Perspective on the Martini model

Marrink, Siewert J.; Tieleman, D. Peter

doi:10.1039/c3cs60093a

Cited by 1,084 publications

(1,396 citation statements)

References 337 publications

(412 reference statements)

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“…Even though current CG force fields have some limitations 45 , here they appear to provide a reliable method to visualize and quantify membrane properties that are otherwise extremely difficult to obtain with structural methods. Moreover, in vitro binding assays demonstrate that the computed properties correlate remarkably well with the membrane adhesive properties of model peptides of the ALPS motif family.…”

Section: Discussionmentioning

confidence: 99%

A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment

et al. 2014

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Two parameters of biological membranes, curvature and lipid composition, direct the recruitment of many peripheral proteins to cellular organelles. Although these traits are often studied independently, it is their combination that generates the unique interfacial properties of cellular membranes. Here, we use a combination of in vivo, in vitro and in silico approaches to provide a comprehensive map of how these parameters modulate membrane adhesive properties. The correlation between the membrane partitioning of model amphipathic helices and the distribution of lipid-packing defects in membranes of different shape and composition explains how macroscopic membrane properties modulate protein recruitment by changing the molecular topography of the membrane interfacial region. Furthermore, our results suggest that the range of conditions that can be obtained in a cellular context is remarkably large because lipid composition and curvature have, under most circumstances, cumulative effects.

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Section: Discussionmentioning

confidence: 99%

A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment

et al. 2014

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“…Although properties of lipid membranes are generally well described by this model, 14 the parameterization of ions, in particular Ca 2+ , has been done at a rather qualitative level mainly due to lack of suitable experimental targets. An accurate description of the interplay between ions and membranes remains a challenge even for fine-grain models.…”

Section: Discussionmentioning

confidence: 99%

Simulation of polyethylene glycol and calcium-mediated membrane fusion

Pannuzzo

Jong

Raudino

et al. 2014

The Journal of Chemical Physics

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Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study J. Chem. Phys. 138, 234901 (2013) We report on the mechanism of membrane fusion mediated by polyethylene glycol (PEG) and Ca 2+ by means of a coarse-grained molecular dynamics simulation approach. Our data provide a detailed view on the role of cations and polymer in modulating the interaction between negatively charged apposed membranes. The PEG chains cause a reduction of the inter-lamellar distance and cause an increase in concentration of divalent cations. When thermally driven fluctuations bring the membranes at close contact, a switch from cis to trans Ca 2+ -lipid complexes stabilizes a focal contact acting as a nucleation site for further expansion of the adhesion region. Flipping of lipid tails induces subsequent stalk formation. Together, our results provide a molecular explanation for the synergistic effect of Ca 2+ and PEG on membrane fusion. © 2014 AIP Publishing LLC.

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“…For example, in the MARTINI coarse-grained model, every amino acid is represented as one bead. [62][63][64] Brownian dynamics simulations, in addition to coarsegrained molecular dynamics simulations, can also provide a faster route to understanding intermolecular interactions in protein solutions. These simulations are performed in absence of the solvent.…”

Section: Multi-scale Molecular Simulations Of Antibody Solutions To Umentioning

confidence: 99%

Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development

Tomar

Kumar

Singh

et al. 2016

mAbs

162

145

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Effective translation of breakthrough discoveries into innovative products in the clinic requires proactive mitigation or elimination of several drug development challenges. These challenges can vary depending upon the type of drug molecule. In the case of therapeutic antibody candidates, a commonly encountered challenge is high viscosity of the concentrated antibody solutions. Concentration-dependent viscosity behaviors of mAbs and other biologic entities may depend on pairwise and higher-order intermolecular interactions, non-native aggregation, and concentration-dependent fluctuations of various antibody regions. This article reviews our current understanding of molecular origins of viscosity behaviors of antibody solutions. We discuss general strategies and guidelines to select low viscosity candidates or optimize lead candidates for lower viscosity at early drug discovery stages. Moreover, strategies for formulation optimization and excipient design are also presented for candidates already in advanced product development stages. Potential future directions for research in this field are also explored.

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Perspective on the Martini model

Cited by 1,084 publications

References 337 publications

A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment

A sub-nanometre view of how membrane curvature and composition modulate lipid packing and protein recruitment

Simulation of polyethylene glycol and calcium-mediated membrane fusion

Molecular basis of high viscosity in concentrated antibody solutions: Strategies for high concentration drug product development

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