The functions of many proteins are regulated through allostery, whereby effector binding at a distal site changes the functional activity (e.g., substrate binding affinity or catalytic efficiency) at ...the active site. Most allosteric studies have focused on thermodynamic properties, in particular, substrate binding affinity. Changes in substrate binding affinity by allosteric effectors have generally been thought to be mediated by conformational transitions of the proteins or, alternatively, by changes in the broadness of the free energy basin of the protein conformational state without shifting the basin minimum position. When effector binding changes the free energy landscape of a protein in conformational space, the change affects not only thermodynamic properties but also dynamic properties, including the amplitudes of motions on different time scales and rates of conformational transitions. Here we assess the roles of conformational dynamics in allosteric regulation. Two cases are highlighted where NMR spectroscopy and molecular dynamics simulation have been used as complementary approaches to identify residues possibly involved in allosteric communication. Perspectives on contentious issues, for example, the relationship between picosecond–nanosecond local and microsecond–millisecond conformational exchange dynamics, are presented.
Biomolecular droplets formed through phase separation have a tendency to fuse. The speed with which fusion occurs is a direct indicator of condensate liquidity, which is key to both cellular ...functions and diseases. Using a dual‐trap optical tweezers setup, we found the fusion speeds of four types of droplets to differ by two orders of magnitude. The order of fusion speed correlates with the fluorescence of thioflavin T, which in turn reflects the macromolecular packing density inside droplets. Unstructured protein or polymer chains pack loosely and readily rearrange, leading to fast fusion. In contrast, structured protein domains pack more closely and have to break extensive contacts before rearrangement, corresponding to slower fusion. This molecular interpretation for disparate fusion speeds provides mechanistic insight into the assembly and aging of biomolecular droplets.
The tendency of biomolecular droplets to fuse is key to cellular functions and diseases. Using optical tweezers, fluorescence microscopy, and theoretical modeling, we have begun to unravel the molecular origin for disparate fusion speeds among different biomolecular droplets. Fusion speed is dictated by macromolecular packing density inside droplets, which can be reported by thioflavin T fluorescence.
The relationship between muscle wasting and mortality risk in the general population remains unclear. Our study was conducted to examine and quantify the associations between muscle wasting and ...all‐cause and cause‐specific mortality risks. PubMed, Web of Science and Cochrane Library were searched until 22 March 2023 for main data sources and references of retrieved relevant articles. Prospective studies investigating the associations of muscle wasting with risks of all‐cause and cause‐specific mortality in the general population were eligible. A random‐effect model was used to calculate the pooled relative risk (RR) and 95% confidence intervals (CIs) for the lowest versus normal categories of muscle mass. Subgroup analyses and meta‐regression were performed to investigate the potential sources of heterogeneities among studies. Dose–response analyses were conducted to evaluate the relationship between muscle mass and mortality risk. Forty‐nine prospective studies were included in the meta‐analysis. A total of 61 055 deaths were ascertained among 878 349 participants during the 2.5‐ to 32‐year follow‐up. Muscle wasting was associated with higher mortality risks of all causes (RR = 1.36, 95% CI, 1.28 to 1.44, I2 = 94.9%, 49 studies), cardiovascular disease (CVD) (RR = 1.29, 95% CI, 1.05 to 1.58, I2 = 88.1%, 8 studies), cancer (RR = 1.14, 95% CI, 1.02 to 1.27, I2 = 38.7%, 3 studies) and respiratory disease (RR = 1.36, 95% CI, 1.11 to 1.67, I2 = 62.8%, 3 studies). Subgroup analyses revealed that muscle wasting, regardless of muscle strength, was significantly associated with a higher all‐cause mortality risk. Meta‐regression showed that risks of muscle wasting‐related all‐cause mortality (P = 0.06) and CVD mortality (P = 0.09) were lower in studies with longer follow‐ups. An approximately inverse linear dose–response relationship was observed between mid‐arm muscle circumference and all‐cause mortality risk (P < 0.01 for non‐linearity). Muscle wasting was associated with higher mortality risks of all causes, CVD, cancer and respiratory disease in the general population. Early detection and treatment for muscle wasting might be crucial for reducing mortality risk and promoting healthy longevity.
Objective
To investigate how physical exercise (PE) would affect brain‐derived neurotrophic factor (BDNF) in randomized controlled trials (RCTs) of healthy subjects.
Methods
Seven databases (PubMed, ...Web of Science, Cochrane, Embase, PsycINFO, CINAHL, SPORTDiscus) were searched for RCTs assessing the effects of PE on serum and/or plasma BDNF until December 18, 2021. Meta‐analysis was performed by random‐effects method with standardized mean difference (SMD) and 95% confidence intervals (CIs). Subgroup analysis and meta‐regression analysis were conducted to investigate the potential source of heterogeneity. Trim and fill method, and leave‐one‐out cross‐validation were conducted.
Results
Eventually, 21 articles, involving 809 participants, were included in the meta‐analysis. Overall, both acute (5 trials, SMD: 1.20, 95% CI: 0.36 to 2.04, p = .005) and long‐term (17 trials, SMD: 0.68, 95% CI: 0.27 to 1.08, p = .001) PE had significant positive effects on BDNF levels. Via subgroup analysis, studies of long‐term PE with larger sample sizes, female participants, participants older than 60 years, and aerobic exercise contributed to a more pronounced improvement on BDNF levels than that found when all studies were combined.
Conclusion
Both acute and long‐term PE had significant positive effects on circulating BDNF in healthy subjects. This review suggests that acute exercise and long‐term aerobic exercise are powerful forms of PE to enhance neurotrophic effect, especially for female subjects or subjects over 60 years.
Recent experiments inside cells and in cytomimetic conditions have demonstrated that the crowded environments found therein can significantly reshape the energy landscapes of individual protein ...molecules and their oligomers. The resulting shifts in populations of conformational and oligomeric states have numerous biological consequences, e.g., concerning the efficiency of replication and transcription, the development of aggregation-related diseases, and the efficacy of small-molecule drugs. Some of the effects of crowding can be anticipated from hard-particle theoretical models, but the in vitro and in vivo measurements indicate that these effects are often subtle and complex. These observations, coupled with recent computational studies at the atomistic level, suggest that the latter detailed modeling may be required to yield a quantitative understanding on the influence of crowded cellular environments.
Membraneless organelles, corresponding to the droplet phase upon liquid–liquid phase separation (LLPS) of protein or protein–RNA mixtures, mediate myriad cellular functions. Cells use a variety of ...biochemical signals such as expression level and posttranslational modification to regulate droplet formation and dissolution, but the physical basis of the regulatory mechanisms remains illdefined and quantitative assessment of the effects is largely lacking. Our computational study predicted that the strength of attraction by droplet-forming proteins dictates whether and how macromolecular regulators promote or suppress LLPS. We experimentally tested this prediction, using the pentamers of SH3 domains and proline-rich motifs (SH3₅ and PRM₅) as droplet-forming proteins. Determination of the changes in phase boundary and the partition coefficients in the droplet phase over a wide range of regulator concentrations yielded both a quantitative measure and a mechanistic understanding of the regulatory effects. Three archetypical classes of regulatory effects were observed. Ficoll 70 at high concentrations indirectly promoted SH3₅–PRM₅ LLPS, by taking up volume in the bulk phase and thereby displacing SH3₅ and PRM₅ into the droplet phase. Lysozyme had a moderate partition coefficient and suppressed LLPS by substituting weaker attraction with SH3₅ for the stronger SH3₅–PRM₅ attraction in the droplet phase. By forming even stronger attraction with PRM₅, heparin at low concentrations partitioned heavily into the droplet phase and promoted LLPS. These characteristics were recapitulated by computational results of patchy particle models, validating the identification of the 3 classes of macromolecular regulators as volume-exclusion promotors, weak-attraction suppressors, and strong-attraction promotors.
Tau, as typical of intrinsically disordered proteins (IDPs), binds to multiple targets including microtubules and acidic membranes. The latter two surfaces are both highly negatively charged, raising ...the prospect of mimicry in their binding by tau. The tau‐microtubule complex was recently determined by cryo‐electron microscopy. Here, we used molecular dynamics simulations to characterize the dynamic binding of tau K19 to an acidic membrane. This IDP can be divided into three repeats, each containing an amphipathic helix. The three amphipathic helices, along with flanking residues, tether the protein to the membrane interface. The separation between and membrane positioning of the amphipathic helices in the simulations are validated by published EPR data. The membrane contact probabilities of individual residues in tau show both similarities to and distinctions from native contacts with microtubules. In particular, a Lys that is conserved among the repeats forms similar interactions with membranes and with microtubules, as does a conserved Val. This partial mimicry facilitates both the membrane anchoring of microtubules by tau and the transfer of tau from membranes to microtubules.
Phase-separated biomolecular condensates must respond agilely to biochemical and environmental cues in performing their wide-ranging cellular functions, but our understanding of condensate dynamics ...is lagging. Ample evidence now indicates biomolecular condensates as viscoelastic fluids, where shear stress relaxes at a finite rate, not instantaneously as in viscous liquids. Yet the fusion dynamics of condensate droplets has only been modeled based on viscous liquids, with fusion time given by the viscocapillary ratio (viscosity over interfacial tension). Here we used optically trapped polystyrene beads to measure the viscous and elastic moduli and the interfacial tensions of four types of droplets. Our results challenge the viscocapillary model, and reveal that the relaxation of shear stress governs fusion dynamics. These findings likely have implications for other dynamic processes such as multiphase organization, assembly and disassembly, and aging.
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