We use quantized molecular dynamics simulations to characterize the role of enzyme vibrations in facilitating dihydrofolate reductase hydride transfer. By sampling the full ensemble of reactive trajectories, we are able to quantify and distinguish between statistical and dynamical correlations in the enzyme motion. We demonstrate the existence of nonequilibrium dynamical coupling between protein residues and the hydride tunneling reaction, and we characterize the spatial and temporal extent of these dynamical effects. Unlike statistical correlations, which give rise to nanometer-scale coupling between distal protein residues and the intrinsic reaction, dynamical correlations vanish at distances beyond 4-6 Å from the transferring hydride. This work finds a minimal role for nonlocal vibrational dynamics in enzyme catalysis, and it supports a model in which nanometer-scale protein fluctuations statistically modulate-or gate-the barrier for the intrinsic reaction.enzyme dynamics | hydrogen tunneling | path integral | ring polymer molecular dynamics P rotein motions are central to enzyme catalysis, with conformational changes on the micro-and millisecond timescale wellestablished to govern progress along the catalytic cycle (1, 2). Less is known about the role of faster, atomic-scale fluctuations that occur in the protein environment of the active site. The textbook view of enzyme-catalyzed reaction mechanisms neglects the functional role of such fluctuations and describes a static protein environment that both scaffolds the active-site region and reduces the reaction barrier (3). This view has grown controversial amid evidence that active-site chemistry is coupled to motions in the enzyme (4-6), and it has been explicitly challenged by recent proposals that enzyme-catalyzed reactions are driven by vibrational excitations that channel energy into the intrinsic reaction coordinate (7,8) or promote reactive tunneling (9, 10). In the following, we combine quantized molecular dynamics and rareevent sampling methods to determine the mechanism by which protein motions couple to reactive tunneling in dihydrofolate reductase and to clarify the role of nonequilibrium vibrational dynamics in enzyme catalysis.Manifestations of enzyme motion include both statistical and dynamical correlations. Statistical correlations are properties of the equilibrium ensemble and describe, for example, the degree to which fluctuations in the spatial position of one atom are influenced by fluctuations in another; these correlations govern the free-energy (FE) landscape and determine the transition state theory kinetics of the system (6). Dynamical correlations are properties of the time-evolution of the system and describe coupling between inertial atomic motions, as in a collective vibrational mode. Compelling evidence for long-ranged (i.e., nanometer-scale) networks of statistical correlations in enzymes emerges from genomic analysis (11), molecular dynamics simulations (11-13), and kinetic studies of double-mutant enzymes (14-16). But the rol...

Calcium carbonate (CaCO 3 ) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO 3 skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO 3 biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO 3 biomineralizing organisms.

SignificanceProtein fluctuations and hydrogen-bond networks play an important—although incompletely understood—role in facilitating efficient biological electron transfer (ET). Experimental mutagenesis results provide evidence for the role of protein motions in Ru-modified azurin ET, a quintessential example of biological ET. A recently developed nonadiabatic molecular dynamics method allows for exploration of the nature of protein fluctuations, providing insight into the conformational motions that accompany ET in Ru-modified azurin. In particular, a fluctuating hydrogen-bond network is identified that transiently ruptures to allow for donor–acceptor compression during ET.

We present evidence of exceptional preservation in the nacre and prismatic layers of a 66 Ma bivalve shell using photoemission electron spectromicroscopy (PEEM). PEEM is a novel method to assess in situ the quality of mineralogical and organic preservation. The analysis is non-invasive and non-destructive, providing spatially explicit maps of microstructure, organics and mineral components, and the crystallographic orientation in mollusk shells. Comparison of a Late Cretaceous and a modern shell demonstrates that the 66 Ma shell (1) preserves original aragonite and calcite crystals in nacre and prismatic layers, respectively, (2) maintains nearly identical mineral microstructure and crystal orientations, and (3) preserves interprismatic proteins. Remarkably, interprismatic proteins are preserved with intact peptide bonds, and suggest an abundance of the amino acid glycine. These findings in a 66 Ma shell support the exceptional quality of organic preservation documented here, which may prove to be relatively common among fossil shells that preserve nacre. PEEM analysis is useful for understanding taphonomic processes influencing shell and molecular fossil preservation over geologic time scales, and contributes to our knowledge of molluscan physiology, biomineralization, evolution, and diagenesis.

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