Simulation of polyethylene glycol and calcium-mediated membrane fusion

Pannuzzo, Martina; Jong, Djurre H. de; Raudino, Antonio; Marrink, Siewert J.

doi:10.1063/1.4869176

Cited by 48 publications

(44 citation statements)

References 37 publications

(46 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The parameters for Na + and Cl – were taken from Marrink et al For Ca 2+ , a well‐tested Martini model is not available yet. Here, Ca 2+ was simply modeled as Na + with +2 e , as this has been used before in other published studies . As in most applications, the standard water model was taken from Marrink et al The parameters for LPS are those defined in Hsu et al Note that a few bonds with large force constants in the original LPS models were replaced with constraints to improve stability and allow larger integration time steps .…”

Section: Methodsmentioning

confidence: 99%

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

et al. 2017

Self Cite

View full text Add to dashboard Cite

A complex cell envelope, composed of a mixture of lipid types including complex lipopolysaccharides, protects bacteria from the external environment. Clearly, the proteins embedded within the various components of the cell envelope have an intricate relationship with their local environment. Therefore, to obtain meaningful results, molecular simulations need to mimic as far as possible this chemically heterogeneous system. However, setting up such systems for computational studies is far from trivial, and consequently the vast majority of simulations of outer membrane proteins still rely on oversimplified phospholipid membrane models. This work presents an update of CHARMM-GUI Martini Maker for coarse-grained modeling and simulation of complex bacterial membranes with lipopolysaccharides. The qualities of the outer membrane systems generated by Martini Maker are validated by simulating them in bilayer, vesicle, nanodisc, and micelle environments (with and without outer membrane proteins) using the Martini force field. We expect this new feature in Martini Maker to be a useful tool for modeling large, complicated bacterial outer membrane systems in a user-friendly manner.

show abstract

Section: Methodsmentioning

confidence: 99%

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…This allows an exact timing of membrane fusion by addition of bivalent (typically calcium) ions. These do not only shield the lipids' negative charges but may also bridge the opposing membranes by binding two negatively charged lipids to one bivalent ion (Böckmann and Grubmüller, 2004; Pannuzzo et al, 2014). Investigations of the interactions between anionic PIP2 lipids and syntaxin were found to drastically depend on Ca 2+ .…”

Section: Importance Of Protein-lipid Interactions For Membrane Fusionmentioning

confidence: 99%

The Multifaceted Role of SNARE Proteins in Membrane Fusion

2017

View full text Add to dashboard Cite

Membrane fusion is a key process in all living organisms that contributes to a variety of biological processes including viral infection, cell fertilization, as well as intracellular transport, and neurotransmitter release. In particular, the various membrane-enclosed compartments in eukaryotic cells need to exchange their contents and communicate across membranes. Efficient and controllable fusion of biological membranes is known to be driven by cooperative action of SNARE proteins, which constitute the central components of the eukaryotic fusion machinery responsible for fusion of synaptic vesicles with the plasma membrane. During exocytosis, vesicle-associated v-SNARE (synaptobrevin) and target cell-associated t-SNAREs (syntaxin and SNAP-25) assemble into a core trans-SNARE complex. This complex plays a versatile role at various stages of exocytosis ranging from the priming to fusion pore formation and expansion, finally resulting in the release or exchange of the vesicle content. This review summarizes current knowledge on the intricate molecular mechanisms underlying exocytosis triggered and catalyzed by SNARE proteins. Particular attention is given to the function of the peptidic SNARE membrane anchors and the role of SNARE-lipid interactions in fusion. Moreover, the regulatory mechanisms by synaptic auxiliary proteins in SNARE-driven membrane fusion are briefly outlined.

show abstract

“…In 2003, Marrink and coworkers developed the coarse‐grained MARTINI force field to model the lipid bilayer explicitly . MARTINI has since been extended to proteins, and was used extensively to study events of the membrane bilayer such as raft formation (reviewed by Bennett & Tieleman), membrane fusion, and supramolecular assemblies in the membrane (like oligomerization of GPCRs). Coarse‐grained simulations are very useful for investigating large‐scale systems with MD, especially in the lipid bilayer, such as drug delivery using nanotubes or fullerenes .…”

Section: Going To Three Dimensionsmentioning

confidence: 99%

Computational modeling of membrane proteins

Leman

Ulmschneider²,

Gray³

2014

Proteins

View full text Add to dashboard Cite

The determination of membrane protein (MP) structures has always trailed that of soluble proteins due to difficulties in their overexpression, reconstitution into membrane mimetics, and subsequent structure determination. The percentage of MP structures in the protein databank (PDB) has been at a constant 1-2% for the last decade. In contrast, over half of all drugs target MPs, only highlighting how little we understand about drug-specific effects in the human body. To reduce this gap, researchers have attempted to predict structural features of MPs even before the first structure was experimentally elucidated. In this review, we present current computational methods to predict MP structure, starting with secondary structure prediction, prediction of trans-membrane spans, and topology. Even though these methods generate reliable predictions, challenges such as predicting kinks or precise beginnings and ends of secondary structure elements are still waiting to be addressed. We describe recent developments in the prediction of 3D structures of both α-helical MPs as well as β-barrels using comparative modeling techniques, de novo methods, and molecular dynamics (MD) simulations. The increase of MP structures has (1) facilitated comparative modeling due to availability of more and better templates, and (2) improved the statistics for knowledge-based scoring functions. Moreover, de novo methods have benefitted from the use of correlated mutations as restraints. Finally, we outline current advances that will likely shape the field in the forthcoming decade.

show abstract

Simulation of polyethylene glycol and calcium-mediated membrane fusion

Cited by 48 publications

References 37 publications

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

The Multifaceted Role of SNARE Proteins in Membrane Fusion

Computational modeling of membrane proteins

Contact Info

Product

Resources

About