Signal transduction across cellular membranes can be mediated by coupling of the clustering of anchored proteins in both leaflets

Effects of protein crowding on membrane systems

Cellular membranes are typically decorated with a plethora of embedded and adsorbed macromolecules, e.g. proteins, that participate in numerous vital processes. With typical surface densities of 30,000 proteins per μm(2) cellular membranes are indeed crowded places that leave only few nanometers of private space for individual proteins. Here, we review recent advances in our understanding of protein crowding in membrane systems. We first give a brief overview on state-of-the-art approaches in experiment and simulation that are frequently used to study crowded membranes. After that, we review how crowding can affect diffusive transport of proteins and lipids in membrane systems. Next, we discuss lipid and protein sorting in crowded membrane systems, including effects like protein cluster formation, phase segregation, and lipid droplet formation. Subsequently, we highlight recent progress in uncovering crowding-induced conformational changes of membranes, e.g. membrane budding and vesicle formation. Finally, we give a short outlook on potential future developments in the field of crowded membrane systems. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

Nanodomain Formation of Ganglioside GM1 in Lipid Membrane: Effects of Cholera Toxin-Mediated Cross-Linking

Cross-linking of specific lipid components by proteins mediates transmembrane signaling and material transport. In this work, we conducted coarse-grained simulation to investigate the interactions of binding units of chorela toxin (CTB) with mixed ganglioside GM1 and dipalmitoylphosphatidylcholine (DPPC) lipid bilayer membrane. We determine that the binding of CTB pentamers cross-links GM1 molecules into protein-sized nanodomains that have distinct lipid order compared with the bulk. The toxin in the nanodomain partially penetrates into the membrane. The local disordering can also transmit across the membrane via lipid coupling. Comparison simulations on CTB binding to a membrane that is composed of various lipid components demonstrate that several factors are responsible for the nanodomain formation: (a) the negatively charged headgroup of a GM1 receptor is responsible for the multivalent binding; (b) the head groups being full of hydrogen-bonding donors and receptors stabilize the GM1 cluster itself and ensure the toxin binding with high affinity; and

Membrane monolayer protrusion mediates a new nanoparticle wrapping pathway

Understanding how nanoparticles (NPs) interact with the lipid membrane is of importance for their potential applications in biomedicine and cytotoxic effects. In this paper, with the aid of computer simulation techniques, we report that NPs can be wrapped by lipid membranes in a pathway different from the conventional endocytic pathway. Our simulation results show that under the conditions of strong NP-membrane adhesion and low membrane tension, NPs can be wrapped by membranes with a pathway regulated by membrane monolayer protrusion. We also find that in the monolayer protrusion mediated wrapping pathway NPs are first trapped in the membrane and the subsequent NP internalization can be achieved by several means, including decreasing the membrane tension, breaking the membrane symmetry between upper and lower leaflets, and exerting an external force on the NPs. The findings from our simulations are well supported by the free energy analysis.

Molecular modeling of membrane tube pearling and the effect of nanoparticle adsorption

DPD simulations suggest that the membrane tube pearling can be regulated by the inner water pressure and NP adsorption.

The role of shape complementarity in the protein-protein interactions

We use a dissipative particle dynamic simulation to investigate the effects of shape complementarity on the protein-protein interactions. By monitoring different kinds of protein shape-complementarity modes, we gave a clear mechanism to reveal the role of the shape complementarity in the protein-protein interactions, i.e., when the two proteins with shape complementarity approach each other, the conformation of lipid chains between two proteins would be restricted significantly. The lipid molecules tend to leave the gap formed by two proteins to maximize the configuration entropy, and therefore yield an effective entropy-induced protein-protein attraction, which enhances the protein aggregation. In short, this work provides an insight into understanding the importance of the shape complementarity in the protein-protein interactions especially for protein aggregation and antibody-antigen complexes. Definitely, the shape complementarity is the third key factor affecting protein aggregation and complex, besides the electrostatic-complementarity and hydrophobic complementarity.

An unusual pathway for the membrane wrapping of rodlike nanoparticles and the orientation- and membrane wrapping-dependent nanoparticle interaction

Although rapid progress has been made in understanding the interaction of nanoparticles (NPs) with lipid membrane, little is known about the interaction between neighboring NPs on the membrane. With the aid of computer simulation techniques, in this work we systematically investigate the membrane mediated interaction between anisotropic NPs with at least one dimension with the size of several nanometers, and find that the interaction between neighboring NPs is orientation- and membrane wrapping-dependent. For rodlike NPs with a weak NP-membrane adhesion strength that the membrane wrapping of NPs occurs at a slow rate and has a limited extent, the orientation-dependent interaction between two neighboring anisotropic NPs arises purely as a result of non-homogeneous distribution of membrane curvature induced by anisotropic NP adsorption. While for rodlike NPs with a strong NP-membrane adhesion, the rapid wrapping rate and extensive wrapping cause the different responses of upper and lower leaflets of the membrane to the NP adsorption, which force the NPs to enter the hydrophobic part of the membrane and lead to the formation of inverted micelles surrounding the NPs. The unusual asymmetrical wrapping also induces orientation-dependent NP interaction, which shows a short-range repulsion, intermediate-range attraction and long-range repulsion for rodlike NPs.