The traditional computational modeling of protein structure, dynamics, and interactions remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation time scales that are still too large to be studied in atomistic detail. Lowering the level of protein representation from all-atom to coarse-grained opens up new possibilities for studying protein systems. In this review we provide an overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions. A more detailed description is given for applications of coarse-grained models suitable for efficient combinations with all-atom simulations in multiscale modeling strategies.

Single-molecule force spectroscopy (SMFS) is a powerful tool to dissect molecular interactions that govern the stability and function of proteins. We applied SMFS to understand the effect of Zn 2؉ on the molecular interactions underlying the structure of rhodopsin. Force-distance curves obtained from SMFS assays revealed the strength and location of molecular interactions that stabilize structural segments within this receptor. The inclusion of ZnCl 2 in SMFS assay buffer increased the stability of most structural segments. This effect was not mimicked by CaCl 2 , CdCl 2 , or CoCl 2 . Thus, Zn 2؉ stabilizes the structure of rhodopsin in a specific manner.Zinc is the second most abundant trace element found in the human body (1) and occurs in high concentrations in the retina (2). Zinc deficiency in humans can lead to vision-related disorders such as poor dark adaptation, night blindness, and retinal degeneration (3). The role of Zn 2ϩ in vision is likely related, in part, to rhodopsin, the light receptor that initiates phototransduction in the rod outer segments (ROS) 5 of retinal photoreceptor cells (4). Rhodopsin can directly associate with this bivalent metal ion (5, 6), and Zn 2ϩ increases the level of rhodopsin phosphorylation (7). Furthermore, changes are observed in the pattern of thermal bleaching and regeneration of rhodopsin by 11-cis-retinal in the presence and absence of Zn 2ϩ (6,8). Therefore, Zn 2ϩ appears to affect the structure and function of rhodopsin.Rhodopsin in native ROS disc membranes has been previously characterized by single-molecule force spectroscopy (SMFS) to reveal the molecular interactions that stabilize the dark state of the receptor (9). The receptor is organized into several stable structural segments that present barriers to unfolding. Forces required to unfold these segments provide a direct measure of the molecular interactions stabilizing the protein in a particular region. SMFS has also been used to characterize the molecular interactions underlying the stability of a few other membrane proteins including bacteriorhodopsin and halorhodopsin from Halobacterium salinarium (10, 11), the sodium/proton antiporter NhaA from Escherichia coli (12), and human aquaporin-1 (13). The sensitivity of SMFS assays enables one to probe the effects of environmental factors like temperature, pH, ion concentration, and oligomeric assembly on the molecular interactions stabilizing a protein (12, 14 -16).In the current study, we use SMFS to monitor the effect of Zn 2ϩ on molecular interactions stabilizing dark-state rhodopsin. Force-distance (F-D) curves obtained from native bovine ROS disc membranes in the presence of Zn 2ϩ revealed that the location of stable structural segments in rhodopsin is unaffected by the inclusion of this bivalent metal ion. However, forces required to unfold these segments in the presence of Zn 2ϩ were significantly increased. Thus, Zn 2ϩ appears to strengthen the molecular interactions that stabilize the native structure of rhodopsin. EXPERIMENTAL PROCEDURESROS Disc...

The γ-secretase complex has a decisive role in the development of Alzheimer's disease, in that it cleaves a precursor to create the amyloid β peptide whose aggregates form the senile plaques encountered in the brains of patients. Γ-secretase is a member of the intramembrane-cleaving proteases which process their transmembrane substrates within the bilayer. Many of the mutations encountered in early onset familial Alzheimer's disease are linked to presenilin 1, the catalytic component of γ-secretase, whose active form requires its endoproteolytic cleavage into N-terminal and C-terminal fragments. Although there is general agreement regarding the topology of the N-terminal fragment, studies of the C-terminal fragment have yielded ambiguous and contradictory results that may be difficult to reconcile in the absence of structural information. Here we present the first structure of the C-terminal fragment of human presenilin 1, as obtained from NMR studies in SDS micelles. The structure reveals a topology where the membrane is likely traversed three times in accordance with the more generally accepted nine transmembrane domain model of presenilin 1, but contains unique structural features adapted to accommodate the unusual intramembrane catalysis. These include a putative half-membrane-spanning helix N-terminally harboring the catalytic aspartate, a severely kinked helical structure toward the C terminus as well as a soluble helix in the assumed-to-be unstructured N-terminal loop.cell-free protein expression | gamma secretase | intramembrane proteolysis | membrane protein structure A lzheimer's disease is the most common form of dementia and affects more than 25 million people worldwide. The most characteristic histological feature of Alzheimer's disease is the presence of long, insoluble amyloid fibrils composed of amyloid β (Aβ) peptide which, either alone or as reservoirs for soluble Aβ oligomers (1, 2), appear to be the primary species responsible for the massive neuronal injury presented in patients. Aβ generation is categorized under an unusual physiological phenomenon termed regulated intramembrane proteolysis. Here, the amyloid precursor protein first sheds its ectodomain mediated by β-secretase. The remaining membrane-bound C-terminal fragment is subsequently processed at a γ-cleavage site by the γ-secretase complex, a multisubunit protease whose minimal essential components include presenilin 1 (PS1) or presenilin-2 (PS2), anterior pharynx-defective, nicastrin, and presenilin enhancer 2 (3). The pathological relevance of this final step lies in the observation that γ-cleavage is variable and can occur after three distinct positions, 38, 40, and 42, whose selection influences the self-aggregating potential of the secreted Aβ peptide. Aβ42, although the minor species, appears to show the strongest potency for oligomerization and represents the majority of Aβ in amyloid plaques (4). Over 150 familial Alzheimer's disease associated mutations (www.molgen.ua.ac.be/ADMutations) have been linked to PS1, the catalyt...

Bacteriorhodopsin (bR) is a membrane protein found in the archae Halobacterium salinarum. Here, we studied wild type bR and especially the triple mutant bR, 3Glu [E9Q/E194Q/E204Q], in combination with wide gap semiconductor TiO2 for their suitability as efficient light harvester in solar cell. Our differential scanning calorimetry data show thermal robustness of bR wild type and 3Glu mutant, which make them good candidates as photosensitizer in solar cells. Molecular modeling indicates that binding of bR to the exposed oxygen atoms of anatase TiO2 is favorable for electron transfer and directed by local, small distance interactions. A solar cell, based on bR wild type and bR triple mutant immobilized on nanocrystalline TiO2 film was successfully constructed. The photocurrent density-photo voltage (J-V) characteristics of bio-sensitized solar cell (BSSC), based on the wild type bR and 3Glu mutant adsorbed on nanocrystalline TiO2 film electrode were measured. The results show that the 3Glu mutant displays better photoelectric performance compared to the wild type bR, giving a short-circuit photocurrent density (J(sc)) of 0.09 mA/cm2 and the open-circuit photovoltage (V(oc)) 0.35 V, under an illumination intensity of 40 mW/cm2.

Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein-peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead.

G-protein-coupled receptors (GPCRs) are important targets for treating severe diseases. However why certain molecules act as activators whereas others, with similar structures, block GPCR activation, is poorly understood since the same molecule can activate one receptor subtype while blocking another closely related receptor. To shed light on these central questions, we used all-atom, long-time-scale molecular dynamics simulations on the κ-opioid and μ-opioid receptors (κOR and μOR). We found that water molecules penetrating into the receptor interior mediate the activating versus blocking effects of a particular ligand-receptor interaction. Both the size and the flexibility of the bound ligand regulated water influx into the receptor. The solvent-accessible inner surface area was found to be a parameter that can help predict the function of the bound ligand.

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs.

The presence of disulfide bonds affects the protein stability and therefore tendency to misfold and form amyloid‐like fibrils. Insulin's three disulfide bridges stabilize the native state and prevent aggregation. Partial proteolysis of insulin releases highly amyloidogenic and inherently disordered two‐chain ‘H‐fragment’ retaining insulin's Cys7A‐Cys7B and Cys6A‐Cys11A disulfide bonds. The abrupt self‐association of H‐fragment monomers into fibrils is suppressed in the presence of disulfide‐reducing agent. These circumstances make the H‐fragment an interesting model to study the impact of disulfide bonds on amyloidogenesis beyond the ‘stabilization‐of‐the‐native‐state’ paradigm. Here, we investigate fibrillization of various synthetic peptides derived from the H‐fragment through modifications of Cys7A‐Cys7B/Cys6A‐Cys11A bonds. In comparison to H‐fragment, aggregation of a two‐chain ‘AB’ analog lacking Cys6A‐Cys11A bond is decelerated, while the alternative removal of Cys7A‐Cys7B bond releases a non‐aggregating B‐chain and a highly amyloidogenic ‘ACC’ fragment containing the intrachain Cys6A‐Cys11A bond. Our analysis, supported by calculations of configurational entropy, suggests that Cys6A‐Cys11A bond is a key factor behind the explosive self‐association of H‐fragment. The bond restricts the conformational space probed by nucleating monomers which is reflected by an approximately 2.4 kJ·mol−1 K−1 decrease in entropy. The fact that the intact Cys6A‐Cys11A bond promotes fibrillization of the H‐fragment is remarkable in light of the previously established role of the same disulfide bond in preventing formation of insulin fibrils. Our results imply that a single disulfide bond within a folded protein and its fragment may play entirely different roles in aggregation and that this role may evolve with progressing phases of misfolding.