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Years ago, we identified a rapid vibrational motion  termed a rate-promoting vibration (RPV) as central to the reaction coordinate of some enzymes. This study addresses two key questions for one example enzyme we have studied, lactate dehydrogenase (LDH): first, what is a lower bound on the RPV’s contribution to catalytic efficiency, and second, what is the mechanism of RPV formation via allosteric transmission. The goal is to understand how we can artificially create such a system. LDH catalyzes the interconversion of pyruvate and lactate via hydride and proton transfer. Altering the motion range between Val31 and Arg106, central residues in the promoting vibration, with a modest constraint reduces the reaction rate (through a raising of the free energy barrier) by over 3 orders of magnitude. Committor analysis shows that shorter distances in the constrained system shift the transition state toward proton transfer, while natural or longer distances favor a transition state formed in hydride transfer. PCA confirms the anticorrelated motion between Val31 and Arg106, aligning with vibrational modes to optimize the reaction path. Critically, we find that a breathing motion among alpha helices is used to create the necessary distance over which a rapid and short RPV can be effective. Network analysis reveals that Val31, Ala34, and Cys35 have higher eigenvector centrality in reactive trajectories, indicating enhanced inter-residue communication. These findings underscore RPVs as crucial modulators of enzymatic function through dynamic and allosteric mechanisms and suggest an approach to the generation of nonbiologic protein catalysts that include a promoting vibration. 

p-Donor/Acceptor charge-transfer (CT) interactions between redox-complementary p-systems often give rise to non-native optical and electronic properties that are beneficial for modern electronics and energy technologies. However, the formation of extended supramolecular p-donor/acceptor stacks capable of long-range charge transport requires ingenious design strategies that can help reinforce otherwise weak p-donor/acceptor noncovalent interactions. Herein, we demonstrate that a large tetragonal prismatic metal–organic cage (MOC28+) having two parallel p-donor tetrakis(4- carboxyphenyl)-Zn-porphyrin (ZnTCPP) faces located B14 Å apart can accommodate up to three redox-complementary planar aromatic guests (either three p-acceptor guests or two p-acceptors surrounding one p-donor guest) between the ZnTCPP faces, forming extended p-donor/acceptor stacks. While empty MOC28+ behaves as an insulator due to the lack of charge delocalization across its large cavity, its inclusion complexes saturated with p-acidic hexaazatriphenylene hexacarbonitrile (HATHCN) and hexacyanotriphenylene (HCTP) displayed noticeably higher electrical conductivity (8.7   10 6 and 1.3   10 6 S m 1, respectively) owing to more facile charge transport through the p-donor/ acceptor stacks composed of the p-acidic guests intercalated between the ZnTCPP faces. Thus, this work demonstrates that tetragonal prismatic metallacages with two parallel electroactive faces can facilitate the creation of extended p-donor/acceptor stacks by encapsulating redox-complementary planar guests, which in turn facilitates through-space charge delocalization, generating non-native electrical conductivity. 

Abstract Accurate positioning of the mitotic spindle within the rounded cell body is critical to physiological maintenance. Mitotic cells encounter confinement from neighboring cells or the extracellular matrix (ECM), which can cause rotation of mitotic spindles and tilting of the metaphase plate (MP). To understand the effect of confinement on mitosis by fibers (ECM confinement), we use flexible ECM-mimicking nanofibers that allow natural rounding of the cell body while confining it to differing levels. Rounded mitotic bodies are anchored in place by actin retraction fibers (RFs) originating from adhesions on fibers. We discover that the extent of confinement influences RF organization in 3D, forming triangular and band-like patterns on the cell cortex under low and high confinement, respectively. Our mechanistic analysis reveals that the patterning of RFs on the cell cortex is the primary driver of the MP rotation. A stochastic Monte Carlo simulation of the centrosome, chromosome, membrane interactions, and 3D arrangement of RFs recovers MP tilting trends observed experimentally. Under high ECM confinement, the fibers can mechanically pinch the cortex, causing the MP to have localized deformations at contact sites with fibers. Interestingly, high ECM confinement leads to low and high MP tilts, which we mechanistically show to depend upon the extent of cortical deformation, RF patterning, and MP position. We identify that cortical deformation and RFs work in tandem to limit MP tilt, while asymmetric positioning of MP leads to high tilts. Overall, we provide fundamental insights into how mitosis may proceed in ECM-confining microenvironments in vivo. 

The relationship between the dynamics and structure of amorphous thin films and nanocomposites near their glass transition is an important problem in soft-matter physics. Here, we develop a simple theoretical approach to describe the density profile and the a-relaxation time of a glycerol-silica nanocomposite (S. Cheng et al., J. Chem. Phys., 2015, 143, 194704). We begin by applying the Derjaguin approximation, where we replace the curved surface of the particle with the planar one; thus, modeling the nanocomposite is reduced to that of a confined thin film. Subsequently, by employing the molecular dynamics (MD) simulation data of Cheng et al., we approximate the density profile of a supported liquid thin film as a stationary solution of a fourth-order partial differential equation (PDE). We then construct an appropriate density functional, from which the density profile emerges through the minimization of free energy. Our final assumption is that of a consistent, temperature-independent scaled density profile, ensuring that the free volume throughout the entire nanocomposite increases with temperature in a smooth, monotonic fashion. Considering the established relationship between glycerol relaxation time and temperature, we can employ Doolittle-type analysis (‘‘naı ¨ ve’’ free-volume model), to calculate the relaxation time based on temperature and film thickness. We then convert the film thickness into the interparticle distance and subsequently the filler volume fraction for the nanocomposites and compare our model predictions with experimental data, resulting in a good agreement. The proposed approach can be easily extended to other nanocomposite and film systems. 

Abstract Multicellular spheroids have shown great promise in 3D biology. Many techniques exist to form spheroids, but how cells take mechanical advantage of native fibrous extracellular matrix (ECM) to form spheroids remains unknown. Here, we identify the role of fiber diameter, architecture, and cell contractility on spheroids’ spontaneous formation and growth in ECM-mimicking fiber networks. We show that matrix deformability revealed through force measurements on aligned fiber networks promotes spheroid formation independent of fiber diameter. At the same time, larger-diameter crosshatched networks of low deformability abrogate spheroid formation. Thus, designing fiber networks of varying diameters and architectures allows spatial patterning of spheroids and monolayers simultaneously. Forces quantified during spheroid formation revealed the contractile role of Rho-associated protein kinase in spheroid formation and maintenance. Interestingly, we observed spheroid–spheroid and multiple spheroid mergers initiated by cell exchanges to form cellular bridges connecting the two spheroids. Unexpectedly, we found large pericyte spheroids contract rhythmically. Transcriptomic analysis revealed striking changes in cell–cell, cell–matrix, and mechanosensing gene expression profiles concordant with spheroid assembly on fiber networks. Overall, we ascertained that contractility and network deformability work together to spontaneously form and pattern 3D spheroids, potentially connecting in vivo matrix biology with developmental, disease, and regenerative biology.