Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II

Adam, Suliman; Knapp-Mohammady, Michaela; Yi, Jun; Bondar, Ana‐Nicoleta

doi:10.1002/jcc.24918

Cited by 23 publications

(24 citation statements)

References 54 publications

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“…Currently, several all-atom and UA FFs are available and validated for all amino acids, several lipid classes, and different solvents (Oostenbrink et al 2004;Zhu et al 2012;Nerenberg and Head-Gordon 2018). Importantly for the photosynthetic community, nowadays several of these FFs have also been derived and validated for photosynthetic pigments and cofactors: most all-atom FFs (such as CHARMM and Amber) have been validated by comparing simulated properties against ab initio calculations (Damjanović et al 2002;Ceccarelli et al 2003;Karki and Roccatano 2011;Cerezo et al 2013;Guerra et al 2015;Adam et al 2018;Kim et al 2018). In the case of the Amber force field for Cars (Prandi et al 2016), this set of parameters has been specifically validated to reproduce selected spectral properties.…”

Section: Atomistic Force Fieldsmentioning

confidence: 99%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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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.Publisher's Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Section: Atomistic Force Fieldsmentioning

confidence: 99%

Molecular dynamics simulations in photosynthesis

Liguori¹,

Croce²,

Marrink

et al. 2020

Photosynth Res

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“… 41 Luthey-Schulten and coworkers optimized the partial charges and bonded parameters for the heme, hexacoordinated with ligands appropriate to Cyt c , relying on both protein X‐ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6‐31G* level. 42 Adam and coauthors have recently carried out a similar optimization of the standard CHARMM parameters, for the Photosystem II, 43 while Soloviov and coauthors added an ad hoc potential term to the CHARMM22 force field to model the ligand-heme interaction in Myoglobin–NO. 44…”

Section: Theoretical Frameworkmentioning

confidence: 99%

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Chillemi

Anselmi

Sanna

et al. 2018

Structural Dynamics

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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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“…The derived Fe 2+ metal charges in the [2FE-2S] cluster were reported to have positive values of 0.590 (FE 2 ) and 0.732 (FE 3 ), which is consistent with previous studies [ 63 ]. However, FE 1 in b-type heme bL was reported to have RESP charges of −0.009, unlike previous studies that reported the RESP charge for Fe 2+ to be 0.16 using the HF/6-31G* charge calculation method [ 64 ]. Additionally, other studies have reported a charge of 0.45 and 1.58 in a-type and c-type heme structures respectively [ 65 , 66 ].…”

Section: Resultsmentioning

confidence: 80%

Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane

Chebon

Sanyanga

Manyumwa

et al. 2021

IJMS

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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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Revised CHARMM force field parameters for iron‐containing cofactors of photosystem II

Cited by 23 publications

References 54 publications

Molecular dynamics simulations in photosynthesis

Molecular dynamics simulations in photosynthesis

Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin

Decoding the Molecular Effects of Atovaquone Linked Resistant Mutations on Plasmodium falciparum Cytb-ISP Complex in the Phospholipid Bilayer Membrane

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