sDMD: An open source program for discontinuous molecular dynamics simulation of protein folding and aggregation

Zheng, Size; Javidpour, Leili; Sahimi, Muhammad; Shing, Katherine S.; Nakano, Aiichiro

doi:10.1016/j.cpc.2019.106873

Cited by 6 publications

(15 citation statements)

References 42 publications

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“…DMD simulations were performed using the software package (sDMD) developed by Zheng and co-workers. , In our simulations, the intra- and intermolecular interactions of protein(s) in the aqueous environment were represented precisely in an implicit water environment using well-calibrated all-atom DMD forcefield parameters published in the literature . Interactions between protein residues and the substrate surface were computed efficiently using the coarse-grained Go-like model − where N stands for the residues’ number in a protein, z i s is the distance between residue I and the surface, and σ i and ϵ i are the van der Waals parameters.…”

Section: Methodsmentioning

confidence: 99%

“…The systems were simulated in a box of 10.0 × 10.0 × 10.0 nm 3 , and surfaces were all on the X – Z plane. Since DMD is event-driven and the solvent is represented only implicitly, it is not straightforward to correlate the simulation time and the temperature with the real time and temperature . To address this issue, instead of applying the real units, we used time step t and reduced temperature T * = T / T s in the simulations .…”

Section: Methodsmentioning

confidence: 99%

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Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

et al. 2021

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Recently, a super uranyl binding protein (SUP) was developed, which exhibits excellent sensitivity/selectivity to bind uranyl ions. It can be immobilized onto a surface in sensing devices to detect uranyl ions. Here, sum frequency generation (SFG) vibrational spectroscopy was applied to probe the interfacial structures of surface-immobilized SUP. The collected SFG spectra were compared to the calculated orientation-dependent SUP SFG spectra using a one-excitonic Hamiltonian approach based on the SUP crystal structures to deduce the most likely surface-immobilized SUP orientation(s). Furthermore, discrete molecular dynamics (DMD) simulation was applied to refine the surface-immobilized SUP conformations and orientations. The immobilized SUP structures calculated from DMD simulations confirmed the SUP orientations obtained from SFG data analyzed based on the crystal structures and were then used for a new round of SFG orientation analysis to more accurately determine the interfacial orientations and conformations of immobilized SUP before and after uranyl ion binding, providing an in-depth understanding of molecular interactions between SUP and the surface and the effect of uranyl ion binding on the SUP interfacial structures. We believe that the developed method of combining SFG measurements, DMD simulation, and Hamiltonian data analysis approach is widely applicable to study biomolecules at solid/liquid interfaces.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

et al. 2021

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“…Despite the aforementioned research, however, the precise underlying mechanisms of the process are still unclear, and the structural information on poly-PR and poly-GR is also limited. In this article, we use discontinuous MD (DMD) simulations combined with all-atom protein models (22) to simulate folding and aggregation of poly-PR and poly-GR proteins. Our goal is to understand at molecular scale the mechanisms of folding and aggregation and the resulting structures of both proteins.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Study of Structure, Folding, and Aggregation of Poly-PR and Poly-GR Proteins

Zheng

Sahimi

Shing

et al. 2021

Biophysical Journal

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“…Detailed information on the discretization of protein−protein interactions in DMD simulations was reported in our previous paper. 66 In the Go-like model, each amino acid residue was simplified as a CG bead with its center of mass located on the α-carbon of the residue in the all-atom model. Thus, in mapping the CG model to the all-atom model, the surface's force acting on each CG bead was assigned to the α-carbon of an amino acid residue and then dissipated by the interactions of the α-carbon atom with its surrounding atoms.…”

Section: Methodsmentioning

confidence: 99%

“…62−65 To achieve sufficient computational efficiency without compromising accuracy and to present protein's secondary structural changes, we integrated the Go-like model 61 into our in-house developed framework of DMD simulations. 66 The original DMD full-atom force field 51 was utilized to compute the intermolecular and intramolecular interactions of proteins precisely and efficiently at the atomistic level. The coarsegrained Go-like model was employed to calculate the peptide/ protein interactions with the surface at the CG level.…”

Section: Introductionmentioning

confidence: 99%

Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface

Zheng

Sajib

Wei

et al. 2021

J. Chem. Theory Comput.

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Fundamental understanding of biomolecular interfacial behavior, such as protein adsorption at the microscopic scale, is critical to broad applications in biomaterials, nanomedicine, and nanoparticle-based biosensing techniques. The goal of achieving both computational efficiency and accuracy presents a major challenge for simulation studies at both atomistic and molecular scales. In this work, we developed a unique, accurate, high-throughput simulation method which, by integrating discontinuous molecular dynamics (DMD) simulations with the Golike protein−surface interaction model, not only solves the dynamics efficiently, but also describes precisely the protein intramolecular and intermolecular interactions at the atomistic scale and the protein−surface interactions at the coarse-grained scale. Using our simulation method and in-house developed software, we performed a systematic study of α-helical ovispirin-1 peptide adsorption on a graphene surface, and our study focused on the effect of surface hydrophobic interactions and π−π stacking on protein adsorption. Our DMD simulations were consistent with full-atom molecular dynamics simulations and showed that a single ovispirin-1 peptide lay down on the flat graphene surface with randomized secondary structure due to strong protein−surface interactions. Peptide aggregates were formed with an internal hydrophobic core driven by strong interactions of hydrophobic residues in the bulk environment. However, upon adsorption, the hydrophobic graphene surface can break the hydrophobic core by denaturing individual peptide structures, leading to disassembling the aggregate structure and further randomizing the ovispirin-1 peptide's secondary structures.

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sDMD: An open source program for discontinuous molecular dynamics simulation of protein folding and aggregation

Cited by 6 publications

References 42 publications

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Molecular Structure of the Surface-Immobilized Super Uranyl Binding Protein

Molecular Dynamics Study of Structure, Folding, and Aggregation of Poly-PR and Poly-GR Proteins

Discontinuous Molecular Dynamics Simulations of Biomolecule Interfacial Behavior: Study of Ovispirin-1 Adsorption on a Graphene Surface

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