Protein misfolding and subsequent self-association are complex, intertwined processes, resulting in development of a heterogeneous population of aggregates closely related to many chronic pathological conditions including Type 2 Diabetes Mellitus and Alzheimer’s disease. To address this issue, here, we develop a theoretical model in the general framework of linear stability analysis. According to this model, self-assemblies of peptides with pronounced conformational flexibility may become, under particular conditions, unstable and spontaneously evolve toward an alternating array of partially ordered and disordered monomers. The predictions of the theory were verified by atomistic molecular dynamics (MD) simulations of islet amyloid polypeptide (IAPP) used as a paradigm of aggregation-prone polypeptides (proteins). Simulations of dimeric, tetrameric, and hexameric human-IAPP self-assemblies at physiological electrolyte concentration reveal an alternating distribution of the smallest domains (of the order of the peptide mean length) formed by partially ordered (mainly β-strands) and disordered (turns and coil) arrays. Periodicity disappears upon weakening of the inter-peptide binding, a result in line with the predictions of the theory. To further probe the general validity of our hypothesis, we extended the simulations to other peptides, the Aβ(1–40) amyloid peptide, and the ovine prion peptide as well as to other proteins (SOD1 dimer) that do not belong to the broad class of intrinsically disordered proteins. In all cases, the oligomeric aggregates show an alternate distribution of partially ordered and disordered monomers. We also carried out Surface Enhanced Raman Scattering (SERS) measurements of hIAPP as an experimental validation of both the theory and in silico simulations.

RhoBTB1 is an atypical Rho GTPase with two BTB domains in addition to its Rho domain. Although most Rho GTPases regulate actin cytoskeletal dynamics, RhoBTB1 is not known to affect cell shape or motility. We report that RhoBTB1 depletion increases prostate cancer cell invasion and induces elongation in Matrigel, a phenotype similar to that induced by depletion of ROCK1 and ROCK2. We demonstrate that RhoBTB1 associates with ROCK1 and ROCK2 and its association with ROCK1 is via its Rho domain. The Rho domain binds to the coiled-coil region of ROCK1 close to its kinase domain. We identify two amino acids within the Rho domain that alter RhoBTB1 association with ROCK1. RhoBTB1 is a substrate for ROCK1, and mutation of putative phosphorylation sites reduces its association with Cullin3, a scaffold for ubiquitin ligases. We propose that RhoBTB1 suppresses cancer cell invasion through interacting with ROCKs, which in turn regulate its association with Cullin3. Via Cullin3, RhoBTB1 has the potential to affect protein degradation.

Prions are self-replicating infectious proteinaceous agents whose conformations are capable of forming amyloid-like aggregate fibrils. Here we present molecular dynamics simulations aimed at investigating the aggregation process of the β-rich H2H3 domain of the ovine prion protein (H2H3-OvPrPSc), known to be the portion of prion protein carrying oligomerization activity.

While targeted therapy against HER2 is an effective first-line treatment in HER2+ breast cancer, acquired resistance remains a clinical challenge. The pseudokinase HER3, heterodimerisation partner of HER2, is widely implicated in the resistance to HER2-mediated therapy. Here, we show that lapatinib, an ATP-competitive inhibitor of HER2, is able to induce proliferation cooperatively with the HER3 ligand neuregulin. This counterintuitive synergy between inhibitor and growth factor depends on their ability to promote atypical HER2-HER3 heterodimerisation. By stabilising a particular HER2 conformer, lapatinib drives HER2-HER3 kinase domain heterocomplex formation. This dimer exists in a head-to-head orientation distinct from the canonical asymmetric active dimer. The associated clustering observed for these dimers predisposes to neuregulin responses, affording a proliferative outcome. Our findings provide mechanistic insights into the liabilities involved in targeting kinases with ATP-competitive inhibitors and highlight the complex role of protein conformation in acquired resistance.

Background: Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5.Results: As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling.Conclusion: Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

Membrane fusion is critical to eukaryotic cellular function and crucial to the entry of enveloped viruses such as influenza and human immunodeficiency virus. Influenza viral entry in the host cell is mediated by a 20-23 amino acid long sequence, called the fusion peptide (FP). Recently, possible structures for the fusion peptide (ranging from an inverted V shaped alpha-helical structure to an alpha-helical hairpin, or to a complete alpha-helix) and their implication in the membrane fusion initiation have been proposed. Despite the large number of studies devoted to the structure of the FP, the mechanism of action of this peptide remains unclear with several mechanisms having been suggested, including the induction of local disorder, promoting membrane curvature, and/or altering local membrane composition.In recent years, several research groups have employed atomistic and/or coarse-grained molecular dynamics (MD) simulations to investigate the matter.In all previous works, the behaviour of a single FP monomer was studied, while in this manuscript, we use a simplified model of a tripeptide (TP) monomer of FP (TFP) instead of a single FP monomer because each Influenza Hemagglutinin contains three FP molecules in the biological system. In this manuscript we report findings targeted at understanding the fusogenic properties and the collective behaviour of these trimers of FP peptides on a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine model membrane. Here we show how the TFP monomers self-assemble into differently sized oligomers in the presence of the membrane. We measure the perturbation to the structure of the phospholipid membrane caused by the presence of these TFP oligomers. Our work (i) shows how self-assembly of TFP in the presence of the membrane induces non negligible deformation to the membrane and (ii) could be a useful starting point to stimulate discussion and further work targeted to fusion pore formation.

Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND) protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

Evolution of bacteria resistant to the most diverse antibiotics is posing one of the major threats to public health. Particular alarm is raised by those genetic lines that develop phenotypes simultaneously resistant to multiple drugs. Among the different mechanisms leading to multidrug resistance, multidrug efflux pumps raise particular concern. These are large macromolecular constructs localised at cell boundaries, which are able to actively bind and transport out of the cell several chemically uncorrelated substrates. In this last decade, computer modelling has proved to be a valuable tool for the investigation of multiple drug-efflux systems at the molecular level. In particular, molecular dynamics simulations unveiled several aspects of the molecular mechanisms governing the recognition and transport of drugs by these systems. Computer-aided protocols constitute a bottom-up reductionist approach that has the privilege of obtaining clean data referring intrinsically to those single parts of the efflux process explicitly taken into account. Combining computational data to the experimental determinations may therefore help in the definition of possible general criteria limiting the action of these systems against both patented and new putative antibiotic agents. Here, we review the most relevant contributions by computational scientists to the understanding of multidrug-efflux systems in the recent past. Particular care is put in the description of the dynamical features of multidrug exporters, a valuable piece of information for which computer modelling represents one of the best investigation tools available at present.

Basic understanding of the means by which multidrug efflux systems can efficiently recognize and transport drugs constitutes a fundamental step toward development of compounds able to tackle the continuous outbreak of new bacterial strains resistant to traditional antibiotics. We applied a series of computational techniques, from molecular docking to molecular dynamics simulations and free energy estimate methods, to determine the differences in the binding properties of imipenem and meropenem, two potent antibiotics of the carbapenem family, to MexB, the RND transporter of the major efflux system of Pseudomonas aeruginosa. We identified and characterized two affinity sites in the periplasmic domain of the transporter, sharing strong similarities with the distal and proximal binding pockets identified in AcrB, the homologue of MexB in Escherichia coli. According to our results, meropenem has a higher affinity to the distal binding pocket than imipenem while both compounds are weakly bound to the proximal pocket. This different behavior is mainly due to the hydration properties of the nonpharmacophore part of the two compounds, being that of imipenem less bulky and hydrophobic. Our data provide for the first time a rationale at molecular level for the experimental evidence indicating meropenem as a compound strongly affected by MexB contrary to imipenem, which is apparently poorly transported by the same pump.

The tripartite efflux pump AcrAB-TolC is responsible for the intrinsic and acquired multidrug resistance in Escherichia coli. Its active part, the homotrimeric transporter AcrB, is in charge of the selective binding of substrates and energy transduction. The presence of several phenilalanine residues in the only binding pocket identified by X-ray has inspired an experimental work where the effects of single point Phe->Ala mutations on the MIC and on the efflux of several antibiotics have been determined [1,2]. Concerning the MICs, interestingly, the mutation F610A has been shown to significantly reduce the minimum inhibitory concentration of doxorubicin and many other substrates, although F610 does not appear to interact strongly with them or to be involved in the squeezing mechanism of the binding pocket suggested as preliminary step of the extrusion process. In this work, we assess the impact of the experimental mutations on the functionality of AcrB by means of computational techniques, using doxorubicin and minocycline as substrates. We found that for F610A the compounds slide deeply inside the binding pocket after mutation, increasing the strength of the interaction. During subsequent conformational alterations of the transporter, the substrates were either not extruded from the binding site or displaced along a direction other than the one associated with extrusion. The other mutations are not able to modify the binding affinity of the substrates, which are kept in positions similar to the ones assumed in the wild type protein. Our study indicates how subtle interactions determine the functionality of multidrug transporters, since decreased transport might not be simplistically correlated to decreased substrate binding affinity. [1] Bohnert, J. A., et al. J. Bacteriol. 2008, 190, 8225-9. [2] Bohnert, J. A.; Schuster, S.; Szymaniak-Vits, M.; Kern, W. V. PlosOne 2011, 6, e21196.

Ligand-receptor interactions are at the basis of the mediation of our physiological responses to a large variety of ligands, such as hormones, neurotransmitters and environmental stimulants, and their tuning represents the goal of a large variety of therapies. Several molecular details of these interactions are still largely unknown. In an effort to shed some light on this important issue, we performed a computational study on the interaction of two related compounds differing by a single methyl group (clozapine and desmethylclozapine) with a [Formula: see text]-opioid receptor. According to experiments, desmethylclozapine is more active than clozapine, providing a system well suited for a comparative study. We investigated stable configurations of the two drugs inside the receptor by simulating their escape routes by molecular dynamics simulations. Our results point out that the action of the compounds might be related to the spatial and temporal distribution of the affinity sites they visit during their permanency. Moreover, no particularly pronounced structural perturbations of the receptor were detected during the simulations, reinforcing the idea of a strong dynamical character of the interaction process, with an important role played by the solvent in addition.

The tripartite efflux pump AcrAB-TolC is responsible for the intrinsic and acquired multidrug resistance in Escherichia coli. Its active part, the homotrimeric transporter AcrB, is in charge of the selective binding of substrates and energy transduction. The mutation F610A has been shown to significantly reduce the minimum inhibitory concentration of doxorubicin and many other substrates, although F610 does not appear to interact strongly with them. Biochemical study of transport kinetics in AcrB is not yet possible, except for some β-lactams, and other techniques should supply this important information. Therefore, in this work, we assess the impact of the F610A mutation on the functionality of AcrB by means of computational techniques, using doxorubicin as substrate. We found that the compound slides deeply inside the binding pocket after mutation, increasing the strength of the interaction. During subsequent conformational alterations of the transporter, doxorubicin was either not extruded from the binding site or displaced along a direction other than the one associated with extrusion. Our study indicates how subtle interactions determine the functionality of multidrug transporters, since decreased transport might not be simplistically correlated to decreased substrate binding affinity.

The importance of delta-opioid receptors as target of a large number of drugs is well recognized, but the molecular details of interaction and action of the compounds are largely unknown. In an effort to shade some light on this important issue we performed an extensive computational study on the interaction of two compounds, clozapine and desmetilclozapine, with a delta-opioid receptor. According to experiments, the lacking of a single methyl group in desmetilclozapine with respect of clozapine makes the former more active than the latter, providing a system well suited for a comparative study. We investigated the escape route of the two drugs from the receptor using molecular dynamics simulations and metadynamics. Our results point out that prolonged interactions of the compounds with specific residues of the receptor do not correlate directly with their activity, having clozapine the longest interactions if compared with desmetilclozapine but being also less active. The action of the compound is related to the spatial distribution of the affinity sites it visits during its permanency. Additionally, the role of long-resident water molecules is discussed. Such information might be useful to provide hints and insights that can be exploited in more structure-and-dynamics-oriented drug design.

All-atom molecular dynamics (MD) simulations are a powerful tool to investigate the structure and function of biomolecular systems. Nonetheless, within the atomistic framework it remains computationally unaffordable to thoroughly sample size and time scales that are critical to most of the biological processes both in vitro and in vivo. Coarse-grained (CG) schemes have been introduced to overcome these limitations; nonetheless, many issues, such as the lack of universality and transferability, still afflict CG models and limit in turn their general applicability to a vast class of relevant biological problems. We introduce a reliable and robust scheme to account for the intrinsic non-radial nature of backbone-backbone interactions in CG molecular dynamics simulations of proteins. Specifically, we define a new CG potential term, which, mimicking the backbone dipole-dipole interactions, is able to naturally stabilize elementary secondary structure motifs, such as α-helices and β-sheets, and to modulate basilar transitions to super-secondary structure assemblies. Moreover, the scheme can properly describe the long-range electrostatic contributions in a multiscale MD framework, contributing to an accurate description of protein-ligand and protein-protein recognition. Thus, this novel scheme represents a promising step towards the development of a CG force field able to take into account intrinsic anisotropy of protein structures, leading to an improved description of the structural and dynamic properties of protein assemblies and networks.

Bacteria, such as E. coli, use multidrug efflux pumps to export toxic substrates through their cell membranes, including antibiotics. The RND transporter of the AcrAB-TolC efflux pump is able to export structurally and chemically different substrates via a functional rotation. The three major states of this rotation cycle were found in several asymmetric crystal structures. After initially analyzing the basic mechanisms of opening of the TolC channel [1] and of substrate extrusion by AcrB [2] separately, we have continued the analysis of the latter one.

We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This term mimics the backbone dipole-dipole interactions and accounts for the needed directionality to form stable folded secondary structure elements. We show that α-helical and β-sheet peptide chains are correctly described in dynamics without the need of introducing any a priori bias potentials or ad hoc parametrizations, which limit broader applicability of CG simulations for proteins. Moreover, our model is able to catch the formation of supersecondary structural motifs, like transitions from long single α-helices to helix-coil-helix or β-hairpin assemblies. This novel scheme requires the structural information of Cα beads only; it does not introduce any additional degrees of freedom to the system and has a general formulation, which allows it to be used in synergy with various CG protocols, leading to an improved description of the structural and dynamic properties of protein assemblies and networks.