The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) ...format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
The Atlantic meridional overturning circulation (AMOC) is a system of ocean currents that has an essential role in Earth's climate, redistributing heat and influencing the carbon cycle
. The AMOC has ...been shown to be weakening in recent years
; this decline may reflect decadal-scale variability in convection in the Labrador Sea, but short observational datasets preclude a longer-term perspective on the modern state and variability of Labrador Sea convection and the AMOC
. Here we provide several lines of palaeo-oceanographic evidence that Labrador Sea deep convection and the AMOC have been anomalously weak over the past 150 years or so (since the end of the Little Ice Age, LIA, approximately AD 1850) compared with the preceding 1,500 years. Our palaeoclimate reconstructions indicate that the transition occurred either as a predominantly abrupt shift towards the end of the LIA, or as a more gradual, continued decline over the past 150 years; this ambiguity probably arises from non-AMOC influences on the various proxies or from the different sensitivities of these proxies to individual components of the AMOC. We suggest that enhanced freshwater fluxes from the Arctic and Nordic seas towards the end of the LIA-sourced from melting glaciers and thickened sea ice that developed earlier in the LIA-weakened Labrador Sea convection and the AMOC. The lack of a subsequent recovery may have resulted from hysteresis or from twentieth-century melting of the Greenland Ice Sheet
. Our results suggest that recent decadal variability in Labrador Sea convection and the AMOC has occurred during an atypical, weak background state. Future work should aim to constrain the roles of internal climate variability and early anthropogenic forcing in the AMOC weakening described here.
Gene replacement therapies utilizing adeno-associated viral (AAV) vectors hold great promise for treating Duchenne muscular dystrophy (DMD). A related approach uses AAV vectors to edit specific ...regions of the DMD gene using CRISPR/Cas9. Here we develop multiple approaches for editing the mutation in dystrophic mdx
mice using single and dual AAV vector delivery of a muscle-specific Cas9 cassette together with single-guide RNA cassettes and, in one approach, a dystrophin homology region to fully correct the mutation. Muscle-restricted Cas9 expression enables direct editing of the mutation, multi-exon deletion or complete gene correction via homologous recombination in myogenic cells. Treated muscles express dystrophin in up to 70% of the myogenic area and increased force generation following intramuscular delivery. Furthermore, systemic administration of the vectors results in widespread expression of dystrophin in both skeletal and cardiac muscles. Our results demonstrate that AAV-mediated muscle-specific gene editing has significant potential for therapy of neuromuscular disorders.
How good is automated protein docking? Kozakov, Dima; Beglov, Dmitri; Bohnuud, Tanggis ...
Proteins, structure, function, and bioinformatics,
December 2013, Volume:
81, Issue:
12
Journal Article
FTMap is a computational mapping server that identifies binding hot spots of macromolecules-i.e., regions of the surface with major contributions to the ligand-binding free energy. To use FTMap, ...users submit a protein, DNA or RNA structure in PDB (Protein Data Bank) format. FTMap samples billions of positions of small organic molecules used as probes, and it scores the probe poses using a detailed energy expression. Regions that bind clusters of multiple probe types identify the binding hot spots in good agreement with experimental data. FTMap serves as the basis for other servers, namely FTSite, which is used to predict ligand-binding sites, FTFlex, which is used to account for side chain flexibility, FTMap/param, used to parameterize additional probes and FTDyn, for mapping ensembles of protein structures. Applications include determining the druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures and providing input for fragment-based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and it is much faster than the more-recent approaches to protein mapping based on mixed molecular dynamics. By using 16 probe molecules, the FTMap server finds the hot spots of an average-size protein in <1 h. As FTFlex performs mapping for all low-energy conformers of side chains in the binding site, its completion time is proportionately longer.
Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1, and BA.2. BA.2 RBD has slightly higher ACE2 affinity than ...BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site; however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focused in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains, and many show broad reactivity with variants of concern.
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•Potent RBD antibodies from Omicron breakthrough vaccinees broadly neutralize VoC•These, possible recall antibodies, are focused in two main clusters•Somatic maturation adapts public antibodies to recover potency•BA.2 > BA.1 ACE2 affinity. BA.2 < BA.1 neutralization by vaccine serum and Vir-S309
Analysis of antibodies from SARS-CoV-2 Omicron breakthrough infections reveals their structural and functional properties as well as ability to neutralize different pandemic strains.
Daily step counts is an intuitive metric that has demonstrated success in motivating physical activity in adults and may hold potential for future public health physical activity recommendations. ...This review seeks to clarify the pattern of the associations between daily steps and subsequent all-cause mortality, cardiovascular disease (CVD) morbidity and mortality, and dysglycemia, as well as the number of daily steps needed for health outcomes.
A systematic review was conducted to identify prospective studies assessing daily step count measured by pedometer or accelerometer and their associations with all-cause mortality, CVD morbidity or mortality, and dysglycemia (dysglycemia or diabetes incidence, insulin sensitivity, fasting glucose, HbA1c). The search was performed across the Medline, Embase, CINAHL, and the Cochrane Library databases from inception to August 1, 2019. Eligibility criteria included longitudinal design with health outcomes assessed at baseline and subsequent timepoints; defining steps per day as the exposure; reporting all-cause mortality, CVD morbidity or mortality, and/or dysglycemia outcomes; adults ≥18 years old; and non-patient populations.
Seventeen prospective studies involving over 30,000 adults were identified. Five studies reported on all-cause mortality (follow-up time 4-10 years), four on cardiovascular risk or events (6 months to 6 years), and eight on dysglycemia outcomes (3 months to 5 years). For each 1000 daily step count increase at baseline, risk reductions in all-cause mortality (6-36%) and CVD (5-21%) at follow-up were estimated across a subsample of included studies. There was no evidence of significant interaction by age, sex, health conditions or behaviors (e.g., alcohol use, smoking status, diet) among studies that tested for interactions. Studies examining dysglycemia outcomes report inconsistent findings, partially due to heterogeneity across studies of glycemia-related biomarker outcomes, analytic approaches, and sample characteristics.
Evidence from longitudinal data consistently demonstrated that walking an additional 1000 steps per day can help lower the risk of all-cause mortality, and CVD morbidity and mortality in adults, and that health benefits are present below 10,000 steps per day. However, the shape of the dose-response relation is not yet clear. Data are currently lacking to identify a specific minimum threshold of daily step counts needed to obtain overall health benefit.
•‘Chameleonic’ behavior is known to be important for the bioavailability of certain macrocyclic drugs.•We show that some degree of chameleonic behavior is required for most oral drugs with ...MW>600–700Da.•A compound likely requires chameleonic properties if either TPSA<0.2×MW, or MPSA in nonpolar environments >140Å2.•Chameleonic behavior potentially explains the improved properties of the high MW Bcl-xL inhibitor ABT263 compared to ABT737.•A change in exposed PSA of ≥0.2MW – 140Å2 is required for effective chameleonic behavior.
Key to the pharmaceutical utility of certain macrocyclic drugs is a ‘chameleonic’ ability to change their conformation to expose polar groups in aqueous solution, but bury them when traversing lipid membranes. Based on analysis of the structures of 20 macrocyclic compounds that are approved oral drugs, we propose that good solubility requires a topological polar surface area (TPSA, in Å2) of ≥0.2×molecular weight (MW). Meanwhile, good passive membrane permeability requires a molecular (i.e., 3D) PSA in nonpolar environments of ≤140Å2. We show that one or other of these limits is almost invariably violated for compounds with MW>600Da, suggesting that some degree of chameleonic behavior is required for most high MW oral drugs.
Neutral detergent fiber (NDF) is the most commonly reported metric for fiber in dairy cattle nutrition. An empirical method, NDF is defined by the procedure used to measure it. The current definitive ...method for NDF treated with amylase (aNDF) is AOAC Official Method 2002.04 performed on dried samples ground through the 1-mm screen of a cutting mill with refluxing and then filtration through Gooch crucibles without (AOAC−; reference method) or with (AOAC+) a glass fiber filter filtration aid. Other methods in use include grinding materials through the 1-mm screen of an abrasion mill, using filtration through a Buchner funnel with a glass fiber filter (Buch), and use of the ANKOM system (ANKOM Technology, Macedon, NY) that simultaneously extracts and filters samples through filter bags with larger (F57) or smaller (F58) particle size retentions. Our objective was to compare the AOAC and alternative methods using samples ground through the 1-mm screens of cutting or abrasion mills. Materials analyzed were 2 alfalfa silages, 2 corn silages, dry ground and high-moisture corn grains, mixed grass hay, ryegrass silage, soybean hulls, calf starter, and sugar beet pulp. Samples were run in duplicate in replicate analytical runs performed on different days by experienced technicians. Compared with cutting mill–ground samples, the aNDF% of dry matter results from abrasion mill–ground samples were or tended to be lower for 8 of 11 samples. Method affected aNDF% results for all materials, with method × grind interactions for 6 of 11 samples. For ash-free aNDF% assessed with cutting mill–ground materials, a priori selected contrasts showed that the number of materials for which methods differed or tended to differ from the AOAC methods were 4 (Buch), 8 (F57), and 3 (F58); and 3 for AOAC– versus AOAC+. However, statistically different does not necessarily mean substantially different. For a given feed and grind, a positive value for the absolute difference between the AOAC– mean and an alternative method mean minus 2 times the standard deviation of AOAC− suggests that values for the alternative method fall outside of the range of results likely to be observed for the reference method. The number of observed positive values for materials processed with cutting and abrasion mills, respectively, were 0 and 2 (AOAC+); 2 and 2 (Buch); 8 and 10 (F57); 4 and 7 (F58); and 0 and 4 (AOAC−). With the materials tested, methods in order of agreement with the reference method were Buch, F58, and F57, which often gave lower values. The AOAC+ gave results similar to AOAC−, substantiating it as an allowed modification of AOAC−. Best agreement between the reference method and variant NDF methods was achieved with the 1-mm screen cutting mill grind. The 1-mm abrasion mill grind produced more aNDF% results that were lower than the reference method but with fewer differences when filter particle retention size was smaller. The use of filters that retain finer particles could be explored to improve comparability of variant NDF methods and grinds. Further evaluation with an expanded set of materials is warranted.
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