Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme

Zhang, Lin; Bai, Shu; Sun, Yan

doi:10.1016/j.jmgm.2011.02.004

Cited by 18 publications

(19 citation statements)

References 51 publications

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“…Therefore, the potential energies provided by these residues are magnified. Moreover, the magnification of the potential energies using Martini force field is also found in our previous study [59]. It is found that the standard Martini force field generates too strong adsorption of lysozyme on the agarose matrix and ligands of hydrophobic charge induction chromatography.…”

Section: Resultssupporting

confidence: 75%

Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex

et al. 2013

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Staphylococcus aureus protein A (SpA) is the most popular affinity ligand for immunoglobulin G1 (IgG1). However, the molecular basis for the dissociation dynamics of SpA-IgG1 complex is unclear. Herein, coarse-grained (CG) molecular dynamics (MD) simulations with the Martini force field were used to study the dissociation dynamics of the complex. The CG-MD simulations were first verified by the agreement in the structural and interactional properties of SpA and human IgG1 (hIgG1) in the association process between the CG-MD and all-atom MD at different NaCl concentrations. Then, the CG-MD simulation studies focused on the molecular insight into the dissociation dynamics of SpA-hIgG1 complex at pH 3.0. It is found that there are four steps in the dissociation process of the complex. First, there is a slight conformational adjustment of helix II in SpA. This is followed by the phenomena that the electrostatic interactions provided by the three hot spots (Glu143, Arg146 and Lys154) of helix II of SpA break up, leading to the dissociation of helix II from the binding site of hIgG1. Subsequently, breakup of the hydrophobic interactions between helix I (Phe132, Tyr133 and His137) in SpA and hIgG1 occurs, resulting in the disengagement of helix I from its binding site of hIgG1. Finally, the non-specific interactions between SpA and hIgG1 decrease slowly till disappearance, leading to the complete dissociation of the SpA-hIgG1 complex. This work has revealed that CG-MD coupled with the Martini force field is an effective method for studying the dissociation dynamics of protein-protein complex.

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Section: Resultssupporting

confidence: 75%

Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex

et al. 2013

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“…180 Martini studies of interactions between soluble proteins are still limited, but do exist, for example on the stability of the spider silk's N-terminal protein domain 181 and of keratin filaments, 182 the stability of engineered nanofibres, 183 the mechanical properties of protein filaments, 184,185 and dissociation of gas phase protein complexes. 186,187 A related application of the Martini model is protein adsorption on solid supports 188,189 or at fluid interfaces. 190 Martini could also be used to screen for protein-ligand interactions in principle.…”

Section: Self-assembly Of Soluble Peptides and Proteinsmentioning

confidence: 99%

Perspective on the Martini model

2013

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The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.

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“…11 Zhang and co-workers reported MD simulation studies of adsorption and conformational transitions within bare cylindrical hydrophobic pores 13 and hydrophobic charge induction chromatography adsorbent pores. 12,14 Furthermore, MD simulation has been applied in a study on surface adsorption and aggregation of lysozyme. 15 In our former work, 16 MD simulations have been successfully employed to study the single component protein adsorption onto an ion-exchange chromatographic media.…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulations of a Binary Protein Mixture Adsorption onto Ion-Exchange Adsorbent

Liang

Fieg

Jakobtorweihen

2015

Ind. Eng. Chem. Res.

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Molecular dynamics (MD) simulations with a coarse-grained model are applied to investigate the binary adsorption of proteins onto an ion-exchange chromatographic medium. In particular, the adsorption of human serum albumin (HSA) and bovine hemoglobin (bHb) on the anion exchanger Q Sepharose FF is studied. Simulations with different initial orientations of the proteins and different protein−protein distances are carried out over a 2000 ns time scale. The protein−ligand potential energies and protein−ligand minimum distances are analyzed, and stable adsorption of HSA but no stable adsorption of bHb is observed. Interactions between HSA and bHb as well as a coupled movement of these two proteins are observed in all simulations. Because of the interaction between these two proteins, their rotations and adjustments to reach a favorable adsorption configuration are hindered. The competition is further indicated by changing adsorption sites on the HSA surface. The interaction and aggregation of the two proteins are investigated in detail.

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Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme

Cited by 18 publications

References 51 publications

Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex

Molecular Basis for the Dissociation Dynamics of Protein A-Immunoglobulin G1 Complex

Perspective on the Martini model

Molecular Dynamics Simulations of a Binary Protein Mixture Adsorption onto Ion-Exchange Adsorbent

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