazaridis, Themis Journal of the American Chemical Society, Vol. 133, Issue 43 https://doi.org/10.1021/ja205811f	journal	October 2011
Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc ₁ Arnarez, Clement; Mazat, Jean-Pierre; Elezgaray, Juan Journal of the American Chemical Society, Vol. 135, Issue 8 https://doi.org/10.1021/ja310577u	journal	February 2013
All-Atom Molecular Dynamics Simulation of Photosystem II Embedded in Thylakoid Membrane Ogata, Koji; Yuki, Taichi; Hatakeyama, Makoto Journal of the American Chemical Society, Vol. 135, Issue 42 https://doi.org/10.1021/ja404317d	journal	October 2013
Rotation Triggers Nucleotide-Independent Conformational Transition of the Empty β Subunit of F ₁ -ATPase Czub, Jacek; Grubmüller, Helmut Journal of the American Chemical Society, Vol. 136, Issue 19 https://doi.org/10.1021/ja500120m	journal	May 2014
Theoretical Description of the Primary Proton-Coupled Electron Transfer Reaction in the Cytochrome bc₁ Complex Barragan, Angela M.; Soudackov, Alexander V.; Luthey-Schulten, Zaida Journal of the American Chemical Society, Vol. 143, Issue 2 https://doi.org/10.1021/jacs.0c07799	journal	January 2021
How the pH Controls Photoprotection in the Light-Harvesting Complex of Mosses Pedraza-González, Laura; Cignoni, Edoardo; D’Ascenzi, Jacopo Journal of the American Chemical Society, Vol. 145, Issue 13 https://doi.org/10.1021/jacs.3c00377	journal	March 2023
Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c ₂ Singharoy, Abhishek; Barragan, Angela M.; Thangapandian, Sundarapandian Journal of the American Chemical Society, Vol. 138, Issue 37 https://doi.org/10.1021/jacs.6b01193	journal	September 2016
Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases Singharoy, Abhishek; Chipot, Christophe; Moradi, Mahmoud Journal of the American Chemical Society, Vol. 139, Issue 1 https://doi.org/10.1021/jacs.6b10744	journal	December 2016
Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I Gupta, Chitrak; Khaniya, Umesh; Chan, Chun Kit Journal of the American Chemical Society, Vol. 142, Issue 20 https://doi.org/10.1021/jacs.9b13450	journal	April 2020
A Multiscale Coarse-Graining Method for Biomolecular Systems Izvekov, Sergei; Voth, Gregory A. The Journal of Physical Chemistry B, Vol. 109, Issue 7 https://doi.org/10.1021/jp044629q	journal	February 2005
Cytochrome c ₂ Exit Strategy: Dissociation Studies and Evolutionary Implications Pogorelov, Taras V.; Autenrieth, Felix; Roberts, Elijah The Journal of Physical Chemistry B, Vol. 111, Issue 3 https://doi.org/10.1021/jp064973i	journal	January 2007
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge The Journal of Physical Chemistry B, Vol. 111, Issue 27 https://doi.org/10.1021/jp071097f	journal	July 2007
Effects of Mutational (Lys to Ala) Surface Charge Changes on the Redox Properties of Electrode-Immobilized Cytochrome c Battistuzzi, Gianantonio; Borsari, Marco; Bortolotti, Carlo Augusto The Journal of Physical Chemistry B, Vol. 111, Issue 34 https://doi.org/10.1021/jp0730343	journal	August 2007
Simulations of the Two-Dimensional Electronic Spectroscopy of the Photosystem II Reaction Center Lewis, K. L. M.; Fuller, F. D.; Myers, J. A. The Journal of Physical Chemistry A, Vol. 117, Issue 1 https://doi.org/10.1021/jp3081707	journal	December 2012
Molecular Organization of Cytochrome c ₂ near the Binding Domain of Cytochrome bc ₁ Studied by Electron Spin–Lattice Relaxation Enhancement Pietras, Rafał; Sarewicz, Marcin; Osyczka, Artur The Journal of Physical Chemistry B, Vol. 118, Issue 24 https://doi.org/10.1021/jp503339g	journal	June 2014
All-Atom Molecular Dynamics Simulation of a Photosystem I/Detergent Complex Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul The Journal of Physical Chemistry B, Vol. 118, Issue 40 https://doi.org/10.1021/jp507157e	journal	September 2014
Identification of Ubiquinol Binding Motifs at the Q _o -Site of the Cytochrome bc ₁ Complex Barragan, Angela M.; Crofts, Antony R.; Schulten, Klaus The Journal of Physical Chemistry B, Vol. 119, Issue 2 https://doi.org/10.1021/jp510022w	journal	November 2014
Red Shift of the Zero Crossing in the CD Spectra of the LH2 Antenna Complex of Rhodopseudomonas acidophila : A Structure-Based Study Koolhaas, M. H. C.; van der Zwan, G.; Frese, R. N. The Journal of Physical Chemistry B, Vol. 101, Issue 37 https://doi.org/10.1021/jp963368k	journal	September 1997
Coupling of Phosphorylation to Electron and Hydrogen Transfer by a Chemi-Osmotic type of Mechanism Mitchell, Peter Nature, Vol. 191, Issue 4784 https://doi.org/10.1038/191144a0	journal	July 1961
Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria McDermott, G.; Prince, S. M.; Freer, A. A. Nature, Vol. 374, Issue 6522 https://doi.org/10.1038/374517a0	journal	April 1995
Structural changes linked to proton translocation by subunit c of the ATP synthase Rastogi, Vinit K.; Girvin, Mark E. Nature, Vol. 402, Issue 6759 https://doi.org/10.1038/46224	journal	November 1999
Arrangement of electron transport chain components in bovine mitochondrial supercomplex I ₁ III ₂ IV ₁ : Cryo-EM of respiratory chain supercomplex Althoff, Thorsten; Mills, Deryck J.; Popot, Jean-Luc The EMBO Journal, Vol. 30, Issue 22 https://doi.org/10.1038/emboj.2011.324	journal	September 2011
Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution Liu, Zhenfeng; Yan, Hanchi; Wang, Kebin Nature, Vol. 428, Issue 6980 https://doi.org/10.1038/nature02373	journal	March 2004
The native architecture of a photosynthetic membrane Bahatyrova, Svetlana; Frese, Raoul N.; Siebert, C. Alistair Nature, Vol. 430, Issue 7003 https://doi.org/10.1038/nature02823	journal	August 2004
Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å Umena, Yasufumi; Kawakami, Keisuke; Shen, Jian-Ren Nature, Vol. 473, Issue 7345 https://doi.org/10.1038/nature09913	journal	April 2011
Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures Arai, Satoshi; Saijo, Shinya; Suzuki, Kano Nature, Vol. 493, Issue 7434 https://doi.org/10.1038/nature11778	journal	January 2013
Lessons from nature about solar light harvesting Scholes, Gregory D.; Fleming, Graham R.; Olaya-Castro, Alexandra Nature Chemistry, Vol. 3, Issue 10 https://doi.org/10.1038/nchem.1145	journal	September 2011
Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex Van Eerden, Floris J.; Melo, Manuel N.; Frederix, Pim W. J. M. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15214	journal	May 2017
Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre Zhang, Lu; Silva, Daniel-Adriano; Zhang, Houdao Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5170	journal	June 2014
Stochastic modelling for quantitative description of heterogeneous biological systems Wilkinson, Darren J. Nature Reviews Genetics, Vol. 10, Issue 2 https://doi.org/10.1038/nrg2509	journal	February 2009
Molecular dynamics simulations of biomolecules Karplus, Martin; McCammon, J. Andrew Nature Structural Biology, Vol. 9, Issue 9 https://doi.org/10.1038/nsb0902-646	journal	September 2002
Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase Böckmann, Rainer A.; Grubmüller, Helmut Nature Structural Biology https://doi.org/10.1038/nsb760	journal	February 2002
Membrane organization of photosystem I complexes in the most abundant phototroph on Earth MacGregor-Chatwin, C.; Jackson, P. J.; Sener, M. Nature Plants, Vol. 5, Issue 8 https://doi.org/10.1038/s41477-019-0475-z	journal	July 2019
Cryo-EM structure of the Blastochloris viridis LH1–RC complex at 2.9 Å Qian, Pu; Siebert, C. Alistair; Wang, Peiyi Nature, Vol. 556, Issue 7700 https://doi.org/10.1038/s41586-018-0014-5	journal	April 2018
Martini 3: a general purpose force field for coarse-grained molecular dynamics Souza, Paulo C. T.; Alessandri, Riccardo; Barnoud, Jonathan Nature Methods, Vol. 18, Issue 4 https://doi.org/10.1038/s41592-021-01098-3	journal	March 2021
The structure of the stress-induced photosystem I–IsiA antenna supercomplex Toporik, Hila; Li, Jin; Williams, Dewight Nature Structural & Molecular Biology, Vol. 26, Issue 6 https://doi.org/10.1038/s41594-019-0228-8	journal	May 2019
A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand binding potencies Wang, Jing; Ishchenko, Alexey; Zhang, Wei Scientific Reports, Vol. 12, Issue 1 https://doi.org/10.1038/s41598-022-05875-8	journal	February 2022
Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels Arnarez, C.; Marrink, S. J.; Periole, X. Scientific Reports, Vol. 3, Issue 1 https://doi.org/10.1038/srep01263	journal	February 2013
From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII) Liguori, Nicoletta; Periole, Xavier; Marrink, Siewert J. Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep15661	journal	October 2015
Dark States in the Light-Harvesting complex 2 Revealed by Two-dimensional Electronic Spectroscopy Ferretti, Marco; Hendrikx, Ruud; Romero, Elisabet Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep20834	journal	February 2016
Polarizability of the active site of cytochrome c reduces the activation barrier for electron transfer Dinpajooh, Mohammadhasan; Martin, Daniel R.; Matyushov, Dmitry V. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep28152	journal	June 2016
Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes Linnanto, Juha; Korppi-Tommola, Jouko Phys. Chem. Chem. Phys., Vol. 8, Issue 6 https://doi.org/10.1039/B513086G	journal	January 2006
Spin decontamination of broken-symmetry density functional theory calculations: deeper insight and new formulations Ferré, Nicolas; Guihéry, Nathalie; Malrieu, Jean-Paul Physical Chemistry Chemical Physics, Vol. 17, Issue 22 https://doi.org/10.1039/C4CP05531D	journal	January 2015
Derivation of coarse-grained simulation models of chlorophyll molecules in lipid bilayers for applications in light harvesting systems Debnath, Ananya; Wiegand, Sabine; Paulsen, Harald Physical Chemistry Chemical Physics, Vol. 17, Issue 34 https://doi.org/10.1039/C5CP01140J	journal	January 2015
Photosynthetic diode: electron transport rectification by wetting the quinone cofactor Martin, Daniel R.; Matyushov, Dmitry V. Physical Chemistry Chemical Physics, Vol. 17, Issue 35 https://doi.org/10.1039/C5CP03397G	journal	January 2015
A highly stable and scalable photosynthetic reaction center–graphene hybrid electrode system for biomimetic solar energy transduction Zhang, Haojie; Carey, Anne-Marie; Jeon, Ki-Wan Journal of Materials Chemistry A, Vol. 5, Issue 13 https://doi.org/10.1039/C6TA10458D	journal	January 2017
Multiscale QM/MM molecular dynamics simulations of the trimeric major light-harvesting complex II Maity, Sayan; Daskalakis, Vangelis; Elstner, Marcus Physical Chemistry Chemical Physics, Vol. 23, Issue 12 https://doi.org/10.1039/D1CP01011E	journal	January 2021
The origin of unidirectional charge separation in photosynthetic reaction centers: nonadiabatic quantum dynamics of exciton and charge in pigment–protein complexes Tamura, Hiroyuki; Saito, Keisuke; Ishikita, Hiroshi Chemical Science, Vol. 12, Issue 23 https://doi.org/10.1039/D1SC01497H	journal	January 2021
Trapping of protein cargo molecules inside DNA origami nanocages Scherf, Merle; Scheffler, Florian; Maffeo, Christopher Nanoscale, Vol. 14, Issue 48 https://doi.org/10.1039/D2NR05356J	journal	January 2022
Million-atom molecular dynamics simulations reveal the interfacial interactions and assembly of plant PSII-LHCII supercomplex Mao, Ruichao; Zhang, Han; Bie, Lihua RSC Advances, Vol. 13, Issue 10 https://doi.org/10.1039/D2RA08240C	journal	January 2023
Parallel tempering: Theory, applications, and new perspectives Earl, David J.; Deem, Michael W. Physical Chemistry Chemical Physics, Vol. 7, Issue 23 https://doi.org/10.1039/b509983h	journal	January 2005
Local and density fitting approximations within the short-range/long-range hybrid scheme: application to large non-bonded complexes Goll, Erich; Leininger, Thierry; Manby, Frederick R. Physical Chemistry Chemical Physics, Vol. 10, Issue 23 https://doi.org/10.1039/b804672g	journal	January 2008
Exploring cryo-electron microscopy with molecular dynamics Vant, John W.; Sarkar, Daipayan; Nguyen, Jonathan Biochemical Society Transactions, Vol. 50, Issue 1 https://doi.org/10.1042/BST20210485	journal	February 2022
Meta-generalized gradient approximation: Explanation of a realistic nonempirical density functional Perdew, John P.; Tao, Jianmin; Staroverov, Viktor N. The Journal of Chemical Physics, Vol. 120, Issue 15 https://doi.org/10.1063/1.1665298	journal	April 2004
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes Janosi, Lorant; Kosztin, Ioan; Damjanović, Ana The Journal of Chemical Physics, Vol. 125, Issue 1 https://doi.org/10.1063/1.2210481	journal	July 2006
A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu Grimme, Stefan; Antony, Jens; Ehrlich, Stephan The Journal of Chemical Physics, Vol. 132, Issue 15 https://doi.org/10.1063/1.3382344	journal	April 2010
An efficient internally contracted multiconfiguration–reference configuration interaction method Werner, Hans‐Joachim; Knowles, Peter J. The Journal of Chemical Physics, Vol. 89, Issue 9 https://doi.org/10.1063/1.455556	journal	November 1988
A combination of Kohn–Sham density functional theory and multi-reference configuration interaction methods Grimme, Stefan; Waletzke, Mirko The Journal of Chemical Physics, Vol. 111, Issue 13 https://doi.org/10.1063/1.479866	journal	October 1999
Perspective: Coarse-grained models for biomolecular systems Noid, W. G. The Journal of Chemical Physics, Vol. 139, Issue 9 https://doi.org/10.1063/1.4818908	journal	September 2013
Long-range correlation energy calculated from coupled atomic response functions Ambrosetti, Alberto; Reilly, Anthony M.; DiStasio, Robert A. The Journal of Chemical Physics, Vol. 140, Issue 18 https://doi.org/10.1063/1.4865104	journal	May 2014
Redesign of the DFT/MRCI Hamiltonian Lyskov, Igor; Kleinschmidt, Martin; Marian, Christel M. The Journal of Chemical Physics, Vol. 144, Issue 3 https://doi.org/10.1063/1.4940036	journal	January 2016
Redox potential replica exchange molecular dynamics at constant pH in AMBER: Implementation and validation Cruzeiro, Vinícius Wilian D.; Amaral, Marcos S.; Roitberg, Adrian E. The Journal of Chemical Physics, Vol. 149, Issue 7 https://doi.org/10.1063/1.5027379	journal	August 2018
The atomistic modeling of light-harvesting complexes from the physical models to the computational protocol Cignoni, Edoardo; Slama, Vladislav; Cupellini, Lorenzo The Journal of Chemical Physics, Vol. 156, Issue 12 https://doi.org/10.1063/5.0086275	journal	March 2022
Replica exchange with solute tempering: A method for sampling biological systems in explicit water Liu, P.; Kim, B.; Friesner, R. A. Proceedings of the National Academy of Sciences, Vol. 102, Issue 39 https://doi.org/10.1073/pnas.0506346102	journal	September 2005
Crystal structure of the yeast cytochrome bc1 complex with its bound substrate cytochrome c Lange, C.; Hunte, C. Proceedings of the National Academy of Sciences, Vol. 99, Issue 5 https://doi.org/10.1073/pnas.052704699	journal	March 2002
Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle Sener, M. K.; Olsen, J. D.; Hunter, C. N. Proceedings of the National Academy of Sciences, Vol. 104, Issue 40 https://doi.org/10.1073/pnas.0706861104	journal	September 2007
Torsional elasticity and energetics of F1-ATPase Czub, J.; Grubmuller, H. Proceedings of the National Academy of Sciences, Vol. 108, Issue 18 https://doi.org/10.1073/pnas.1018686108	journal	April 2011
Proton transfer via a transient linear water-molecule chain in a membrane protein Freier, E.; Wolf, S.; Gerwert, K. Proceedings of the National Academy of Sciences, Vol. 108, Issue 28 https://doi.org/10.1073/pnas.1104735108	journal	June 2011
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis Nogales, J.; Gudmundsson, S.; Knight, E. M. Proceedings of the National Academy of Sciences, Vol. 109, Issue 7 https://doi.org/10.1073/pnas.1117907109	journal	January 2012
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I Kaila, V. R. I.; Wikstrom, M.; Hummer, G. Proceedings of the National Academy of Sciences, Vol. 111, Issue 19 https://doi.org/10.1073/pnas.1319156111	journal	April 2014
Redox-induced activation of the proton pump in the respiratory complex I Sharma, Vivek; Belevich, Galina; Gamiz-Hernandez, Ana P. Proceedings of the National Academy of Sciences, Vol. 112, Issue 37 https://doi.org/10.1073/pnas.1503761112	journal	September 2015
Multiscale model of light harvesting by photosystem II in plants Amarnath, Kapil; Bennett, Doran I. G.; Schneider, Anna R. Proceedings of the National Academy of Sciences, Vol. 113, Issue 5 https://doi.org/10.1073/pnas.1524999113	journal	January 2016
Biophysical comparison of ATP synthesis mechanisms shows a kinetic advantage for the rotary process Anandakrishnan, Ramu; Zhang, Zining; Donovan-Maiye, Rory Proceedings of the National Academy of Sciences, Vol. 113, Issue 40 https://doi.org/10.1073/pnas.1608533113	journal	September 2016
Redox-coupled quinone dynamics in the respiratory complex I Warnau, Judith; Sharma, Vivek; Gamiz-Hernandez, Ana P. Proceedings of the National Academy of Sciences, Vol. 115, Issue 36 https://doi.org/10.1073/pnas.1805468115	journal	August 2018
Escaping free-energy minima Laio, A.; Parrinello, M. Proceedings of the National Academy of Sciences, Vol. 99, Issue 20 https://doi.org/10.1073/pnas.202427399	journal	September 2002
Molecular mechanism and energetics of coupling between substrate binding and product release in the F ₁ -ATPase catalytic cycle Badocha, Michał; Wieczór, Miłosz; Marciniak, Antoni Proceedings of the National Academy of Sciences, Vol. 120, Issue 8 https://doi.org/10.1073/pnas.2215650120	journal	February 2023
Stark effect spectroscopy of Rhodobacter sphaeroides and Rhodopseudomonas viridis reaction centers Lockhart, D. J.; Boxer, S. G. Proceedings of the National Academy of Sciences, Vol. 85, Issue 1 https://doi.org/10.1073/pnas.85.1.107	journal	January 1988
Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets Goss, P. J. E.; Peccoud, J. Proceedings of the National Academy of Sciences, Vol. 95, Issue 12 https://doi.org/10.1073/pnas.95.12.6750	journal	June 1998
Rigid Core and Flexible Terminus: STRUCTURE OF SOLUBILIZED LIGHT-HARVESTING CHLOROPHYLL a/b COMPLEX (LHCII) MEASURED BY EPR Dockter, Christoph; Müller, André H.; Dietz, Carsten Journal of Biological Chemistry, Vol. 287, Issue 4 https://doi.org/10.1074/jbc.M111.307728	journal	December 2011
Single-molecule Analysis of F0F1-ATP Synthase Inhibited by N,N-Dicyclohexylcarbodiimide Toei, Masashi; Noji, Hiroyuki Journal of Biological Chemistry, Vol. 288, Issue 36 https://doi.org/10.1074/jbc.M113.482455	journal	September 2013
Structure of Complex III with Bound Cytochrome c in Reduced State and Definition of a Minimal Core Interface for Electron Transfer Solmaz, Sozanne R. N.; Hunte, Carola Journal of Biological Chemistry, Vol. 283, Issue 25 https://doi.org/10.1074/jbc.M710126200	journal	April 2008
Demonstration of Short-lived Complexes of Cytochrome c with Cytochrome bc1 by EPR Spectroscopy Sarewicz, Marcin; Borek, Arkadiusz; Daldal, Fevzi Journal of Biological Chemistry, Vol. 283, Issue 36 https://doi.org/10.1074/jbc.M802174200	journal	September 2008
The Organization of LH2 Complexes in Membranes from Rhodobacter sphaeroides Olsen, John D.; Tucker, Jaimey D.; Timney, John A. Journal of Biological Chemistry, Vol. 283, Issue 45 https://doi.org/10.1074/jbc.M804824200	journal	August 2008
Single-molecule analysis reveals rotational substeps and chemo-mechanical coupling scheme of Enterococcus hirae V1-ATPase Iida, Tatsuya; Minagawa, Yoshihiro; Ueno, Hiroshi Journal of Biological Chemistry, Vol. 294, Issue 45 https://doi.org/10.1074/jbc.RA119.008947	journal	November 2019
Identification of plant-based hexokinase 2 inhibitors: combined molecular docking and dynamics simulation studies Khan, Asifa; Mohammad, Taj; Shamsi, Anas Journal of Biomolecular Structure and Dynamics, Vol. 40, Issue 20 https://doi.org/10.1080/07391102.2021.1942217	journal	June 2021
Recent development and application of constant pH molecular dynamics Chen, Wei; Morrow, Brian H.; Shi, Chuanyin Molecular Simulation, Vol. 40, Issue 10-11 https://doi.org/10.1080/08927022.2014.907492	journal	May 2014
QM/MM free energy simulations: recent progress and challenges Lu, Xiya; Fang, Dong; Ito, Shingo Molecular Simulation, Vol. 42, Issue 13 https://doi.org/10.1080/08927022.2015.1132317	journal	July 2016
Physics of microswimmers—single particle motion and collective behavior: a review Elgeti, J.; Winkler, R. G.; Gompper, G. Reports on Progress in Physics, Vol. 78, Issue 5 https://doi.org/10.1088/0034-4885/78/5/056601	journal	April 2015
Specific roles of protein-phospholipid interactions in the yeast cytochrome bc1 complex structure Lange, C. The EMBO Journal, Vol. 20, Issue 23 https://doi.org/10.1093/emboj/20.23.6591	journal	December 2001
Projection structure of the photosynthetic reaction centre-antenna complex of Rhodospirillum rubrum at 8.5 A resolution Jamieson, S. J. The EMBO Journal, Vol. 21, Issue 15 https://doi.org/10.1093/emboj/cdf410	journal	August 2002
General random matrix approach to account for the effect of static disorder on the spectral properties of light harvesting systems Şener, Melih K.; Schulten, Klaus Physical Review E, Vol. 65, Issue 3 https://doi.org/10.1103/PhysRevE.65.031916	journal	March 2002
Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study Damjanović, Ana; Kosztin, Ioan; Kleinekathöfer, Ulrich Physical Review E, Vol. 65, Issue 3 https://doi.org/10.1103/PhysRevE.65.031919	journal	March 2002
Flow pattern in the vicinity of self-propelling hot Janus particles Bickel, Thomas; Majee, Arghya; Würger, Alois Physical Review E, Vol. 88, Issue 1 https://doi.org/10.1103/PhysRevE.88.012301	journal	July 2013
Dynamical Clustering and Phase Separation in Suspensions of Self-Propelled Colloidal Particles Buttinoni, Ivo; Bialké, Julian; Kümmel, Felix Physical Review Letters, Vol. 110, Issue 23 https://doi.org/10.1103/PhysRevLett.110.238301	journal	June 2013
Density-Functional Theory for Time-Dependent Systems Runge, Erich; Gross, E. K. U. Physical Review Letters, Vol. 52, Issue 12 https://doi.org/10.1103/PhysRevLett.52.997	journal	March 1984
Unified Approach for Molecular Dynamics and Density-Functional Theory Car, R.; Parrinello, M. Physical Review Letters, Vol. 55, Issue 22 https://doi.org/10.1103/PhysRevLett.55.2471	journal	November 1985
Self-Motile Colloidal Particles: From Directed Propulsion to Random Walk Howse, Jonathan R.; Jones, Richard A. L.; Ryan, Anthony J. Physical Review Letters, Vol. 99, Issue 4 https://doi.org/10.1103/PhysRevLett.99.048102	journal	July 2007
Active Particles in Complex and Crowded Environments Bechinger, Clemens; Di Leonardo, Roberto; Löwen, Hartmut Reviews of Modern Physics, Vol. 88, Issue 4 https://doi.org/10.1103/RevModPhys.88.045006	journal	November 2016
Lateral Segregation of Photosystem I in Cyanobacterial Thylakoids MacGregor-Chatwin, Craig; Sener, Melih; Barnett, Samuel F. H. The Plant Cell, Vol. 29, Issue 5 https://doi.org/10.1105/tpc.17.00071	journal	March 2017
The End of Moore's Law: A New Beginning for Information Technology Theis, Thomas N.; Wong, H. -S. Philip Computing in Science & Engineering, Vol. 19, Issue 2 https://doi.org/10.1109/MCSE.2017.29	journal	March 2017
Anton 2: Raising the Bar for Performance and Programmability in a Special-Purpose Molecular Dynamics Supercomputer Shaw, David E.; Grossman, J. P.; Bank, Joseph A. SC14: International Conference for High Performance Computing, Networking, Storage and Analysis https://doi.org/10.1109/SC.2014.9	conference	November 2014
Lessons learned about steered molecular dynamics simulations and free energy calculations Boubeta, Fernando Martín; Contestín García, Rocío María; Lorenzo, Ezequiel Norberto Chemical Biology & Drug Design, Vol. 93, Issue 6 https://doi.org/10.1111/cbdd.13485	journal	February 2019
Quantitative proteomic analysis of intracytoplasmic membrane development in Rhodobacter sphaeroides: Proteomics of membrane assembly in Rba. sphaeroides Jackson, Philip J.; Lewis, Hilary J.; Tucker, Jaimey D. Molecular Microbiology, Vol. 84, Issue 6 https://doi.org/10.1111/j.1365-2958.2012.08074.x	journal	May 2012
Connectivity of centermost chromatophores in Rhodobacter sphaeroides bacteria Noble, Jade M.; Lubieniecki, Johann; Savitzky, Benjamin H. Molecular Microbiology, Vol. 109, Issue 6 https://doi.org/10.1111/mmi.14077	journal	September 2018
Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V _o complex Roh, Soung-Hun; Shekhar, Mrinal; Pintilie, Grigore Science Advances, Vol. 6, Issue 41 https://doi.org/10.1126/sciadv.abb9605	journal	October 2020
Structure of a symmetric photosynthetic reaction center–photosystem Gisriel, Christopher; Sarrou, Iosifina; Ferlez, Bryan Science, Vol. 357, Issue 6355 https://doi.org/10.1126/science.aan5611	journal	July 2017
Physics makes rules, evolution rolls the dice Camargo, Chico Science, Vol. 361, Issue 6399 https://doi.org/10.1126/science.aat7776	journal	July 2018
ATP Synthase Junge, Wolfgang; Nelson, Nathan Annual Review of Biochemistry, Vol. 84, Issue 1 https://doi.org/10.1146/annurev-biochem-060614-034124	journal	June 2015
Biomolecular Simulation: A Computational Microscope for Molecular Biology Dror, Ron O.; Dirks, Robert M.; Grossman, J. P. Annual Review of Biophysics, Vol. 41, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155245	journal	June 2012
Equilibrium Sampling in Biomolecular Simulations Zuckerman, Daniel M. Annual Review of Biophysics, Vol. 40, Issue 1 https://doi.org/10.1146/annurev-biophys-042910-155255	journal	June 2011
Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications Jing, Zhifeng; Liu, Chengwen; Cheng, Sara Y. Annual Review of Biophysics, Vol. 48, Issue 1 https://doi.org/10.1146/annurev-biophys-070317-033349	journal	May 2019
Coarse-Graining Methods for Computational Biology Saunders, Marissa G.; Voth, Gregory A. Annual Review of Biophysics, Vol. 42, Issue 1 https://doi.org/10.1146/annurev-biophys-083012-130348	journal	May 2013
The Cytochrome bc ₁ Complex: Function in the Context of Structure Crofts, Antony R. Annual Review of Physiology, Vol. 66, Issue 1 https://doi.org/10.1146/annurev.physiol.66.032102.150251	journal	March 2004
Structural and Functional Proteomics of Intracytoplasmic Membrane Assembly in *Rhodobacter sphaeroides* Woronowicz, Kamil; Harrold, John W.; Kay, Joseph M. Journal of Molecular Microbiology and Biotechnology, Vol. 23, Issue 1-2 https://doi.org/10.1159/000346520	journal	January 2013
Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours Jumper, John M.; Faruk, Nabil F.; Freed, Karl F. PLOS Computational Biology, Vol. 14, Issue 12 https://doi.org/10.1371/journal.pcbi.1006578	journal	December 2018
Cisplatin Induces a Mitochondrial-ROS Response That Contributes to Cytotoxicity Depending on Mitochondrial Redox Status and Bioenergetic Functions Marullo, Rossella; Werner, Erica; Degtyareva, Natalya PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0081162	journal	November 2013
The Influence of Protein-Protein Interactions on the Organization of Proteins within Thylakoid Membranes Tremmel, I. G.; Weis, E.; Farquhar, G. D. Biophysical Journal, Vol. 88, Issue 4 https://doi.org/10.1529/biophysj.104.045666	journal	April 2005
Theory of Optical Spectra of Photosystem II Reaction Centers: Location of the Triplet State and the Identity of the Primary Electron Donor Raszewski, Grzegorz; Saenger, Wolfram; Renger, Thomas Biophysical Journal, Vol. 88, Issue 2 https://doi.org/10.1529/biophysj.104.050294	journal	February 2005
A Protein Dynamics Study of Photosystem II: The Effects of Protein Conformation on Reaction Center Function Vasil’ev, Sergej; Bruce, Doug Biophysical Journal, Vol. 90, Issue 9 https://doi.org/10.1529/biophysj.105.076075	journal	May 2006
Using Metadynamics to Understand the Mechanism of Calmodulin/Target Recognition at Atomic Detail Fiorin, G.; Pastore, A.; Carloni, P. Biophysical Journal, Vol. 91, Issue 8 https://doi.org/10.1529/biophysj.106.086611	journal	October 2006
Molecular dynamics simulation reveals how phosphorylation of tyrosine 26 of phosphoglycerate mutase 1 upregulates glycolysis and promotes tumor growth Wang, Yan; Cai, Wen-Sheng; Chen, Luonan Oncotarget, Vol. 8, Issue 7 https://doi.org/10.18632/oncotarget.14517	journal	January 2017
Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses Singharoy, Abhishek; Chipot, Chris; Ekimoto, Toru Frontiers in Physiology, Vol. 10 https://doi.org/10.3389/fphys.2019.00046	journal	February 2019
Molecular System Bioenergetics—New Aspects of Metabolic Research Saks, Valdur International Journal of Molecular Sciences, Vol. 10, Issue 8 https://doi.org/10.3390/ijms10083655	journal	August 2009
The Role of Bioenergetics in Neurodegeneration Strope, Taylor A.; Birky, Cole J.; Wilkins, Heather M. International Journal of Molecular Sciences, Vol. 23, Issue 16 https://doi.org/10.3390/ijms23169212	journal	August 2022
The “mitochondrial stress responses”: the “Dr. Jekyll and Mr. Hyde” of neuronal disorders Rimessi, Alessandro; Patergnani, Simone; Morciano, Giampaolo Neural Regeneration Research, Vol. 17, Issue 12 https://doi.org/10.4103/1673-5374.339473	journal	January 2022
Overall energy conversion efficiency of a photosynthetic vesicle Sener, Melih; Strumpfer, Johan; Singharoy, Abhishek eLife, Vol. 5 https://doi.org/10.7554/eLife.09541	journal	August 2016
Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps Singharoy, Abhishek; Teo, Ivan; McGreevy, Ryan eLife, Vol. 5 https://doi.org/10.7554/eLife.16105	journal	July 2016

Similar Records

Respiratory syncytial virus increases lung cellular bioenergetics in neonatal C57BL/6 mice

Journal Article · 2014 · Virology · OSTI ID:22435031

Albawardi, Alia; Almarzooqi, Saeeda; Benedict, Sheela; +1 more

Multiscale modeling and cinematic visualization of photosynthetic energy conversion processes from electronic to cell scales

Journal Article · 2020 · Parallel Computing · OSTI ID:1850691

Sener, Melih; Levy, Stuart; Stone, John E.; +8 more

Atomic detail visualization of photosynthetic membranes with GPU-accelerated ray tracing

Journal Article · 2016 · Parallel Computing · OSTI ID:1371005

Stone, John E.; Sener, Melih; Vandivort, Kirby L.; +13 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
electron transport
photosynthesis
simulation

Title: Perspective on Integrative Simulations of Bioenergetic Domains

Citation Formats

References (240)

Similar Records

Related Subjects