Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.

AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca2+-impermeable, or GluA2-lacking and Ca2+-permeable1. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies2, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes.

Correction: The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

[This corrects the article DOI: 10.1371/journal.ppat.1010631.].

The structural role of SARS-CoV-2 genetic background in the emergence and success of spike mutations: The case of the spike A222V mutation.

The S:A222V point mutation, within the G clade, was characteristic of the 20E (EU1) SARS-CoV-2 variant identified in Spain in early summer 2020. This mutation has since reappeared in the Delta subvariant AY.4.2, raising questions about its specific effect on viral infection. We report combined serological, functional, structural and computational studies characterizing the impact of this mutation. Our results reveal that S:A222V promotes an increased RBD opening and slightly increases ACE2 binding as compared to the parent S:D614G clade. Finally, S:A222V does not reduce sera neutralization capacity, suggesting it does not affect vaccine effectiveness.

Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.

ProDy 2.0: increased scale and scope after 10 years of protein dynamics modelling with Python.

SUMMARY: ProDy, an integrated application programming interface developed for modelling and analysing protein dynamics, has significantly evolved in recent years in response to the growing data and needs of the computational biology community. We present major developments that led to ProDy 2.0: (i) improved interfacing with databases and parsing new file formats, (ii) SignDy for signature dynamics of protein families, (iii) CryoDy for collective dynamics of supramolecular systems using cryo-EM density maps and (iv) essential site scanning analysis for identifying sites essential to modulating global dynamics. AVAILABILITY AND IMPLEMENTATION: ProDy is open-source and freely available under MIT License from https://github.com/prody/ProDy. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Allosteric interactions in the parathyroid hormone GPCR-arrestin complex formation.

Peptide ligands of class B G-protein-coupled receptors act via a two-step binding process, but the essential mechanisms that link their extracellular binding to intracellular receptor-arrestin interactions are not fully understood. Using NMR, crosslinking coupled to mass spectrometry, signaling experiments and computational approaches on the parathyroid hormone (PTH) type 1 receptor (PTHR), we show that initial binding of the PTH C-terminal part constrains the conformation of the flexible PTH N-terminal signaling epitope before a second binding event occurs. A 'hot-spot' PTH residue, His9, that inserts into the PTHR transmembrane domain at this second step allosterically engages receptor-arrestin coupling. A conformational change in PTHR intracellular loop 3 permits favorable interactions with ß-arrestin's finger loop. These results unveil structural determinants for PTHR-arrestin complex formation and reveal that the two-step binding mechanism proceeds via cooperative fluctuations between ligand and receptor, which extend to other class B G-protein-coupled receptors.

Structural and Dynamic Effects of PTEN C-Terminal Tail Phosphorylation.

The phosphatase and tensin homologue deleted on chromosome 10 (PTEN) tumor suppressor gene encodes a tightly regulated dual-specificity phosphatase that serves as the master regulator of PI3K/AKT/mTOR signaling. The carboxy-terminal tail (CTT) is key to regulation and harbors multiple phosphorylation sites (Ser/Thr residues 380-385). CTT phosphorylation suppresses the phosphatase activity by inducing a stable, closed conformation. However, little is known about the mechanisms of phosphorylation-induced CTT-deactivation dynamics. Using explicit solvent microsecond molecular dynamics simulations, we show that CTT phosphorylation leads to a partially collapsed conformation, which alters the secondary structure of PTEN and induces long-range conformational rearrangements that encompass the active site. The active site rearrangements prevent localization of PTEN to the membrane, precluding lipid phosphatase activity. Notably, we have identified phosphorylation-induced allosteric coupling between the interdomain region and a hydrophobic site neighboring the active site in the phosphatase domain. Collectively, the results provide a mechanistic understanding of CTT phosphorylation dynamics and reveal potential druggable allosteric sites in a previously believed clinically undruggable protein.

Does HMB Enhance Body Composition in Athletes? A Systematic Review and Meta-analysis.

ABSTRACT: Holland, BM, Roberts, BM, Krieger, JW, and Schoenfeld, BJ. Does HMB enhance body composition in athletes? A systematic review and meta-analysis. J Strength Cond Res 36(2): 585-592, 2022-The purpose of this article was to systematically review and meta-analyze the current literature to determine the effects of HMB on body composition in athletes. Studies were deemed eligible for inclusion if they met the following criteria: (a) were an experimental design published in a peer-reviewed, English-language journal; (b) included human athletic populations; (c) assessed body mass (BM), fat mass (FM), or fat-free mass (FFM) using a validated measure; (d) and had a minimum supplementation period of 4 weeks. Separate analyses were performed for BM, FM, and FFM using robust variance random-effects meta-regression for multilevel data structures, with adjustments for small samples. The final analysis of BM comprised a total of 208 subjects from 7 studies. Analysis of FFM and FM encompassed 5 studies comprising 161 subjects and 5 studies comprising 128 subjects, respectively. The principal finding of this analysis suggests HMB may have a small, positive impact on FFM in athletes (0.30 ± 0.13; 95% confidence interval [CI]: -0.07 to 0.68; p = 0.08), although this seems specific to when protein intake is suboptimal (<1.6 g·kg-1·d-1). Consistent with previous research on athletes, HMB demonstrated no significant effect on BM (-0.02 ± 0.04; 95% CI: -0.14 to 0.10; p = 0.70) and a small, nonsignificant effect on FM (-0.33 ± 0.23; 95% CI: -0.96 to 0.31; p = 0.22). More research is required to establish HMB's influence on FFM in athletes. It is also important to consider the dosage of HMB and training parameters of athletes because these will likely influence the efficacy of supplementation.

Sweetened beverage taxes: Economic benefits and costs according to household income.

Taxing sweetened beverages has emerged as an important and effective policy for addressing their overconsumption. However, taxes may place a greater economic burden on people with lower incomes. We assess the degree to which sweetened beverage taxes in three large US cities placed an inequitable burden on populations with lower incomes by assessing spending on beverage taxes by income after taxes have been implemented, as well as any net transfer of funds towards lower income populations once allocation of tax revenue is considered. We find that while lower income populations pay a higher percentage of their income in beverage taxes, there is no difference in absolute spending on beverage taxes per capita, and that there is a sizable net transfer of funds towards programs targeting lower income populations. Thus, when considering both population-level taxes paid and sufficiently targeted allocations of tax revenues, a sweetened beverage tax may have characteristics of an equitable public policy.

Sugar-Sweetened Beverage Reduction Policies: Progress and Promise.

Evidence showing the effectiveness of policies to reduce the consumption of sugar-sweetened beverages (SSBs) is growing. SSBs are one of the largest sources of added sugar in the diet and are linked to multiple adverse health conditions. This review presents a framework illustrating the various types of policies that have been used to reduce SSB exposure and consumption; policies are organized into four categories (financial, information, defaults, and availability) and take into consideration crosscutting policy considerations (feasibility, impact, and equity). Next, for each category, we describe a specific example and provide evidence of impact. Finally, we discuss crosscutting policy considerations, the challenge of choosing among the various policy options, and important areas for future research. Notably, no single policy will reduce SSB consumption to healthy levels, so an integrated policy approach that adapts to changing market and consumption trends; evolving social, political, and public health needs; and emerging science is critical.

Countermarketing About Fruit Drinks, Alone or With Water Promotion: A 2019 Randomized Controlled Trial in Latinx Parents.

Objectives. To test whether fruit drink countermarketing messages alone or combined with water promotion messages reduce Latinx parents' purchases of fruit drinks for children aged 0 to 5 years. Methods. We performed a 3-arm randomized controlled online trial enrolling 1628 Latinx parents in the United States during October and November 2019. We assessed the effect of culturally tailored fruit drink countermarketing messages (fruit drink‒only group), countermarketing and water promotion messages combined (combination group), or car-seat safety messages (control) delivered via Facebook groups for 6 weeks on parental beverage choices from a simulated online store. Results. The proportion of parents choosing fruit drinks decreased by 13.7 percentage points in the fruit drink‒only group (95% confidence interval [CI] = -20.0, -7.4; P < .001) and by 19.2 percentage points in the combination group (95% CI = -25.0, -13.4; P < .001) relative to control. Water selection increased in both groups. Conclusions. Fruit drink countermarketing messages, alone or combined with water promotion messages, significantly decreased parental selection of fruit drinks and increased water selection for their children. Public Health Implications. Countermarketing social media messages may be an effective and low-cost intervention for reducing parents' fruit drink purchases for their children. (Am J Public Health. 2021;111(11):1997-2007. https://doi.org/10.2105/AJPH.2021.306488).

A meta-regression of the effects of resistance training frequency on muscular strength and hypertrophy in adults over 60 years of age.

Resistance training is a commonly used strategy for improving both athletic performance and general health. While the contribution of resistance training intensity and volume to muscle strength and hypertrophy have been extensively investigated, training frequency only recently received sufficient attention, especially in older adults. A meta-regression was conducted to compare muscle strength and hypertrophic adaptations to resistance training programmes performed with different training frequencies in adults over 60 years of age. The systematic literature search identified 14 articles for meta-regression. For each outcome, an effect size (ES) was calculated as the pre-test-post-test change, divided by the pooled pre-test standard deviation (SD). Random-effects meta-regressions for multilevel data structures, using study as the clustering variable, were performed using package metafor in R. Maximal strength shows a significant effect of frequency (p = 0.001), with an increase in effect size of 0.14 for every day increase in frequency (CI: 0.08, 0.21). For muscle hypertrophy, no significant effect of frequency was found (p = 0.67). Considering that muscle hypertrophy was not affected, while maximum strength was only slightly improved with additional training days, it seems unlikely that more than two weekly resistance training sessions would provide any further benefits for older adults.

Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.

Recent studies have drawn attention to the evolution of protein dynamics, in addition to sequence and structure, based on the premise structure-encodes-dynamics-encodes-function. Of interest is to understand how functional differentiation is accomplished while maintaining the fold, or how intrinsic dynamics plays out in the evolution of structural variations and functional specificity. We performed a systematic computational analysis of 26,899 proteins belonging to 116 CATH superfamilies. Characterizing cooperative mechanisms and convergent/divergent features that underlie the shared/differentiated dynamics of family members required a methodology that lends itself to efficient analyses of large ensembles of proteins. We therefore introduced, SignDy, an integrated pipeline for evaluating the signature dynamics of families based on elastic network models. Our analysis confirmed that family members share conserved, highly cooperative (global) modes of motion. Importantly, our analysis discloses a subset of motions that sharply distinguishes subfamilies, which lie in a low-to-intermediate frequency regime of the mode spectrum. This regime has maximal impact on functional differentiation of families into subfamilies, while being evolutionarily conserved among subfamily members. Notably, the high-frequency end of the spectrum also reveals evolutionary conserved features across and within subfamilies; but in sharp contrast to global motions, high-frequency modes are minimally collective. Modulation of robust/conserved global dynamics by low-to-intermediate frequency fluctuations thus emerges as a versatile mechanism ensuring the adaptability of selected folds and the specificity of their subfamilies. SignDy further allows for dynamics-based categorization as a new layer of information relevant to distinctive mechanisms of action of subfamilies, beyond sequence or structural classifications.

Sex Differences in Resistance Training: A Systematic Review and Meta-Analysis.

Roberts, BM, Nuckols, G, and Krieger, JW. Sex differences in resistance training: A systematic review and meta-analysis. J Strength Cond Res 34(5): 1448-1460, 2020-The purpose of this study was to determine whether there are different responses to resistance training for strength or hypertrophy in young to middle-aged males and females using the same resistance training protocol. The protocol was pre-registered with PROSPERO (CRD42018094276). Meta-analyses were performed using robust variance random effects modeling for multilevel data structures, with adjustments for small samples using package robumeta in R. Statistical significance was set at P < 0.05. The analysis of hypertrophy comprised 12 outcomes from 10 studies with no significant difference between males and females (effect size [ES] = 0.07 ± 0.06; P = 0.31; I = 0). The analysis of upper-body strength comprised 19 outcomes from 17 studies with a significant effect favoring females (ES = -0.60 ± 0.16; P = 0.002; I = 72.1). The analysis of lower-body strength comprised 23 outcomes from 23 studies with no significant difference between sexes (ES = -0.21 ± 0.16; P = 0.20; I = 74.7). We found that males and females adapted to resistance training with similar effect sizes for hypertrophy and lower-body strength, but females had a larger effect for relative upper-body strength. Given the moderate effect size favoring females in the upper-body strength analysis, it is possible that untrained females display a higher capacity to increase upper-body strength than males. Further research is required to clarify why this difference occurs only in the upper body and whether the differences are due to neural, muscular, motor learning, or are an artifact of the short duration of studies included.

Comparison of Multifrequency Bioelectrical Impedance vs. Dual-Energy X-ray Absorptiometry for Assessing Body Composition Changes After Participation in a 10-Week Resistance Training Program.

Schoenfeld, BJ, Nickerson, BS, Wilborn, CD, Urbina, SL, Hayward, SB, Krieger, J, Aragon, AA, and Tinsley, G. Comparison of multifrequency bioelectrical impedance vs. dual-energy x-ray absorptiometry for assessing body composition changes after participation in a 10-week resistance training program. J Strength Cond Res 34(3): 678-688, 2020-The purpose of this study was to assess the ability of multifrequency bioelectrical impedance analysis (MF-BIA) to determine alterations in total and segmental body composition across a 10-week resistance training (RT) program in comparison with the criterion reference dual-energy X-ray absorptiometry (DXA). Twenty-one young male volunteers (mean ± SD; age = 22.9 ± 3.0 years; height = 175.5 ± 5.9 cm; body mass = 82.9 ± 13.6 kg; body mass index = 26.9 ± 3.6) performed an RT program that included exercises for all major muscle groups. Body composition was assessed using both methods before and after the intervention; change scores were determined by subtracting pre-test values from post-test values for percent body fat ([INCREMENT]%BF), fat mass ([INCREMENT]FM), and fat-free mass ([INCREMENT]FFM). Mean changes were not significantly different when comparing MF-BIA with DXA for [INCREMENT]%BF (-1.05 vs. -1.28%), [INCREMENT]FM (-1.13 vs. -1.19 kg), and FFM (0.10 vs. 0.37 kg, respectively). Both methods showed strong agreement for [INCREMENT]%BF (r = 0.75; standard error of the estimate [SEE] = 1.15%), [INCREMENT]FM (r = 0.84; SEE 1.0 kg), and [INCREMENT]FFM (r = 0.71; SEE of 1.5 kg). The 2 methods were poor predictors of each other in regards to changes in segmental measurements. Our data indicate that MF-BIA is an acceptable alternative for tracking changes in FM and FFM during a combined diet and exercise program in young, athletic men, but segmental lean mass measurements must be interpreted with circumspection.

Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.

Accurate modeling of structural dynamics of proteins and their differentiation across different species can help us understand generic mechanisms of function shared by family members and the molecular basis of the specificity of individual members. We focused here on the family of lipoxygenases, enzymes that catalyze lipid oxidation, the mammalian and bacterial structures of which have been elucidated. We present a systematic method of approach for characterizing the sequence, structure, dynamics, and allosteric signaling properties of these enzymes using a combination of structure-based models and methods and bioinformatics tools applied to a data set of 88 structures. The analysis elucidates the signature dynamics of the lipoxygenase family and its differentiation among members, as well as key sites that enable its adaptation to specific substrate binding and allosteric activity.

Perceptions of the possible health and economic impacts of Seattle's sugary beverage tax.

BACKGROUND: Taxes on sugary beverages are an emerging strategy to improve health by reducing consumption and raising revenues to support community wellbeing. However, taxes may have unintended consequences, and perceptions of these consequences may affect attitudes towards this policy. METHODS: In June 2017, the Seattle City Council passed an ordinance imposing a tax on sugary beverages, effective January 1, 2018. Between October and December 2017, we recruited 851 adults in Seattle to complete a survey (telephone or online) about support for the tax and their perceptions of tax-related health and economic impacts. We first analyzed data for the full sample. We then tested for differences in participants' responses by household income level (< 260% Federal Poverty Level [FPL], ≥ 260% FPL) and across race/ethnicities using chi-square tests. Analyses used population weights and adjusted for multiple comparisons, using the Holm-Bonferroni Sequential Correction (p < 0.01). RESULTS: A majority of participants supported the sugary beverage tax (59%; 95% Confidence Interval [CI]: 55, 63%) and believed that the tax would improve public health (56%; CI: 52, 60%). Most participants believed that the tax would not negatively affect small businesses (52%; CI: 48, 56%) nor result in job loss (66%; CI: 62, 70%). Most participants also perceived that the tax would not negatively impact their own finances (79%; CI: 75, 82%). However, fewer lower-income (48%; CI: 42, 53%), versus higher-income participants (61%; CI: 55, 66%), perceived that the tax would improve public health, would not result in job loss (lower-income: 58%; CI: 53, 64%; higher-income: 71%; CI: 66, 75%) and would not negatively affect their own finances (lower-income: 68%; CI: 62, 73%; higher-income: 85%; CI: 81, 88%). Compared to non-Hispanic Whites, (82%; CI: 79, 86%), a smaller proportion of non-Hispanic Blacks (63%; 95% CI: 48, 75%), and Hispanics (67%; 95% CI: 51, 79%), perceived that the tax would have negative consequences for their own family finances. CONCLUSIONS: A majority of respondents supported the sugary beverage tax in Seattle. Lower-income participants were more concerned about potential financial consequences. Further evaluation of the extent to which unintended consequences occur is needed.

How many times per week should a muscle be trained to maximize muscle hypertrophy? A systematic review and meta-analysis of studies examining the effects of resistance training frequency.

Training frequency is considered an important variable in the hypertrophic response to regimented resistance exercise. The purpose of this paper was to conduct a systematic review and meta-analysis of experimental studies designed to investigate the effects of weekly training frequency on hypertrophic adaptations. Following a systematic search of PubMed/MEDLINE, Scoups, and SPORTDiscus databases, a total of 25 studies were deemed to meet inclusion criteria. Results showed no significant difference between higher and lower frequency on a volume-equated basis. Moreover, no significant differences were seen between frequencies of training across all categories when taking into account direct measures of growth, in those considered resistance-trained, and when segmenting into training for the upper body and lower body. Meta-regression analysis of non-volume-equated studies showed a significant effect favoring higher frequencies, although the overall difference in magnitude of effect between frequencies of 1 and 3+ days per week was modest. In conclusion, there is strong evidence that resistance training frequency does not significantly or meaningfully impact muscle hypertrophy when volume is equated. Thus, for a given training volume, individuals can choose a weekly frequency per muscle groups based on personal preference.

Resistance Training Frequencies of 3 and 6 Times Per Week Produce Similar Muscular Adaptations in Resistance-Trained Men.

Saric, J, Lisica, D, Orlic, I, Grgic, J, Krieger, JW, Vuk, S, and Schoenfeld, BJ. Resistance training frequencies of 3 and 6 times per week produce similar muscular adaptations in resistance-trained men. J Strength Cond Res 33(7S): S122-S129, 2019-We examined the effects of resistance training (RT) frequency performed 3 times per week (RT3) vs. RT performed 6 times per week (RT6) under volume-equated conditions in resistance-trained men. Twenty-seven men were randomly allocated to RT3 (n = 14) or RT6 (n = 13). The supervised training intervention lasted for 6 weeks. Upper- and lower-body strength were assessed using the 1 repetition maximum test. Also, muscular endurance (60% 1 repetition maximum performed to momentary failure) and muscle thickness (elbow flexors, elbow extensors, rectus femoris, and vastus intermedius) were measured before and after intervention. Pre-to-post intervention, both groups increased upper-body strength (RT3: +4%; RT6: +6%) and lower-body strength (RT3: +22%; RT6: +18%) with no significant between-group differences. No significant pre-to-post intervention increases in muscular endurance were seen in either of the training groups. Both groups increased elbow extensor thickness (RT3: +14%; RT6: +11%), rectus femoris thickness (RT3: +5%; RT6: +6%), and vastus intermedius thickness (RT3: +10%; RT6: +11%) with no significant between-group differences. Only the RT3 group significantly increased elbow flexor thickness from pre-to-post intervention (+7%). When training volume is equated, it seems that RT performed either 3 or 6 times per week can result in similar strength gains over a 6-week training period. Furthermore, under volume-equated conditions, comparable hypertrophy results may also be expected with both RT frequencies. Finally, no changes were seen in muscular endurance possibly because of the considerable interindividual variability in responses. The findings presented herein might be of interest to coaches, exercise practitioners, athletes, and recreational trainees.

Association of 100% fruit juice consumption and 3-year weight change among postmenopausal women in the in the Women's Health Initiative.

The association between drinking 100% fruit juice and long-term weight gain is controversial and has been investigated in few studies. We examined whether 100% fruit juice consumption was associated with weight change in a large prospective cohort of postmenopausal women. We analyzed data from 49,106 postmenopausal women in the United States enrolled in the Women's Health Initiative between 1993 and 1998. Food frequency questionnaires at baseline and year 3 assessed food and beverage intake. Body weight was measured at in-person clinic visits. We used linear mixed effects modeling to determine the association between change in 100% fruit juice consumption and 3-year weight change over the same time period. Covariates of interest included age, demographic factors, smoking, body mass index, hormone replacement therapy, lifestyle factors, change in whole fruit intake, and change in sugar-sweetened beverage intake. The mean weight change was 3.2 lbs. over 3 years. In multivariable adjusted analyses, each 1 serving/day increase in 100% fruit juice intake was associated with a 3-year weight gain of 0.39 lbs. (95% confidence interval: 0.10, 0.69). In conclusion, an increase in 100% fruit juice consumption was associated with a small amount of long-term weight gain in postmenopausal women.