Autonomic Regulation in Musculoskeletal Pain

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DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against “traditional” protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting), operates by comparing the topography of the protein surface when “viewed” from a vantage point inside the protein against the topography of a bound ligand when “viewed” from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers “on-the-fly” during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a “pose recapitulation” experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site). Whereas the previous version of DARC docked only one of these inhibitors to within 2 Å RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001). Collectively then, we find that the five enhancements described here – which together make up DARC 2.0 – lead to dramatically improved speed and performance relative to the original DARC method

Класифікація засобів публічного адміністрування в сфері лотереї

Лиськов М. О. Класифікація засобів публічного адміністрування в сфері лотереї / М. О. Лиськов // Актуальні проблеми держави і права : зб. наук. пр. / редкол.: В. В. Завальнюк (голов. ред.) [та ін.]. – Одеса : Видавничий дім "Гельветика", 2017. – Вип. 78. – С. 86-91.В даній науковій статті досліджено поняття "засобів публічного адміністрування в сфері лотереї", визначено їх особливості та види. Серед засобів публічного адміністрування лотерейної сфери виділено: 1) ліцензування господарської діяльності у сфері лотереї; 2) контроль та нагляд у сфері лотереї; 3) державна монополія на регулювання лотерейної сфери; 4) сертифікація грального обладнання та програмного забезпечення до нього; 5) відповідальність за порушення правил лотерейної сфери.Класификация средств публичного администрирования в сфере лотереи. В данной научной статье исследовано понятие "средств публичного администрирования в сфере лотереи", определены их особенности и виды. Среди средств публичного администрирования лотерейной сферы выделено: 1) лицензирование хозяйственной деятельности в сфере лотереи; 2) контроль и надзор в сфере лотереи; 3) государственная монополия на регулирование лотерейной сферы; 4) сертификация игрового оборудования и программного обеспечения к нему; 5) ответственность за нарушение правил лотерейной сферы.Classification of public administration in the field of lotteries. In this scientific article the term „means of public administration in the area of lotteries“, defined by their features and types. Among the means of public administration lottery areas highlighted: 1) licensing of economic activities in the lottery; 2) control and supervision in the lottery; 3) state monopoly on the regulation of lottery areas; 4) certification of gambling equipment and software to it; 5) liability for violation of lottery sector

Minihepcidins are rationally designed small peptides that mimic hepcidin activity in mice and may be useful for the treatment of iron overload

Iron overload is the hallmark of hereditary hemochromatosis and a complication of iron-loading anemias such as β-thalassemia. Treatment can be burdensome and have significant side effects, and new therapeutic options are needed. Iron overload in hereditary hemochromatosis and β-thalassemia intermedia is caused by hepcidin deficiency. Although transgenic hepcidin replacement in mouse models of these diseases prevents iron overload or decreases its potential toxicity, natural hepcidin is prohibitively expensive for human application and has unfavorable pharmacologic properties. Here, we report the rational design of hepcidin agonists based on the mutagenesis of hepcidin and the hepcidin-binding region of ferroportin and computer modeling of their docking. We identified specific hydrophobic/aromatic residues required for hepcidin-ferroportin binding and obtained evidence in vitro that a thiol-disulfide interaction between ferroportin C326 and the hepcidin disulfide cage may stabilize binding. Guided by this model, we showed that 7–9 N-terminal amino acids of hepcidin, including a single thiol cysteine, comprised the minimal structure that retained hepcidin activity, as shown by the induction of ferroportin degradation in reporter cells. Further modifications to increase resistance to proteolysis and oral bioavailability yielded minihepcidins that, after parenteral or oral administration to mice, lowered serum iron levels comparably to those after parenteral native hepcidin. Moreover, liver iron concentrations were lower in mice chronically treated with minihepcidins than those in mice treated with solvent alone. Minihepcidins may be useful for the treatment of iron overload disorders

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

Bryan S. Der, Ron Jacak, Brian Kuhlman, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, Andrew D. Ellington , Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas, United States of AmericaChristien Kluwe, Aleksandr E. Miklos, George Georgiou, Andrew D. Ellington, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of AmericaAleksandr E. Miklos, Andrew D. Ellington , Applied Research Laboratories, University of Texas at Austin, Austin, Texas, United States of AmericaSergey Lyskov, Jeffrey J. Gray, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of AmericaBrian Kuhlman, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of AmericaReengineering protein surfaces to exhibit high net charge, referred to as “supercharging”, can improve reversibility of unfolding by preventing aggregation of partially unfolded states. Incorporation of charged side chains should be optimized while considering structural and energetic consequences, as numerous mutations and accumulation of like-charges can also destabilize the native state. A previously demonstrated approach deterministically mutates flexible polar residues (amino acids DERKNQ) with the fewest average neighboring atoms per side chain atom (AvNAPSA). Our approach uses Rosetta-based energy calculations to choose the surface mutations. Both protocols are available for use through the ROSIE web server. The automated Rosetta and AvNAPSA approaches for supercharging choose dissimilar mutations, raising an interesting division in surface charging strategy. Rosetta-supercharged variants of GFP (RscG) ranging from −11 to −61 and +7 to +58 were experimentally tested, and for comparison, we re-tested the previously developed AvNAPSA-supercharged variants of GFP (AscG) with +36 and −30 net charge. Mid-charge variants demonstrated ~3-fold improvement in refolding with retention of stability. However, as we pushed to higher net charges, expression and soluble yield decreased, indicating that net charge or mutational load may be limiting factors. Interestingly, the two different approaches resulted in GFP variants with similar refolding properties. Our results show that there are multiple sets of residues that can be mutated to successfully supercharge a protein, and combining alternative supercharge protocols with experimental testing can be an effective approach for charge-based improvement to refolding.This work was supported by the Defense Advanced Research Projects Agency (HR-0011-10-1-0052 to A.E.) and the Welch Foundation (F-1654 to A.E.), the National Institutes of Health grants GM073960 (B.K.) and R01-GM073151 (J.G. and S.L.), the Rosetta Commons (S.L.), the National Science Foundation graduate research fellowship (2009070950 to B.D.), the UNC Royster Society Pogue fellowship (B.D.), and National Institutes of Health grant T32GM008570 for the UNC Program in Molecular and Cellular Biophysics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Center for Systems and Synthetic BiologyCellular and Molecular BiologyApplied Research LaboratoriesEmail: [email protected]

Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)

The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org

Efficient enumeration of bosonic configurations with applications to the calculation of non-radiative rates

This work presents algorithms for the efficient enumeration of configuration spaces following Boltzmann-like statistics, with example applications to the calculation of non-radiative rates, and an open-source implementation. Configuration spaces are found in several areas of physics, particularly wherever there are energy levels that possess variable occupations. In bosonic systems, where there are no upper limits on the occupation of each level, enumeration of all possible configurations is an exceptionally hard problem. We look at the case where the levels need to be filled to satisfy an energy criterion, for example, a target excitation energy, which is a type of knapsack problem as found in combinatorics. We present analyses of the density of configuration spaces in arbitrary dimensions and how particular forms of kernel can be used to envelope the important regions. In this way, we arrive at three new algorithms for enumeration of such spaces that are several orders of magnitude more efficient than the naive brute force approach. Finally, we show how these can be applied to the particular case of internal conversion rates in a selection of molecules and discuss how a stochastic approach can, in principle, reduce the computational complexity to polynomial time

Study of oxygen-ion conductivity and luminescence in the ZrO2-Nd2O3 system : impact of local heterogeneity

Stabilized fluorites and pyrochlores with different types of substitution in the (Nd2O3 ? ZrO2 system (NdZrO)) have been studied by Raman spectroscopy, X-ray diffraction, and impedance spectroscopy methods. Ionic and proton conductivity maps for 9 compositions in the NdZrO system are presented. Oxygen partial pressure measurements show a typical ionic conductor behavior, with a significantly increase of conductivity for (Nd2?xZrx)Zr2O7+x/2 (x = 1.27) fluorite and (Nd2?xZrx)Zr2O7+x/2 (x = 0.4, 0.2) pyrochlores. For the same compositions the strong luminescence was observed. Strong luminescence and high oxygenion conductivity of these solid solutions can be associated with the presence of phases with the different degree of structural disorder (tetragonal phase, fluorite) in local nanodomains in fluorite or pyrochlore matrix in the ZrO2 ? Nd2Zr2O7 region. Really, Raman spectra of (Nd2?xZrx)Zr2O7+x/2 (x = 0.5 ? 0.2) solid solutions demonstrated the fluorite + pyrochlore structural type in the short-range order. Fluorite nanodomains in pyrochlore matrix (ZrO2 ? Nd2Zr2O7 region) resulting from an order?disorder transition can only be detected at a radiation wavelength comparable to the fluorite nanodomain size. Thus, using Raman spectroscopy the broad isomorphism range in the ZrO2 ? Nd2Zr2O7 system has been shown to be nonuniform.371C-9F16-EBDE | Eduarda GomesN/