Fibronectin module FNIII9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FNIII9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (?1e), FN III9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FNIII9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FNIII9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved

Thermodynamics and Structural Characterization of BAR domain dimerization from MD simulations

Protein-protein interactions are essential steps in nearly all biological processes. The BAR domain proteins are a large family that interact with one another in solution and on the membrane to help drive membrane remodeling. Here the binding thermodynamics of homodimerization between the Lsp1 BAR domain proteins in solution, is studied using MD simulations. By combining coarse-grained protein models with enhanced sampling through metadynamics, we are able to construct a free-energy surface describing the bound vs unbound states along multiple collective variables. From these surfaces, the KD values are computed as well as the relative entropic and enthalpic contributions. In addition, the results are verified to be robust under variations to the parameter selections in the metadynamics approach. The stuctural intermediates encountered during the binding process are also characterized. With these results, a rich and quantitative perspective on the binding thermodynamics of moderately strong protein-protein interactions is provided, that is representative of a wide range of protein contacts that are critical for cell biology

Membrane models for molecular simulations of peripheral membrane proteins

Peripheral membrane proteins (PMPs) bind temporarily to the surface of biological membranes. They also exist in a soluble form and their tertiary structure is often known. Yet, their membrane-bound form and their interfacial-binding site with membrane lipids remain difficult to observe directly. Their binding and unbinding mechanism, the conformational changes of the PMPs and their influence on the membrane structure are notoriously challenging to study experimentally. Molecular dynamics simulations are particularly useful to fill some knowledge-gaps and provide hypothesis that can be experimentally challenged to further our understanding of PMP-membrane recognition. Because of the time-scales of PMP-membrane binding events and the computational costs associated with molecular dynamics simulations, membrane models at different levels of resolution are used and often combined in multiscale simulation strategies. We here review membrane models belonging to three classes: atomistic, coarse-grained and implicit. Differences between models are rooted in the underlying theories and the reference data they are parameterized against. The choice of membrane model should therefore not only be guided by its computational efficiency. The range of applications of each model is discussed and illustrated using examples from the literature.publishedVersio

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 ms provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified th

Visualizing Biological Membrane Organization and Dynamics

International audienc

Computational investigations of protein dynamics and its implication in cellular functions: two cases on membrane sculpting by protein complexes and molecular origin of Parkinson's disease

Proteins are complex machineries dedicated to drive many functions in eukaryotic cells. In this article, two cases of protein dynamics and their implications to cellular functions are discussed with computational approaches: membrane sculpting by F-BAR domains and transient β-hairpin structure in α-synuclein. Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called “scaffolding” mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domain’s 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. The molecular dynamics study others, thereby, both a large-scale picture of membrane sculpting by F-BAR domain lattices as well as atomic-level dynamic information about the involvement of the individual F-BAR domain and its interactions with partner F-BAR domains and membrane in the sculpting process. Parkinson’s disease is a common neurodegenerative disorder that originates from the intrinsically disordered peptide α-synuclein aggregating into fibrils. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 150 μs in aggregated time) using a hybrid-resolution model, PACE, to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts and 3J(HNHCα )-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-Amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.Ope

Functional characterization of the inverse FBAR-containing proteins srGAP1 and Carom

The Slit-Robo GTPase activating protein family (srGAPs) consists of four members and are important multi-domain adaptor proteins, which are involved in axonal pathfinding and various other neuronal processes. This thesis explores the function of the human srGAP1 protein as well as its zebrafish homolog in three ways: 1) examining of the membrane deforming activity of the FBAR domain, 2) analysing the specific activity of the srGAP1 GAP domain towards three members of RhoGTPases, and 3) identifying potential novel interaction partners for the srGAP1 protein with the intention to determine new pathway involvements for the protein. The work presented in this thesis shows that the srGAP1 FBAR domain can induce vesicle deformation in vesicle-based in vitro assays. Compared to the results of another FBAR domain-containing protein, the Carom protein, the srGAP1 FBAR domain is less potent in inducing invaginations of giant unilamellar vesicles. Both proteins do not induce formation of tubules as seen for classical FBAR domains, but lead to invaginations of the vesicles. Based on these results both proteins can be assigned to the recently found inverse FBAR subfamily. This work also measures the intrinsic GTP hydrolysis accelerating activity of the srGAP1 GAP domain with different NMR approaches. A comparison of the srGAP1 GAP domains of human and zebrafish showed species-specific interaction with Cdc42. Cross-interactions between the GAP domains and Cdc42 from different organism, namely human and zebrafish, was observed to a low extent. Finally, this work identifies possible new interaction partners for the srGAP1 protein with mass spectrometry analysis, which indicate that the srGAP1 protein might have a more complex and diverse role than assumed so far