Molecular simulations and visualization: introduction and overview

Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building

The Eighth Central European Conference "Chemistry towards Biology": snapshot

The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on 28 August – 1 September 2016The Eighth Central European Conference "Chemistry towards Biology" was held in Brno, Czech Republic, on 28 August-1 September 2016 to bring together experts in biology, chemistry and design of bioactive compounds; promote the exchange of scientific results, methods and ideas; and encourage cooperation between researchers from all over the world. The topics of the conference covered "Chemistry towards Biology", meaning that the event welcomed chemists working on biology-related problems, biologists using chemical methods, and students and other researchers of the respective areas that fall within the common scope of chemistry and biology. The authors of this manuscript are plenary speakers and other participants of the symposium and members of their research teams. The following summary highlights the major points/topics of the meeting

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Applications of nuclear magnetic resonance spectroscopy: from drug discovery to protein structure and dynamics.

The versatility of nuclear magnetic resonance (NMR) spectroscopy is apparent when presented with diverse applications to which it can contribute. Here, NMR is used i) as a screening/ validation tool for a drug discovery program targeting the Phosphatase of Regenerating Liver 3 (PRL3), ii) to characterize the conformational heterogeneity of p53 regulator, Murine Double Minute X (MDMX), and iii) to characterize the solution dynamics of guanosine monophosphate kinase (GMPK). Mounting evidence suggesting roles for PRL3 in oncogenesis and metastasis has catapulted it into prominence as a cancer drug target. Yet, despite significant efforts, there are no PRL3 small molecule inhibitors currently in clinical trials. This work combines screening of an FDA-approved drug panel and the identification of binders by protein-observed NMR. FDA-approved drugs salirasib and candesartan were identified as potent inhibitors in in vitro inhibition and migration assays while a weak inhibitor, olsalazine, was identified by NMR as the first small molecule inhibitor to directly bind PRL3. NMR was also used to validate the binding of additional compounds identified as experimental PRL3 inhibitors. Thienopyridone, a potent experimental inhibitor, did not show direct binding to PRL3 but instead inhibited phosphatase activity via redox mechanism. NMR also revealed that other experimental inhibitors did not engage PRL3. Thus, there remains a need to identify potent PRL3-directed inhibitors. Meanwhile, molecular modeling revealed a putative druggable site that has not been thoroughly explored before. The current study provides some scaffolds such as candesartan and particularly, olsalazine, the only binder identified, that could be the starting point of further drug discovery efforts, as well as a putative site that can be targeted in silico. MDMX, a negative regulator of p53, is another important therapeutic target in cancer, along with the homologous protein, MDM2. Inhibitors that block the MDM2-p53 interaction have been identified and despite similarities in the binding site of these homologous proteins, these inhibitors are ineffective against MDMX. It is hypothesized that the flexibility of MDMX contributes to this significant difference in response to inhibitors, despite comparable affinity to their endogenous target, p53. Examination of available inhibitor-bound structures of MDMX reveal a conserved pharmacophore but the structures adopt distinct conformations away from the binding site. This implies that global motions of the protein might contribute to molecular recognition. The conformational heterogeneity in MDMX was further confirmed by collecting residual dipolar couplings (RDCs). Further investigations on both MDMX and MDM2 are necessary to uncover whether the flexibility of MDMX contributes to the differential binding to inhibitors. Finally, NMR relaxation methods and state-of-the-art high-power Carr-Purcell-Meiboom Gill (CPMG) relaxation dispersion measurements, the first documented application on an enzyme, were used to characterize the solution dynamics of GMPK and the changes in dynamics upon GMP binding. Substrate binding resulted in restricting the amplitudes of motion for backbone amide bonds within the picosecond-nanosecond timescale. Meanwhile, CPMG showed dispersion in both in the absence and presence of GMP, such that substrate binding did not quench dynamics within the microsecond-millisecond timescale. Interestingly, more residues are observed to have dispersion in the bound form, some near the C-terminal of helix 3, which has previously been proposed to be involved in product release. Current studies show that substrate binding affect different timescales of protein motion. Future work shall follow how motions within different timescales are affected as GMPK processes its substrates – such as, for instance, binding of ATP analogs within the ATP binding site or simultaneous occupancy of both substrate binding pockets. This paves the way for a complete picture of the relationship of function and dynamics in the conformational enzymatic cycle of a bi-substrate enzyme using GMPK as a model. The current work illustrates some of the diverse applications of NMR on three unique systems that are also drug targets. Information collected here can be leveraged on future structure and dynamics studies as well as drug discovery efforts targeting any of these proteins

Uncertainty quantification in classical molecular dynamics

Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach has begun to advance from being a computer-based means of rationalizing experimental observations to producing apparently credible predictions for a number of real-world applications within industrial sectors such as advanced materials and drug discovery. However, key aspects concerning the reproducibility of the method have not kept pace with the speed of its uptake in the scientific community. Here, we present a discussion of uncertainty quantification for molecular dynamics simulation designed to endow the method with better error estimates that will enable it to be used to report actionable results. The approach adopted is a standard one in the field of uncertainty quantification, namely using ensemble methods, in which a sufficiently large number of replicas are run concurrently, from which reliable statistics can be extracted. Indeed, because molecular dynamics is intrinsically chaotic, the need to use ensemble methods is fundamental and holds regardless of the duration of the simulations performed. We discuss the approach and illustrate it in a range of applications from materials science to ligand-protein binding free energy estimation. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'

Molecular Dynamics Simulations of the Bacterial Outer Membrane Channels TolC and OprM & dxTuber, a Biomolecular Cavity Detection Tool based on Protein and Solvent Dynamics

The multidrug resistance of bacteria is a serious phenomenon in current medical treatment. Beginning with the introduction of antibiotics more and more bacterial strains achieved resistance against these chemical compounds and over the years a competition between antibiotic drug discovery and bacterial drug resistance arose. The well studied Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa serve in this work as a model organisms for bacterial resistance against antibiotics. Both bacteria evolved multidrug resistant strains through several strategies, including the expelling of harming compounds through efflux systems. The over expression of these efflux systems in the bacterial membranes are responsible for resistance against many antibiotic compounds. The AcrA/B-TolC efflux system induces resistance of E.coli against a broad range of antibiotics. Ranging from the inner membrane towards the outer membrane, the efflux system spans the entire periplasmic space. The system consists of the inner membrane transporter AcrB, the membrane fusion protein AcrA and the outer membrane channel TolC. TolC itself cooperates with several inner membrane transporters and facilitates the export of harming compounds across the outer membrane. Due to this versatility TolC could become a target of drug treatment. A disabled or blocked TolC could prevent drug extrusion via systems that use TolC as an exit gate. At the time of writing the gating functionality of TolC is not known in detail. To gain insights into TolC functionality two series of unbiased molecular dynamics (MD) simulations were performed. Whereas the first series was carried out in absence of AcrB the second one was executed in presence of the AcrB docking domain (AcrB-DD). For the first series unbiased MD simulations between 150-300 ns in a Palmitoyloleoylphosphatidylethanolamine (POPE) / NaCl / water environment were calculated. In most of these simulations TolC opens and closes freely on extracellular side hinting at the absence of a gating functionality on this side. On periplasmic side a double aspartate ring restricts substrate passage in all simulations and grasping-like motions were noticed for the tip loops of helix 7 & 8. A consecutive binding of two sodium ions inside the lower periplasmic part of TolC occured in one simulation, which induced a stabilized closed state on periplasmic side. TolC remained closed on periplasmic side unless all ions were removed from the simulation box indicating a sodium dependent lock on this side. For the second series of MD simulations we added the AcrB-DD to the previously described system setup based on orientations of a previously published data driven modeled structure. Four unbiased 150 ns MD simulations were calculated and in one of these simulations the docking domain spontaneously docks onto TolC. The latter simulation was extended to a simulation time of 1.05 μs resulting in a tighter binding between AcrB and TolC with regards to the modeled structure. A preferred open conformation on extracellular hints analogue to TolC only simulations at the absence of a lock on extracellular side. On the AcrB-facing side TolC's tip loops located at helix 7 & 8 opened up and were stabilized by the AcrB docking domain. However, the double aspartate ring remained closed until the end of the simulation, meaning that either the simulation time is too short to observe an opening of TolC or that another part of the AcrA/B-TolC efflux system is missing to open TolC. In Pseudomonas aeruginosa OprM had been identified as a TolC homologue protein. OprM is part of the multidrug efflux system MexA/B-OprM and acts as an exit duct for several inner membrane transporters. Also for OprM the gating mechanisms are not known in detail at time of writing. To explore OprM's gating mechanisms it has been simulated in a POPE / NaCl / water environment. During all five 200 ns long MD simulations OprM opens and closes freely on extracellular side suggesting also for OprM the absence of a gating mechanism on extracellular side. The tip loops of helix 7 & 8 on periplasmic side open up in a way comparable to TolC simulations and in contrast to TolC no closing motions were noticed for these helices for OprM. In OprM a single aspartate ring limits substrate passage on the inner membrane facing side of OprM. In contrast to TolC simulations a slight opening of this aspartate ring was measured in all five simulations. The absence of heightened sodium densities near the periplasmic entrance regions could mean that either longer simulation time is needed to observe a sodium induced closure of OprM or that the periplasmic access is regulated only by the aspartate ring. Despite the absence of heightened sodium densities in the aspartate ring region, clear peaks of high sodium densities identified sodium pockets between the equatorial region and the aspartate ring region formed by Asp171 and Asp230. Voids inside of proteins can indicate substrate binding sites, ion pockets, pathways through channel proteins, their open and closed states and active sites. Over the years numerous cavity detection tools have been introduced to identify and highlight these voids. All available cavity detection tools were based on static structures and present cavities for single protein conformations only. With dxTuber we developed and introduced a novel cavity detection tool based on an ensemble of protein conformations. It uses averaged protein and solvent density maps, which are derived from MD trajectories, as input. With this technique protein dynamics are taken into account and cavities are detected through the separation of protein external solvent from protein internal solvent. Protein internal solvent can be grouped into cavities and stored in the commonly used PDB file format. Individual cavities can be separated via the atom name field of the PDB file format. dxTuber itself can calculate cavity volume and the cross-sectional area of a single cavity along a principle axis. For convenience a graphical user interface (GUI) and a command line interface (CLI) of dxTuber are released under the GPL v2

The Global Benefits of Open Research

The 2018 MPDI Writing Prize invited early stage researchers who are not native English speakers to write on the subject of "the global benefits of open research". Six prizes were awarded, however there were many more entries. This book collates many of those entries and contains inspiring, thought-provoking and original viewpoints of open science through the eyes of those conducting research on a daily basi