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Mejuto-Zaera C, Tzeli D, Williams-Young D, Tubman NM, Matoušek M, Brabec J, Veis L, Xantheas SS, de Jong WA. The Effect of Geometry, Spin, and Orbital Optimization in Achieving Accurate, Correlated Results for Iron-Sulfur Cubanes. J Chem Theory Comput 2022; 18:687-702. [PMID: 35034448 DOI: 10.1021/acs.jctc.1c00830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Iron-sulfur clusters comprise an important functional motif in the catalytic centers of biological systems, capable of enabling important chemical transformations at ambient conditions. This remarkable capability derives from a notoriously complex electronic structure that is characterized by a high density of states that is sensitive to geometric changes. The spectral sensitivity to subtle geometric changes has received little attention from correlated, large active space calculations, owing partly to the exceptional computational complexity for treating these large and correlated systems accurately. To provide insight into this aspect, we report the first Complete Active Space Self Consistent Field (CASSCF) calculations for different geometries of the [Fe(II/III)4S4(SMe)4]-2 clusters using two complementary, correlated solvers: spin-pure Adaptive Sampling Configuration Interaction (ASCI) and Density Matrix Renormalization Group (DMRG). We find that the previously established picture of a double-exchange driven magnetic structure, with minute energy gaps (<1 mHa) between consecutive spin states, has a weak dependence on the underlying geometry. However, the spin gap between the singlet and the spin state 2S + 1 = 19, corresponding to a maximal number of Fe-d electrons being unpaired and of parallel spin, is strongly geometry dependent, changing by a factor of 3 upon slight deformations that are still within biologically relevant parameters. The CASSCF orbital optimization procedure, using active spaces as large as 86 electrons in 52 orbitals, was found to reduce this gap compared to typical mean-field orbital approaches. Our results show the need for performing large active space calculations to unveil the challenging electronic structure of these complex catalytic centers and should serve as accurate starting points for fully correlated treatments upon inclusion of dynamical correlation outside the active space.
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Affiliation(s)
- Carlos Mejuto-Zaera
- University of California, Berkeley, California 94720, United States.,Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Demeter Tzeli
- Laboratory of Physical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens 15784, Greece.,Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, Vas. Constantinou 48, Athens 11635, Greece
| | - David Williams-Young
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Norm M Tubman
- Quantum Artificial Intelligence Lab. (QuAIL), Exploration Technology Directorate, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Mikuláš Matoušek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Jiri Brabec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, v.v.i., Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Sotiris S Xantheas
- Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, United States.,Department of Chemistry, University of Washington, Seattle, Washington 98185, United States
| | - Wibe A de Jong
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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da Silva TU, Pougy KDC, Albuquerque MG, da Silva Lima CH, Machado SDP. Development of parameters compatible with the CHARMM36 force field for [Fe 4S 4] 2+ clusters and molecular dynamics simulations of adenosine-5'-phosphosulfate reductase in GROMACS 2019. J Biomol Struct Dyn 2020; 40:3481-3491. [PMID: 33183173 DOI: 10.1080/07391102.2020.1847687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
DFT calculations were used to obtain parameters compatible with the CHARMM36 force field for iron-sulfur clusters (Fe-S) of the type [Fe4S4]2+ that are coordinated to dissimilatory adenosine-5'-phosphosulfate reductase (APSrAB). Classical molecular dynamics (MD) simulations were performed on two APSrAB systems to validate the parameters and verify the stability of the studied systems. The time analysis of the parameters inserted into the force field was in reasonable agreement with the experimental X-ray diffraction data. The analysis of the time evolution of the studied systems indicated that these systems and, in particular, the clusters in their respective cavities had a good stability and were in agreement with what was observed in previous works. The parameters obtained provide the basis for the study of APSrAB as well as other systems that contain [Fe4S4]2+ through the CHARMM36 force field.
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Teo RD, Migliore A, Beratan DN. Mutation effects on charge transport through the p58c iron-sulfur protein. Chem Sci 2020; 11:7076-7085. [PMID: 33250976 PMCID: PMC7690218 DOI: 10.1039/d0sc02245d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
Growing experimental evidence indicates that iron–sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe4S4] clusters, mediated by proteins and DNA, may convey signals to coordinate enzyme action. Human primase is a well studied [Fe4S4] protein, and its p58c domain (which contains an [Fe4S4] cluster) plays a role in the initiation of DNA replication. The Y345C mutation in p58c is linked to gastric tumors and may influence the protein-mediated charge transport. The complexity of protein–DNA systems, and the intricate electronic structure of [Fe4S4] clusters, have impeded progress into understanding functional charge transport in these systems. In this study, we built force fields to describe the high potential [Fe4S4] cluster in both oxidation states. The parameterization is compatible with AMBER force fields and enabled well-balanced molecular dynamics simulations of the p58c–RNA/DNA complex relevant to the initiation of DNA replication. Using the molecular mechanics Poisson–Boltzmann and surface area solvation method on the molecular dynamics trajectories, we find that the p58c mutation induces a modest change in the p58c–duplex binding free energy in agreement with recent experiments. Through kinetic modeling and analysis, we identify key features of the main charge transport pathways in p58c. In particular, we find that the Y345C mutation partially changes the composition and frequency of the most efficient (and potentially relevant to the biological function) charge transport pathways between the [Fe4S4] cluster and the duplex. Moreover, our approach sets the stage for a deeper understanding of functional charge transfer in [Fe4S4] protein–DNA complexes. Functional electron transfer between the [Fe4S4] cluster and the nucleic acid is impacted by a Y345C mutation in the p58c subunit of human primase.![]()
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Affiliation(s)
- Ruijie D Teo
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - Agostino Migliore
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ;
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA . ; .,Department of Physics , Duke University , Durham , North Carolina 27708 , USA.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , USA
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Guo Y, Li H, He LL, Zhao DX, Gong LD, Yang ZZ. Theoretical reflections on the structural polymorphism of the oxygen-evolving complex in the S2 state and the correlations to substrate water exchange and water oxidation mechanism in photosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:833-846. [DOI: 10.1016/j.bbabio.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/25/2017] [Accepted: 08/02/2017] [Indexed: 11/29/2022]
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Guo Y, Li H, He LL, Zhao DX, Gong LD, Yang ZZ. The open-cubane oxo–oxyl coupling mechanism dominates photosynthetic oxygen evolution: a comprehensive DFT investigation on O–O bond formation in the S4state. Phys Chem Chem Phys 2017; 19:13909-13923. [DOI: 10.1039/c7cp01617d] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
How is O2created in nature? Comprehensive DFT investigations determine the dominance of the open-cubane oxo–oxyl coupling mechanism over alternative possibilities.
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Affiliation(s)
- Yu Guo
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Hui Li
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Lan-Lan He
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Li-Dong Gong
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering
- Liaoning Normal University
- Dalian 116029
- People's Republic of China
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Perrin BS, Niu S, Ichiye T. Calculating standard reduction potentials of [4Fe-4S] proteins. J Comput Chem 2013; 34:576-82. [PMID: 23115132 PMCID: PMC3570669 DOI: 10.1002/jcc.23169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/20/2012] [Accepted: 09/30/2012] [Indexed: 11/08/2022]
Abstract
The oxidation-reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combination of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Shuqiang Niu
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
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Electronic structure of the unique [4Fe-3S] cluster in O2-tolerant hydrogenases characterized by 57Fe Mossbauer and EPR spectroscopy. Proc Natl Acad Sci U S A 2012; 110:483-8. [PMID: 23267108 DOI: 10.1073/pnas.1202575110] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Iron-sulfur clusters are ubiquitous electron transfer cofactors in hydrogenases. Their types and redox properties are important for H(2) catalysis, but, recently, their role in a protection mechanism against oxidative inactivation has also been recognized for a [4Fe-3S] cluster in O(2)-tolerant group 1 [NiFe] hydrogenases. This cluster, which is uniquely coordinated by six cysteines, is situated in the proximity of the catalytic [NiFe] site and exhibits unusual redox versatility. The [4Fe-3S] cluster in hydrogenase (Hase) I from Aquifex aeolicus performs two redox transitions within a very small potential range, forming a superoxidized state above +200 mV vs. standard hydrogen electrode (SHE). Crystallographic data has revealed that this state is stabilized by the coordination of one of the iron atoms to a backbone nitrogen. Thus, the proximal [4Fe-3S] cluster undergoes redox-dependent changes to serve multiple purposes beyond classical electron transfer. In this paper, we present field-dependent (57)Fe-Mössbauer and EPR data for Hase I, which, in conjunction with spectroscopically calibrated density functional theory (DFT) calculations, reveal the distribution of Fe valences and spin-coupling schemes for the iron-sulfur clusters. The data demonstrate that the electronic structure of the [4Fe-3S] core in its three oxidation states closely resembles that of corresponding conventional [4Fe-4S] cubanes, albeit with distinct differences for some individual iron sites. The medial and distal iron-sulfur clusters have similar electronic properties as the corresponding cofactors in standard hydrogenases, although their redox potentials are higher.
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Niu S, Ichiye T. Insight into environmental effects on bonding and redox properties of [4Fe-4S] clusters in proteins. J Am Chem Soc 2009; 131:5724-5. [PMID: 19341280 DOI: 10.1021/ja900406j] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The large differences in redox potentials between the HiPIPs and ferredoxins are generally attributed to hydrogen bonds and electrostatic effects from the protein and solvent. Recent ligand K-edge X-ray absorption studies by Solomon and co-workers show that the Fe-S covalencies of [4Fe-4S] clusters in the two proteins differ considerably apparently because of hydrogen bonds from water, indicating electronic effects may be important. However, combined density function theory (DFT) and photoelectron spectroscopy studies by our group and Wang and co-workers indicate that hydrogen bonds tune the potential of [4Fe-4S] clusters by mainly electrostatics. The DFT studies here rationalize both results, namely that the observed change in the Fe-S covalency is due to differences in ligand conformation between the two proteins rather than hydrogen bonds. Moreover, the ligand conformation affects the calculated potentials by approximately 100 mV and, thus, is a heretofore unconsidered means of tuning the potential.
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Affiliation(s)
- Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, DC 20057-1227, USA
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