Becksteinlab/GromacsWrapper: Release 0.8.0

Beckstein, Oliver; Lacerda, Pedro; Domański, Jan; Dotson, David; Heavey, Thomas; White, Andrew J. P.; Gowers, Richard; Linke, Max; Kenney, I J; Cody,; Fan, Shujie; Somogyi, Andy; denniej,; Loche, Philip; Mohebifar, Mohamad; Berg, Andrej

doi:10.5281/zenodo.2654393

“…Inc. 2015). Other python packages used for the illustration are numpy (Harris et al 2020), mdtraj (McGibbon et al 2015, PyEMMA (Scherer et al 2015), and GROMACS Wrapper (Beckstein et al 2019;Chavan and Barton 2020).…”

Section: Simulation Detailsmentioning

confidence: 99%

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

Saini

¹

,

Globisch

²

,

Franke

³

et al. 2021

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The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.

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pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics

Voronin¹,

Schug²

2021

JOSS

2

0

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Proteins are complex biomolecules which fulfill a wide range of critical tasks in living organisms. Studying and understanding their structure, function, and dynamics is essential for life sciences and can be applied for, e.g., disease control or advanced drug design. Molecular Dynamics (MD) is a computational method relying on physical models to simulate biomolecular systems. Movements of all atoms can be 'viewed' like a movie and analyzed to improve the understanding of specific interactions or complement experimental measurements. Replica Exchange (REX) is a powerful method used to enhance the sampling of protein conformations and generates large amounts of data.

show abstract

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

Saini¹

2021

Preprint

0

View full text Add to dashboard Cite

The structural basis for the stability of the trimeric form of the light harvesting complex (LHCII), a pigmented protein from green plants pivotal for photosynthesis, remains elusive till date. The protein embedded in a dipalmitoylphosphatidylcholine (DPPC) lipid membrane is investigated using all-atom molecular dynamics simulations to find out the interactions responsible for the structural integrity of the trimer and its relation to antenna function. Central association of chlorophyll a (CLA) molecules near the LHCII chains is attributed to a conserved coordination between the Mg of CLA and the oxygen of a specific residue of the first helix of a chain. The residue forms a salt-bridge with the fourth helix of the same chain of the trimer, not of the monomer. In an earlier experiment, three residues (WYR) at each chain of the trimer have been found indispensable for the trimerization and referred to as trimerization motif. We find that the residues of the trimerization motif are connected to the lipids or pigments by a chain of interactions rather than a direct contact. Synergistic effects of sequentially located hydrogen bonds and salt-bridges within monomers of the trimer keep the trimer conformation stable in association with the pigments or the lipids. These interactions are exclusively present in the pigmented trimer and not present in the monomer or in the unpigmented trimer. Thus, our results provide a molecular basis for the inherent stability of the LHCII trimer in a lipid membrane and explain many pre-existing experimental data.

show abstract

Becksteinlab/GromacsWrapper: Release 0.8.0

Cited by 3 publications

References 0 publications

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics

Interactions Determining the Structural Integrity of the Trimer of Plant Light Harvesting Complex in Lipid Membranes

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