1
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Cui C, Jiang M, Jain N, Das S, Lo YH, Kermani AA, Pipatpolkai T, Sun J. Structural basis of human NOX5 activation. Nat Commun 2024; 15:3994. [PMID: 38734761 PMCID: PMC11088703 DOI: 10.1038/s41467-024-48467-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
NADPH oxidase 5 (NOX5) catalyzes the production of superoxide free radicals and regulates physiological processes from sperm motility to cardiac rhythm. Overexpression of NOX5 leads to cancers, diabetes, and cardiovascular diseases. NOX5 is activated by intracellular calcium signaling, but the underlying molecular mechanism of which - in particular, how calcium triggers electron transfer from NADPH to FAD - is still unclear. Here we capture motions of full-length human NOX5 upon calcium binding using single-particle cryogenic electron microscopy (cryo-EM). By combining biochemistry, mutagenesis analyses, and molecular dynamics (MD) simulations, we decode the molecular basis of NOX5 activation and electron transfer. We find that calcium binding to the EF-hand domain increases NADPH dynamics, permitting electron transfer between NADPH and FAD and superoxide production. Our structural findings also uncover a zinc-binding motif that is important for NOX5 stability and enzymatic activity, revealing modulation mechanisms of reactive oxygen species (ROS) production.
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Affiliation(s)
- Chenxi Cui
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Meiqin Jiang
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Nikhil Jain
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Sourav Das
- Department of Chemical Biology & Therapeutics, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Yu-Hua Lo
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Ali A Kermani
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA
| | - Tanadet Pipatpolkai
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 673371, Singapore, Singapore.
| | - Ji Sun
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN38105, USA.
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2
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Pirnia A, Maqdisi R, Mittal S, Sener M, Singharoy A. Perspective on Integrative Simulations of Bioenergetic Domains. J Phys Chem B 2024; 128:3302-3319. [PMID: 38562105 DOI: 10.1021/acs.jpcb.3c07335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
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, 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.
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Affiliation(s)
- Adam Pirnia
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Ranel Maqdisi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
| | - Sumit Mittal
- VIT Bhopal University, Sehore 466114, Madhya Pradesh, India
| | - Melih Sener
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
- Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhishek Singharoy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1004, United States
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3
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Lee C, Yang J, Kwon S, Seok C. GalaxyDock2-HEME: Protein-ligand docking for heme proteins. J Comput Chem 2023; 44:1369-1380. [PMID: 36809651 DOI: 10.1002/jcc.27092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/20/2023] [Accepted: 02/08/2023] [Indexed: 02/23/2023]
Abstract
Prediction of protein-ligand binding poses is an essential component for understanding protein-ligand interactions and computer-aided drug design. Various proteins involve prosthetic groups such as heme for their functions, and adequate consideration of the prosthetic groups is vital for protein-ligand docking. Here, we extend the GalaxyDock2 protein-ligand docking algorithm to handle ligand docking to heme proteins. Docking to heme proteins involves increased complexity because the interaction of heme iron and ligand has covalent nature. GalaxyDock2-HEME, a new protein-ligand docking program for heme proteins, has been developed based on GalaxyDock2 by adding an orientation-dependent scoring term to describe heme iron-ligand coordination interaction. This new docking program performs better than other noncommercial docking programs such as EADock with MMBP, AutoDock Vina, PLANTS, LeDock, and GalaxyDock2 on a heme protein-ligand docking benchmark set in which ligands are known to bind iron. In addition, docking results on two other sets of heme protein-ligand complexes in which ligands do not bind iron show that GalaxyDock2-HEME does not have a high bias toward iron binding compared to other docking programs. This implies that the new docking program can distinguish iron binders from noniron binders for heme proteins.
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Affiliation(s)
- Changsoo Lee
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Jinsol Yang
- Galux Inc, Gwanak-gu, Seoul, Republic of Korea
| | - Sohee Kwon
- Galux Inc, Gwanak-gu, Seoul, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.,Galux Inc, Gwanak-gu, Seoul, Republic of Korea
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4
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In silico investigation of cytochrome bc1 molecular inhibition mechanism against Trypanosoma cruzi. PLoS Negl Trop Dis 2023; 17:e0010545. [PMID: 36689459 PMCID: PMC9894551 DOI: 10.1371/journal.pntd.0010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 02/02/2023] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Chagas' disease is a neglected tropical disease caused by the kinetoplastid protozoan Trypanosoma cruzi. The only therapies are the nitroheterocyclic chemicals nifurtimox and benznidazole that cause various adverse effects. The need to create safe and effective medications to improve medical care remains critical. The lack of verified T. cruzi therapeutic targets hinders medication research for Chagas' disease. In this respect, cytochrome bc1 has been identified as a promising therapeutic target candidate for antibacterial medicines of medical and agricultural interest. Cytochrome bc1 belongs to the mitochondrial electron transport chain and transfers electrons from ubiquinol to cytochrome c1 by the action of two catalytic sites named Qi and Qo. The two binding sites are highly selective, and specific inhibitors exist for each site. Recent studies identified the Qi site of the cytochrome bc1 as a promising drug target against T. cruzi. However, a lack of knowledge of the drug mechanism of action unfortunately hinders the development of new therapies. In this context, knowing the cause of binding site selectivity and the mechanism of action of inhibitors and substrates is crucial for drug discovery and optimization processes. In this paper, we provide a detailed computational investigation of the Qi site of T. cruzi cytochrome b to shed light on the molecular mechanism of action of known inhibitors and substrates. Our study emphasizes the action of inhibitors at the Qi site on a highly unstructured portion of cytochrome b that could be related to the biological function of the electron transport chain complex.
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5
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Yang X, Wu W, Chen X, Wu F, Fan S, Yu P, Mao L. A versatile artificial metalloenzyme scaffold enabling direct bioelectrocatalysis in solution. SCIENCE ADVANCES 2022; 8:eabo3315. [PMID: 36322668 PMCID: PMC9629707 DOI: 10.1126/sciadv.abo3315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Artificial metalloenzymes (ArMs) are commonly designed with protein scaffolds containing buried coordination pockets to achieve substrate specificity and product selectivity for homogeneous reactions. However, their reactivities toward heterogeneous transformations are limited because interfacial electron transfers are hampered by the backbone shells. Here, we introduce bacterial small laccase (SLAC) as a new protein scaffold for constructing ArMs to directly catalyze electrochemical transformations. We use molecular dynamics simulation, x-ray crystallography, spectroscopy, and computation to illustrate the scaffold-directed assembly of an oxo-bridged dicobalt motif on protein surface. The resulting ArM in aqueous phase catalyzes electrochemical water oxidation without mediators or electrode modifications. Mechanistic investigation reveals the role of SLAC scaffold in defining the four-electron transfer pathway from water to oxygen. Furthermore, we demonstrate that SLAC-based ArMs implemented with Ni2+, Mn2+, Ru3+, Pd2+, or Ir3+ also enable direct bioelectrocatalysis of water electrolysis. Our study provides a versatile and generalizable route to complement heterogeneous repertoire of ArMs for expanded applications.
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Affiliation(s)
- Xiaoti Yang
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjie Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Chen
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilong Fan
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
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6
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Han Z, Wu F, Yu P, Mao L. Computer-Aided Rational Construction of Mediated Bioelectrocatalysis with π-Conjugated (Hetero)cyclic Molecules: Toward Promoted Distant Electron Tunneling and Improved Biosensing. Anal Chem 2022; 94:8033-8040. [PMID: 35604848 DOI: 10.1021/acs.analchem.2c01289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Highly π-conjugated (hetero)cyclic molecules having delocalized orbitals and tunable charge mobilities are attractive redox relays for mediated bioelectrocatalysis in manifold applications. As rigid molecules, their dynamics within the soft but confined intraprotein space becomes the crucial determinant of the enzyme-mediator electron-tunneling efficiency. However, it is rarely investigated in designing the mediated interface with a particular biocatalyst (e.g., oxidoreductase), which remains an empirical but try-and-error process. Herein, we present the computer-aided exploration of interactions between a flavin-containing reductive synthase and structurally diverse π-extended (hetero)cyclic mediators to realize reversed bioelectrocatalytic oxidation at low overpotentials. Compared to ring-fused systems with unbroken molecular planarity, heteroatom-bridged cyclic, and rotatable conjugated structures (e.g., indophenols) can experience unusually large dynamic torsion under biased forces of hydrogen bonding with enzyme residues. This behavior led to fast intraprotein reorientation (<50 ps) that shortened the electron-tunneling distance from 12 to 9 Å. Meanwhile, the lowest unoccupied molecular orbital level upon molecular torsion was decreased by 0.5 eV to further promote electron abstraction from the reduced flavin cofactor. An efficient distant electron tunneling also obviated mediator transport through the substrate channel, thus avoiding competitive inhibition on enzyme kinetics to broaden the operating concentration range. The resulting bioelectrocatalytic interface enables low-potential biosensing of glutamate with improved selectivity. Our finding provides new structural insights into constructing efficient long-range heterogeneous charge transport with biomacromolecular catalysts.
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Affiliation(s)
- Zhongjie Han
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Wu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Yu
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- Beijing National Laboratory for Molecular Science, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,College of Chemistry, Beijing Normal University, Beijing 100875, China
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7
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Lu LN, Liu C, Yang ZZ, Zhao DX. Refined models of coordination between Al3+/Mg2+ and enzyme in molecular dynamics simulation in terms of ABEEM polarizable force field. J Mol Graph Model 2022; 114:108190. [DOI: 10.1016/j.jmgm.2022.108190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/04/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
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8
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Exploring the folding energy landscapes of heme proteins using a hybrid AWSEM-heme model. J Biol Phys 2022; 48:37-53. [PMID: 35000062 PMCID: PMC8866609 DOI: 10.1007/s10867-021-09596-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/03/2021] [Indexed: 10/29/2022] Open
Abstract
Heme is an active center in many proteins. Here we explore computationally the role of heme in protein folding and protein structure. We model heme proteins using a hybrid model employing the AWSEM Hamiltonian, a coarse-grained forcefield for the protein chain along with AMBER, an all-atom forcefield for the heme. We carefully designed transferable force fields that model the interactions between the protein and the heme. The types of protein-ligand interactions in the hybrid model include thioester covalent bonds, coordinated covalent bonds, hydrogen bonds, and electrostatics. We explore the influence of different types of hemes (heme b and heme c) on folding and structure prediction. Including both types of heme improves the quality of protein structure predictions. The free energy landscape shows that both types of heme can act as nucleation sites for protein folding and stabilize the protein folded state. In binding the heme, coordinated covalent bonds and thioester covalent bonds for heme c drive the heme toward the native pocket. The electrostatics also facilitates the search for the binding site.
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9
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Chebon-Bore L, Sanyanga TA, Manyumwa CV, Khairallah A, Tastan Bishop Ö. Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane. Int J Mol Sci 2021; 22:2138. [PMID: 33670016 PMCID: PMC7926518 DOI: 10.3390/ijms22042138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/19/2022] Open
Abstract
Atovaquone (ATQ) is a drug used to prevent and treat malaria that functions by targeting the Plasmodium falciparum cytochrome b (PfCytb) protein. PfCytb catalyzes the transmembrane electron transfer (ET) pathway which maintains the mitochondrial membrane potential. The ubiquinol substrate binding site of the protein has heme bL, heme bH and iron-sulphur [2FE-2S] cluster cofactors that act as redox centers to aid in ET. Recent studies investigating ATQ resistance mechanisms have shown that point mutations of PfCytb confer resistance. Thus, understanding the resistance mechanisms at the molecular level via computational approaches incorporating phospholipid bilayer would help in the design of new efficacious drugs that are also capable of bypassing parasite resistance. With this knowledge gap, this article seeks to explore the effect of three drug resistant mutations Y268C, Y268N and Y268S on the PfCytb structure and function in the presence and absence of ATQ. To draw reliable conclusions, 350 ns all-atom membrane (POPC:POPE phospholipid bilayer) molecular dynamics (MD) simulations with derived metal parameters for the holo and ATQ-bound -proteins were performed. Thereafter, simulation outputs were analyzed using dynamic residue network (DRN) analysis. Across the triplicate MD runs, hydrophobic interactions, reported to be crucial in protein function were assessed. In both, the presence and absence of ATQ and a loss of key active site residue interactions were observed as a result of mutations. These active site residues included: Met 133, Trp136, Val140, Thr142, Ile258, Val259, Pro260 and Phe264. These changes to residue interactions are likely to destabilize the overall intra-protein residue communication network where the proteins' function could be implicated. Protein dynamics of the ATQ-bound mutant complexes showed that they assumed a different pose to the wild-type, resulting in diminished residue interactions in the mutant proteins. In summary, this study presents insights on the possible effect of the mutations on ATQ drug activity causing resistance and describes accurate MD simulations in the presence of the lipid bilayer prior to conducting inhibitory drug discovery for the PfCytb-iron sulphur protein (Cytb-ISP) complex.
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Affiliation(s)
| | | | | | | | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140, South Africa; (L.C.-B.); (T.A.S.); (C.V.M.); (A.K.)
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10
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Lešnik S, Hodošček M, Bren U, Stein C, Bondar AN. Potential Energy Function for Fentanyl-Based Opioid Pain Killers. J Chem Inf Model 2020; 60:3566-3576. [DOI: 10.1021/acs.jcim.0c00185] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Samo Lešnik
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, D-14195 Berlin, Germany
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova ulica 17, SI-2000 Maribor, Slovenia
| | - Milan Hodošček
- National Institute of Chemistry Slovenia, Theory Department, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Urban Bren
- University of Maribor, Faculty of Chemistry and Chemical Engineering, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, SI-6000 Koper, Slovenia
| | - Christoph Stein
- Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin Department of Experimental Anesthesiology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, D-14195 Berlin, Germany
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11
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Liguori N, Croce R, Marrink SJ, Thallmair S. Molecular dynamics simulations in photosynthesis. PHOTOSYNTHESIS RESEARCH 2020; 144:273-295. [PMID: 32297102 PMCID: PMC7203591 DOI: 10.1007/s11120-020-00741-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/24/2020] [Indexed: 05/12/2023]
Abstract
Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD.
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Affiliation(s)
- Nicoletta Liguori
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
| | - Roberta Croce
- Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Sebastian Thallmair
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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12
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Govindjee. A sixty-year tryst with photosynthesis and related processes: an informal personal perspective. PHOTOSYNTHESIS RESEARCH 2019; 139:15-43. [PMID: 30343396 DOI: 10.1007/s11120-018-0590-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
After briefly describing my early collaborative work at the University of Allahabad, that had laid the foundation of my research life, I present here some of our research on photosynthesis at the University of Illinois at Urbana-Champaign, randomly selected from light absorption to NADP+ reduction in plants, algae, and cyanobacteria. These include the fact that (i) both the light reactions I and II are powered by light absorbed by chlorophyll (Chl) a of different spectral forms; (ii) light emission (fluorescence, delayed fluorescence, and thermoluminescence) by plants, algae, and cyanobacteria provides detailed information on these reactions and beyond; (iii) primary photochemistry in both the photosystems I (PS I) and II (PS II) occurs within a few picoseconds; and (iv) most importantly, bicarbonate plays a unique role on the electron acceptor side of PS II, specifically at the two-electron gate of PS II. Currently, the ongoing research around the world is, and should be, directed towards making photosynthesis better able to deal with the global issues (such as increasing population, dwindling resources, and rising temperature) particularly through genetic modification. However, basic research is necessary to continue to provide us with an understanding of the molecular mechanism of the process and to guide us in reaching our goals of increasing food production and other chemicals we need for our lives.
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13
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Chillemi G, Anselmi M, Sanna N, Padrin C, Balducci L, Cammarata M, Pace E, Chergui M, Benfatto M. Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2018; 5:054101. [PMID: 30246048 PMCID: PMC6135643 DOI: 10.1063/1.5031806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
We present a detailed analysis of the X-ray absorption near-edge structure (XANES) data on the Fe K-edge of CO Myoglobin based on a combined procedure of Molecular Dynamics (MD) calculations and MXAN (Minuit XANes) data analysis that we call D-MXAN. The ability of performing quantitative XANES data analysis allows us to refine classical force field MD parameters, thus obtaining a reliable tool for the atomic investigation of this important model system for biological macromolecules. The iterative procedure here applied corrects the greatest part of the structural discrepancy between classical MD sampling and experimental determinations. Our procedure, moreover, is able to discriminate between different heme conformational basins visited during the MD simulation, thus demonstrating the necessity of a sampling on the order of tens of nanoseconds, even for an application such X-ray absorption spectroscopy data analysis.
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Affiliation(s)
- Giovanni Chillemi
- Authors to whom correspondence should be addressed: , Telephone: +39 06 44486 706 and , Telephone: +39–06-9403–2884
| | - Massimiliano Anselmi
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | | | - Cristiano Padrin
- CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii 6, 00185 Roma, Italy
| | - Lodovico Balducci
- Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France
| | - Marco Cammarata
- Université de Rennes 1, CNRS, Univ. Bretagne Loire, Institut de Physique de Rennes, UMR 6251, Rennes F-35042, France
| | - Elisabetta Pace
- Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, Italy
| | - Majed Chergui
- Lab. of Ultrafast Spectroscopy (LSU) and Lausanne Centre for Ultrafast Science (LACUS), Ecole Polytechnique Fédérale de Lausanne, ISIC, FSB, Station 6, CH-1015 Lausanne, Switzerland
| | - Maurizio Benfatto
- Laboratori Nazionali di Frascati, INFN- Via E. Fermi 44, 00044 Frascati, Italy
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14
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Wu X, Clavaguera C, Lagardère L, Piquemal JP, de la Lande A. AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms. J Chem Theory Comput 2018; 14:2705-2720. [PMID: 29630819 DOI: 10.1021/acs.jctc.7b01128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the first parameters of the heme redox cofactors for the polarizable AMOEBA force field in both the ferric and ferrous forms. We consider two types of complexes, one with two histidine side chains as axial ligands and one with a histidine and a methionine side chain as ligands. We have derived permanent multipoles from second-order Møller-Plesset perturbation theory (MP2). The sets of parameters have been validated in a first step by comparison of AMOEBA interaction energies of heme and a collection of biologically relevant molecules with MP2 and Density Functional Theory (DFT) calculations. In a second validation step, we consider interaction energies with large aggregates comprising around 80 H2O molecules. These calculations are repeated for 30 structures extracted from semiempirical PM7 DM simulations. Very encouraging agreement is found between DFT and the AMOEBA force field, which results from an accurate treatment of electrostatic interactions. We finally report long (10 ns) MD simulations of cytochromes in two redox states with AMOEBA testing both the 2003 and 2014 AMOEBA water models. These simulations have been carried out with the TINKER-HP (High Performance) program. In conclusion, owing to their ubiquity in biology, we think the present work opens a wide array of applications of the polarizable AMOEBA force field on hemeproteins.
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Affiliation(s)
- Xiaojing Wu
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Carine Clavaguera
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
| | - Louis Lagardère
- Sorbonne Université, CNRS , Institut Parisien de Chimie Physique et Théorique (IP2CT) , 4 Place Jussieu , F-75005 , Paris , France.,Sorbonne Université , Institut des Sciences du Calcul et des Données (ISCD) , 4 place Jussieu , F-75005 , Paris , France
| | - Jean-Philip Piquemal
- Sorbonne Université, CNRS , Laboratoire de Chimie Théorique (LCT) , 4 Place Jussieu , F-75005 , Paris , France.,Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Institut Universitaire de France , 75005 , Paris , France
| | - Aurélien de la Lande
- Laboratoire de Chimie Physique , Université Paris Sud - CNRS, Université Paris Saclay , 15 Avenue Jean Perrin , 91405 Orsay Cedex , France
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Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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