Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events

A cluster of inhibitory residues in the regulatory domain prevents activation of the cystic fibrosis transmembrane conductance regulator

Activation of the cystic fibrosis transmembrane conductance regulator (CFTR) Cl‒ channel requires PKA phosphorylation at the regulatory (R) domain to relieve inhibition of ATP-dependent channel activity. This study aimed to identify the primary inhibitory site that prevents channel activation. CFTR mutants with deletion of residues 760 to 783 (ΔR760-783) elicited constitutive macroscopic and single-channel Cl‒ currents in the presence of ATP before PKA phosphorylation, suggesting that protein segment R760-783 in the R domain blocks CFTR activation. With the background of ΔR760-835, further deletion of R708-759 led to fully active channels in the presence of ATP, but the absence of PKA, suggesting that R708-759 prevents the activation of ΔR760-835-CFTR. R760-783 peptides were unstructured in buffered solutions in CD spectroscopy and the N771P mutation that interrupts the α-helix formation induced no apparent constitutive current before PKA phosphorylation. These data suggest that interpeptide interactions by α-helices likely contribute trivially to the blocking effect of R760-783. CFTR mutants with small deletions or alanine replacements containing any one of residues R766 and S768 in a PKA consensus sequence and M773 and T774 generated PKA-independent CFTR Cl‒ currents. Similarly, introducing the mutations Q767C or T774C into a control CFTR construct produced constitutive CFTR Cl‒ currents by positively charged 2-(trimethylammonium)ethylmethanethiosulfonate modification of target cysteines. Moreover, PKA-independent single-channel activity was evidently observed in R766K-, S768K-, and T774K-CFTR mutants. Therefore, the four residues, R766, S768, M773, and T774, may form an inhibitory module that precludes CFTR activation through side-chain interactions. This inhibitory mechanism might be emulated by other PKA-dependent proteins.

Molecular basis underlying the specificity of an antagonist AA92593 for mammalian melanopsins

Melanopsin functions in intrinsically photosensitive retinal ganglion cells of mammals to regulate circadian clock and pupil constriction. The opsinamide AA92593 has been reported to specifically inhibit mouse and human melanopsin functions as a competitive antagonist against retinal; however, the molecular mechanisms underlying its specificity have not been resolved. In this study, we attempted to identify amino acid residues responsible for the susceptibility of mammalian melanopsins to AA92593. Our cell-based assays confirmed that AA92593 effectively inhibited the light-induced cellular responses of mammalian melanopsins, but not those of non-mammalian vertebrate and invertebrate melanopsins. These results suggest that amino acid residues specifically conserved among mammalian melanopsins are important for the antagonistic effect of AA92593, and we noticed Phe-942.61, Ser-188ECL2, and Ser-2696.52 as candidate residues. Substitutions of these residues reduced the antagonistic effect of AA92593. We conducted docking and molecular dynamics simulations based on the AlphaFold-predicted melanopsin structure. The simulations indicated that Phe-942.61, Ser-188ECL2, and Ser-2696.52 are located at the AA92593-binding site and additionally identified Trp-189ECL2 and Leu-2075.42 interacting with the antagonist. Substitutions of Trp-189ECL2 and Leu-2075.42 affected the antagonistic effect of AA92593. Furthermore, substitutions of these amino acid residues converted the AA92593-insensitive non-mammalian melanopsins susceptible to the antagonist. Based on experiments and molecular simulations, five amino acid residues, at positions 942.61, 188ECL2, 189ECL2, 2075.42, and 2696.52, were found to be responsible for the specific susceptibility of mammalian melanopsins to AA92593.

Recent advances of biocompatible optical nanobiosensors in liquid biopsy: towards early non-invasive diagnosis

Liquid biopsy is a non-invasive diagnostic method that can reduce the risk of complications and offers exceptional benefits in the dynamic monitoring and acquisition of heterogeneous cell population information. Optical nanomaterials with excellent light absorption, luminescence, and photoelectrochemical properties have accelerated the development of liquid biopsy technologies. Owing to the unique size effect of optical nanomaterials, their improved optical properties enable them to exhibit good sensitivity and specificity for mitigating signal interference from various molecules in body fluids. Nanomaterials with biocompatible and optical sensing properties play a crucial role in advancing the maturity and diversification of liquid biopsy technologies. This article offers a comprehensive review of recent advanced liquid biopsy technologies that utilize novel biocompatible optical nanomaterials, including fluorescence, colorimetric, photoelectrochemical, and Raman broad-spectrum-based biosensors. We focused on liquid biopsy for the most significant early biomarkers in clinical medicine, and specifically reviewed reports on the effectiveness of optical nanosensing technology in the detection of real patient samples, which may provide basic evidence for the transition of optical nanosensing technology from engineering design to clinical practice. Furthermore, we introduced the integration of optical nanosensing-based liquid biopsy with modern devices, such as smartphones, to demonstrate the potential of the technology in portable clinical diagnosis.

Unraveling the dynamic slowdown in supercooled water: The role of dynamic disorder in jump motions

When a liquid is rapidly cooled below its melting point without inducing crystallization, its dynamics slow down significantly without noticeable structural changes. Elucidating the origin of this slowdown has been a long-standing challenge. Here, we report a theoretical investigation into the mechanism of the dynamic slowdown in supercooled water, a ubiquitous yet extraordinary substance characterized by various anomalous properties arising from local density fluctuations. Using molecular dynamics simulations, we found that the jump dynamics, which are elementary structural change processes, deviate from Poisson statistics with decreasing temperature. This deviation is attributed to slow variables competing with the jump motions, i.e., dynamic disorder. The present analysis of the dynamic disorder showed that the primary slow variable is the displacement of the fourth nearest oxygen atom of a jumping molecule, which occurs in an environment created by the fluctuations of molecules outside the first hydration shell. As the temperature decreases, the jump dynamics become slow and intermittent. These intermittent dynamics are attributed to the prolonged trapping of jumping molecules within extended and stable low-density domains. As the temperature continues to decrease, the number of slow variables increases due to the increased cooperative motions. Consequently, the jump dynamics proceed in a higher-dimensional space consisting of multiple slow variables, becoming slower and more intermittent. It is then conceivable that with further decreasing temperature, the slowing and intermittency of the jump dynamics intensify, eventually culminating in a glass transition.