Differential modulation of energy landscapes of cyclic AMP receptor protein (CRP) as a regulatory mechanism for class II CRP-dependent promoters.

The Escherichia coli cAMP receptor protein, CRP, is a homodimeric global transcription activator that employs multiple mechanisms to modulate the expression of hundreds of genes. These mechanisms require different interfacial interactions among CRP, RNA, and DNA of varying sequences. The involvement of such a multiplicity of interfaces requires a tight control to ensure the desired phenotype. CRP-dependent promoters can be grouped into three classes. For decades scientists in the field have been puzzled over the differences in mechanisms between class I and II promoters. Using a new crystal structure, IR spectroscopy, and computational analysis, we defined the energy landscapes of WT and 14 mutated CRPs to determine how a homodimeric protein can distinguish nonpalindromic DNA sequences and facilitate communication between residues located in three different activation regions (AR) in CRP that are ∼30 Šapart. We showed that each mutation imparts differential effects on stability among the subunits and domains in CRP. Consequently, the energetic landscapes of subunits and domains are different, and CRP is asymmetric. Hence, the same mutation can exert different effects on ARs in class I or II promoters. The effect of a mutation is transmitted through a network by long-distance communication not necessarily relying on physical contacts between adjacent residues. The mechanism is simply the sum of the consequences of modulating the synchrony of dynamic motions of residues at a distance, leading to differential effects on ARs in different subunits. The computational analysis is applicable to any system and potentially with predictive capability.

The many characters of visual alpha oscillations.

A central feature of human brain activity is the alpha rhythm: a 7-13 Hz oscillation observed most notably over occipitoparietal brain regions during periods of eyes-closed rest. Alpha oscillations covary with changes in visual processing and have been associated with a broad range of neurocognitive functions. In this article, we review these associations and suggest that alpha oscillations can be thought to exhibit at least five distinct 'characters': those of the inhibitor, perceiver, predictor, communicator and stabiliser. In short, while alpha oscillations are strongly associated with reductions in visual attention, they also appear to play important roles in regulating the timing and temporal resolution of perception. Furthermore, alpha oscillations are strongly associated with top-down control and may facilitate transmission of predictions to visual cortex. This is in addition to promoting communication between frontal and posterior brain regions more generally, as well as maintaining ongoing perceptual states. We discuss why alpha oscillations might associate with such a broad range of cognitive functions and suggest ways in which these diverse associations can be studied experimentally.

Nanosecond Dynamics Regulate the MIF-Induced Activity of CD74.

Macrophage migration inhibitory factor (MIF) activates CD74, which leads to severe disorders including inflammation, autoimmune diseases and cancer under pathological conditions. Molecular dynamics (MD) simulations up to one microsecond revealed dynamical correlation between a residue located at the opening of one end of the MIF solvent channel, previously thought to be a consequence of homotrimerization, and residues in a distal region responsible for CD74 activation. Experiments verified the allosteric regulatory site and identified a pathway to this site via the MIF ß-strands. The reported findings provide fundamental insights on a dynamic mechanism that controls the MIF-induced activation of CD74.

Fluorescence Blinking Beyond Nanoconfinement: Spatially Synchronous Intermittency of Entire Perovskite Microcrystals.

Abrupt fluorescence intermittency or blinking is long recognized to be characteristic of single nano-emitters. Extended quantum-confined nanostructures also undergo spatially heterogeneous blinking; however, there is no such precedent in dimensionally unconfined (bulk) materials. Herein, we report multi-level blinking of entire individual organo-lead bromide perovskite microcrystals (volume=0.1-3 µm3 ) under ambient conditions. Extremely high spatiotemporal correlation (>0.9) in intracrystal emission intensity fluctuations signifies effective communication amongst photogenerated carriers at distal locations (up to ca. 4 µm) within each crystal. Fused polycrystalline grains also exhibit this intriguing phenomenon, which is rationalized by correlated and efficient migration of carriers to a few transient nonradiative traps, the nature and population of which determine blinking propensity. Observation of spatiotemporally correlated emission intermittency in bulk semiconductor crystals opens the possibility of designing novel devices involving long-range (mesoscopic) electronic communication.

Dynamically Coupled Residues within the SH2 Domain of FYN Are Key to Unlocking Its Activity.

Src kinase activity is controlled by various mechanisms involving a coordinated movement of kinase and regulatory domains. Notwithstanding the extensive knowledge related to the backbone dynamics, little is known about the more subtle side-chain dynamics within the regulatory domains and their role in the activation process. Here, we show through experimental methyl dynamic results and predicted changes in side-chain conformational couplings that the SH2 structure of Fyn contains a dynamic network capable of propagating binding information. We reveal that binding the phosphorylated tail of Fyn perturbs a residue cluster near the linker connecting the SH2 and SH3 domains of Fyn, which is known to be relevant in the regulation of the activity of Fyn. Biochemical perturbation experiments validate that those residues are essential for inhibition of Fyn, leading to a gain of function upon mutation. These findings reveal how side-chain dynamics may facilitate the allosteric regulation of the different members of the Src kinase family.