Enzymatic transition states and dynamic motion in barrier crossing

Structural and Biochemical Analysis of Butanol Dehydrogenase From Thermotoga maritima

Butanol dehydrogenase (BDH) plays a crucial role in butanol biosynthesis by catalyzing the conversion of butanal to butanol using the coenzyme NAD(P)H. In this study, we observed that BDH from Thermotoga maritima (TmBDH) exhibits dual coenzyme specificity and catalytic activity with NADPH as the coenzyme under highly alkaline conditions. Additionally, a thermal stability analysis on TmBDH demonstrated its excellent activity retention even at elevated temperatures of 80°C. These findings demonstrate the superior thermal stability of TmBDH and suggest that it is a promising candidate for large-scale industrial butanol production. Furthermore, we discovered that TmBDH effectively catalyzes the conversion of aldehydes to alcohols and exhibits a wide range of substrate specificities toward aldehydes, while excluding alcohols. The dimeric state of TmBDH was observed using rapid online buffer exchange native mass spectrometry. Additionally, we analyzed the coenzyme-binding sites and inferred the possible locations of the substrate-binding sites. These results provide insights that improve our understanding of BDHs.

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling

The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.

Computational Investigation of the Covalent Inhibition Mechanism of Bruton's Tyrosine Kinase by Ibrutinib

Covalent inhibitors represent a promising class of therapeutic compounds. Nonetheless, rationally designing covalent inhibitors to achieve a right balance between selectivity and reactivity remains extremely challenging. To better understand the covalent binding mechanism, a computational study is carried out using the irreversible covalent inhibitor of Bruton tyrosine kinase (BTK) ibrutinib as an example. A multi-μs classical molecular dynamics trajectory of the unlinked inhibitor is generated to explore the fluctuations of the compound associated with the kinase binding pocket. Then, the reaction pathway leading to the formation of the covalent bond with the cysteine residue at position 481 via a Michael addition is determined using the string method in collective variables on the basis of hybrid quantum mechanical-molecular mechanical (QM/MM) simulations. The reaction pathway shows a strong correlation between the covalent bond formation and the protonation/deprotonation events taking place sequentially in the covalent inhibition reaction, consistent with a 3-step reaction with transient thiolate and enolates intermediate states. Two possible atomistic mechanisms affecting deprotonation/protonation events from the thiolate to the enolate intermediate were observed: a highly correlated direct pathway involving proton transfer to the Cα of the acrylamide warhead from the cysteine involving one or a few water molecules and a more indirect pathway involving a long-lived enolate intermediate state following the escape of the proton to the bulk solution. The results are compared with experiments by simulating the long-time kinetics of the reaction using kinetic modeling.

Transition Path Sampling Study of Engineered Enzymes That Catalyze the Morita-Baylis-Hillman Reaction: Why Is Enzyme Design so Difficult?

It is hoped that artificial enzymes designed in laboratories can be efficient alternatives to chemical catalysts that have been used to synthesize organic molecules. However, the design of artificial enzymes is challenging and requires a detailed molecular-level analysis to understand the mechanism they promote in order to design efficient variants. In this study, we computationally investigate the mechanism of proficient Morita-Baylis-Hillman enzymes developed using a combination of computational design and directed evolution. The powerful transition path sampling method coupled with in-depth post-processing analysis has been successfully used to elucidate the different chemical pathways, transition states, protein dynamics, and free energy barriers of reactions catalyzed by such laboratory-optimized enzymes. This research provides an explanation for how different chemical modifications in an enzyme affect its catalytic activity in ways that are not predictable by static design algorithms.

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.

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

Proteins exhibit conformational fluctuations and changes over various time scales, ranging from rapid picosecond-scale local atomic motions to slower microsecond-scale global conformational transformations. In the presence of these intricate fluctuations, chemical reactions occur and functions emerge. These conformational fluctuations of proteins are not merely stochastic random motions but possess distinct spatiotemporal characteristics. Moreover, chemical reactions do not always proceed along a single reaction coordinate in a quasi-equilibrium manner. Therefore, it is essential to understand spatiotemporal conformational fluctuations of proteins and the conformational change processes associated with reactions. In this Perspective, we shed light on the complex dynamics of proteins and their role in enzyme catalysis by presenting recent results regarding dynamic couplings and disorder in the conformational dynamics of proteins and rare but rapid enzymatic reaction events obtained from molecular dynamics simulations.

Substrate Positioning Dynamics Involves a Non-Electrostatic Component to Mediate Catalysis

Substrate positioning dynamics (SPD) orients the substrate in the active site, thereby influencing catalytic efficiency. However, it remains unknown whether SPD effects originate primarily from electrostatic perturbation inside the enzyme or can independently mediate catalysis with a significant non-electrostatic component. In this work, we investigated how the non-electrostatic component of SPD affects transition state (TS) stabilization. Using high-throughput enzyme modeling, we selected Kemp eliminase variants with similar electrostatics inside the enzyme but significantly different SPD. The kinetic parameters of these mutants were experimentally characterized. We observed a valley-shaped, two-segment linear correlation between the TS stabilization free energy (converted from kinetic parameters) and substrate positioning index (a metric to quantify SPD). The energy varies by approximately 2 kcal/mol. Favorable SPD was observed for the distal mutant R154W, increasing the proportion of reactive conformations and leading to the lowest activation free energy. These results indicate the substantial contribution of the non-electrostatic component of SPD to enzyme catalytic efficiency.

Targeted Mutation of a Non-catalytic Gating Residue Increases the Rate of Pseudomonas aeruginosa d-Arginine Dehydrogenase Catalytic Turnover

Commercial food and l-amino acid industries rely on bioengineered d-amino acid oxidizing enzymes to detect and remove d-amino acid contaminants. However, the bioengineering of enzymes to generate faster biological catalysts has proven difficult as a result of the failure to target specific kinetic steps that limit enzyme turnover, kcat, and the poor understanding of loop dynamics critical for catalysis. Pseudomonas aeruginosa d-arginine dehydrogenase (PaDADH) oxidizes most d-amino acids and is a good candidate for application in the l-amino acid and food industries. The side chain of the loop L2 E246 residue located at the entrance of the PaDADH active site pocket potentially favors the closed active site conformation and secures the substrate upon binding. This study used site-directed mutagenesis, steady-state, and rapid reaction kinetics to generate the glutamine, glycine, and leucine variants and investigate whether increasing the rate of product release could translate to an increased enzyme turnover rate. Upon E246 mutation to glycine, there was an increased rate of d-arginine turnover kcat from 122 to 500 s-1. Likewise, the kcat values increased 2-fold for the glutamine or leucine variants. Thus, we have engineered a faster biocatalyst for industrial applications by selectively increasing the rate of the PaDADH product release.

Decreased Transition-State Analogue Affinity in Isotopically Heavy MTAN with Increased Catalysis

5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori (HpMTAN) demonstrated faster chemistry when expressed as an isotopically heavy protein, with 2H, 13C, and 15N replacing the bulk of normal isotopes. The inverse heavy enzyme isotope effect has been attributed to improved enzyme-reactant interactions causing more frequent transition-state formation ( Proc. Natl. Acad. Sci. U.S.A. 2021, 118, e2109118118). Transition-state analogues stabilize the transient dynamic geometry of the transition state and inform on transition-state dynamics. Here, a slow-onset, tight-binding transition-state analogue of HpMTAN is characterized with heavy and light enzymes. Dissociation constants for the initial encounter complex (Ki) and for the tightly bound complex after slow-onset inhibition (Ki*) with hexylthio-DADMe-Immucillin-A (HTDIA) gave Ki values for light and heavy HpMTAN = 52 ± 10 and 85 ± 13 pM and Ki* values = 5.9 ± 0.3 and 10.0 ± 1.2 pM, respectively. HTDIA dissociates from heavy HpMTAN at 0.063 ± 0.002 min-1, faster than that from light HpMTAN at 0.032 ± 0.004 min-1. These values are consistent with transition-state formation by an improved catalytic site dynamic search and inconsistent with catalytic efficiency proportional to tight binding of the transition state.

Reactivity Tracking of an Enzyme Progress Coordinate

The reactivity of individual solvent-coupled protein configurations is used to track and resolve the progress coordinate for the core reaction sequence of substrate radical rearrangement and hydrogen atom transfer in the ethanolamine ammonia-lyase (EAL) enzyme from Salmonella enterica. The first-order decay of the substrate radical intermediate is the monitored reaction. Heterogeneous confinement from sucrose hydrates in the mesophase solvent surrounding the cryotrapped protein introduces distributed kinetics in the non-native decay of the substrate radical pair capture substate, which arise from an ensemble of configurational microstates. Reaction rates increase by >103-fold across the distribution to approach that for the native enabled substate for radical rearrangement, which reacts with monotonic kinetics. The native progress coordinate thus involves a collapse of the configuration space to generate optimized reactivity. Reactivity tracking reveals fundamental features of solvent-protein-reaction configurational coupling and leads to a model that refines the ensemble paradigm of enzyme catalysis for strongly adiabatic chemical steps.

Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations

The initial phases of drug discovery - in silico drug design - could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines - so far an unmet and crucial goal - will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.

Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling

Despite initial resistance, it has been increasingly accepted that protein dynamics plays a role in enzymatic catalysis. There have been two lines of research. Some works study slow conformational motions that are not coupled to the reaction coordinate, but guide the system towards catalytically competent conformations. Understanding at the atomistic level how this is accomplished has remained elusive except for a few systems. In this review we focus on fast sub-picosecond motions that are coupled to the reaction coordinate. The use of Transition Path Sampling has allowed us an atomistic description of how these rate-promoting vibrational motions are incorporated in the reaction mechanism. We will also show how we used insights from rate-promoting motions in protein design.

Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase

The influence of protein motions on enzyme catalysis remains a topic of active discussion. Protein motions occur across a variety of time scales, from vibrational fluctuations in femtoseconds, to collective motions in milliseconds. There have been numerous studies that show conformational motions may assist in catalysis, protein folding, and substrate specificity. It is also known through transition path sampling studies that rapid promoting vibrations contribute to enzyme catalysis. Human purine nucleoside phosphorylase (PNP) is one enzyme that contains both an important conformational motion and a rapid promoting vibration. The slower motion in this enzyme is associated with a loop motion, that when open allows substrate entry and product release but closes over the active site during catalysis. We examine the differences between an unconstrained PNP structure and a PNP structure with constraints on the loop motion. To investigate possible coupling between the slow and fast protein dynamics, we employed transition path sampling, reaction coordinate identification, electric field calculations, and free energy calculations reported here.

Dynamical activation of function in metalloenzymes

Formulations of hydrogen tunneling in enzyme-catalysed C-H activation reactions indicate enthalpic barriers to reaction that are independent of chemical steps and dependent on the protein scaffold. A tool to identify catalytically relevant site-specific protein thermal networks has emerged from temperature-dependent hydrogen deuterium exchange (TDHDX). Focusing on mutant enzyme forms with altered activation energies for catalysis, TDHDX provides a comparative analysis of the impact of mutation on Ea for local protein unfolding. Identified thermal networks appear unrelated to protein scaffold conservation and track to the dictates of the catalysed reaction, including sites for metal binding. The positions of thermal networks provide a framework for further understanding of time-dependent, functionally relevant protein motions. Measurement of nanosecond Stokes shifts at the surface of the thermal network in soybean lipoxygenase yields activation energies that are identical to Ea values measured for kcat . This finding identifies a rapid (> nanosecond), long-range and cooperative structural reorganization as the thermal barrier to catalysis. A model for protein dynamics is put forward that integrates broadly distributed protein conformational sampling with protein embedded thermal networks.

DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies

Antibiotic resistance is a global health problem in which mutations occurring in functional proteins render drugs ineffective. The working mechanisms of the arising mutants are seldom apparent; a methodology to decipher these mechanisms systematically would render devising therapies to control the arising mutational pathways possible. Here we utilize C_α-C_β bond vector relaxations obtained from moderate length MD trajectories to determine conduits for functionality of the resistance conferring mutants of Escherichia coli dihydrofolate reductase. We find that the whole enzyme is synchronized to the motions of the substrate, irrespective of the mutation introducing gain-of-function or loss-of function. The total coordination of the motions suggests changes in the hydrogen bond dynamics with respect to the wild type as a possible route to determine and classify the mode-of-action of individual mutants. As a result, nine trimethoprim-resistant point mutations arising frequently in evolution experiments are categorized. One group of mutants that display the largest occurrence (L28R, W30G) work directly by modifying the dihydrofolate binding region. Conversely, W30R works indirectly by the formation of the E139-R30 salt bridge which releases energy resulting from tight binding by distorting the binding cavity. A third group (D27E, F153S, I94L) arising as single, resistance invoking mutants in evolution experiment trajectories allosterically and dynamically affects a hydrogen bonding motif formed at residues 59-69-71 which in turn modifies the binding site dynamics. The final group (I5F, A26T, R98P) consists of those mutants that have properties most similar to the wild type; these only appear after one of the other mutants is fixed on the protein structure and therefore display clear epistasis. Thus, we show that the binding event is governed by the entire enzyme dynamics while the binding site residues play gating roles. The adjustments made in the total enzyme in response to point mutations are what make quantifying and pinpointing their effect a hard problem. Here, we show that hydrogen bond dynamics recorded on sub-μs time scales provide the necessary fingerprints to decipher the various mechanisms at play.

Temperature-dependent hydrogen deuterium exchange shows impact of analog binding on adenosine deaminase flexibility but not embedded thermal networks

The analysis of hydrogen deuterium exchange by mass spectrometry as a function of temperature and mutation (TDHDX-MS) has emerged as a generic and efficient tool for the spatial resolution of protein networks that are proposed to function in the thermal activation of catalysis. In this work, we extend TDHDX from apo-enzyme structures to protein-ligand complexes. Using adenosine deaminase as a prototype, we compared the impacts of a substrate analog (1-deaza-adenosine or DAA) and a very tight-binding inhibitor/transition state analog (pentostatin) at single and multiple temperatures. At a single temperature, we observed different HDX-MS properties for the two ligands, as expected from their 10⁶-fold differences in strength of binding. By contrast, analogous patterns for TDHDX-MS emerge in the presence of both DAA and pentostatin, indicating similar impacts of either ligand on the enthalpic barriers for local protein unfolding. We extended TDHDX to a function-altering mutant of adenosine deaminase in the presence of pentostatin and revealed a protein thermal network that is highly similar to that previously reported for the apo-enzyme (Gao et al., 2020, JACS 142, 19936-19949). Finally, we discuss the differential impacts of pentostatin binding on overall protein flexibility vs. site-specific thermal transfer pathways in the context of models for substrate-induced changes to a distributed protein conformational landscape that act in synergy with embedded protein thermal networks to achieve efficient catalysis.

Transition Path Sampling Based Calculations of Free Energies for Enzymatic Reactions: The Case of Human Methionine Adenosyl Transferase and Plasmodium vivax Adenosine Deaminase

Transition path sampling (TPS) is widely used for the calculations of reaction rates, transition state structures, and reaction coordinates of condensed phase systems. Here we discuss a scheme for the calculation of free energies using the ensemble of TPS reactive trajectories in combination with a window-based sampling technique for enzyme-catalyzed reactions. We calculate the free energy profiles of the reactions catalyzed by the human methionine S-adenosyltransferase (MAT2A) enzyme and the Plasmodium vivax adenosine deaminase (pvADA) enzyme to assess the accuracy of this method. MAT2A catalyzes the formation of S-adenosine-l-methionine following a S_N2 mechanism, and using our method, we estimate the free energy barrier for this reaction to be 16 kcal mol^-1, which is in excellent agreement with the experimentally measured activation energy of 17.27 kcal mol^-1. Furthermore, for the pvADA enzyme-catalyzed reaction we estimate a free energy barrier of 21 kcal mol^-1, and the calculated free energy profile is similar to that predicted from experimental observations. Calculating free energies by employing our simple method within TPS provides significant advantages over methods such as umbrella sampling because it is free from any applied external bias, is accurate compared to experimental measurements, and has a reasonable computational cost.

Molecular Insights into the Intrinsic Dynamics and Their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase

Proteins are intrinsically dynamic and change conformations over a wide range of time scales. While the conformational dynamics have been realized to be important for protein functions, e.g., in activity-stability trade-offs, how they play a role during enzyme catalysis has been of debate over decades. By studying Pin1 peptidyl-prolyl isomerase using extensive molecular dynamics simulations, here we discuss how the slow intrinsic dynamics of Pin1 observed in the NMR relaxation dispersion experiment occur and couple to isomerization reactions in molecular detail. In particular, we analyze the angular correlation functions of the backbone N-H bonds and find that slow conformational transitions occur at about the 3₁₀ helix in the apo state. These events at the helical region further affect the residues at about the ligand binding site. Unfolding of this helix leads to a tight hydrogen bond between the helical region and the ligand binding loop, thus forming a stable coiled structure. The helical and coiled structures are found to be characteristic of the Pin1-ligand complex with the ligand in the trans and cis states, respectively. These results indicate that the changes in the slow dynamics of Pin1 by the isomerization reaction occur via the shift in populations of the helical and coiled states, where the balance is dependent on the ligand isomerization states.

The ω3 scaling of the vibrational density of states in quasi-2D nanoconfined solids

The vibrational properties of crystalline bulk materials are well described by Debye theory, which successfully predicts the quadratic ω² low-frequency scaling of the vibrational density of states. However, the analogous framework for nanoconfined materials with fewer degrees of freedom has been far less well explored. Using inelastic neutron scattering, we characterize the vibrational density of states of amorphous ice confined inside graphene oxide membranes and we observe a crossover from the Debye ω² scaling to an anomalous ω³ behaviour upon reducing the confinement size L. Additionally, using molecular dynamics simulations, we confirm the experimental findings and prove that such a scaling appears in both crystalline and amorphous solids under slab-confinement. We theoretically demonstrate that this low-frequency ω³ law results from the geometric constraints on the momentum phase space induced by confinement along one spatial direction. Finally, we predict that the Debye scaling reappears at a characteristic frequency ω_× = vL/2π, with v the speed of sound of the material, and we confirm this quantitative estimate with simulations.

A description of the vibrational properties of amorphous ice confined in graphene oxide membranes, as an exemplary nanoconfined material, is presented. Inelastic neutron scattering experiments and molecular dynamics simulations show anomalous deviations from standard bulk behavior.

Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu

Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural flexibility in affecting the activation energy barrier of a flexible multidomain enzyme adenylate kinase (AK3L1, UniProtKB: Q9UIJ7). Activation energy profiles of both local (at three different sites along the polypeptide backbone) and global dynamics of the enzyme have been monitored using solvation studies on the subnanosecond time scale and tryptophan quenching studies over the temperature range of 278-323 K, respectively, under crowded conditions (Ficoll 70, Dextran 40, Dextran 70, and PEG 8). This study not only provides the site-specific mapping of dynamics but reveals that the activation energies associated with these local motions undergo a significant decrease in the presence of macromolecular crowders, providing new insights into how crowding affects internal protein dynamics. The crowded scenario also aids in enhancing the coupling between the local and global motions of the enzyme. Moreover, select portions/regions of the enzyme when taken together can well mirror the overall dynamics of the biomolecule, showing possible energy hotspots along the polypeptide backbone.

General principles of secondary active transporter function

Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.

Mechanism for the rare fluctuation that powers protein conformational change

Most functional processes of biomolecules are rare events. Key to a rare event is the rare fluctuation that enables the energy activation process that precedes and powers crossing of the activation barrier. However, the physical nature of this rare fluctuation and how it enables energy activation and subsequently barrier crossing are unknown. We developed a novel metric, the reaction capacity pC, that rigorously defines the beginning and parameterizes the progress of energy activation. This enabled us to identify the rare fluctuation as a special phase-space condition that is necessary and sufficient for initiating systematic energy flow from the non-reaction coordinates into the reaction coordinates. The energy activation of a prototype biomolecular isomerization reaction is dominated by kinetic energy transferring into and accumulating in the reaction coordinates, administered by inertial forces alone. This mechanism for energy activation is fundamentally different from the mechanism suggested by Kramers theory.

Engineered Tryptophan Synthase Balances Equilibrium Effects and Fast Dynamic Effects

Creating efficient and stable enzymes for catalysis in pharmaceutical and industrial laboratories is an important research goal. Arnold et al. used directed evolution to engineer a natural tryptophan synthase to create a mutant that is operable under laboratory conditions without the need for a natural allosteric effector. The use of directed evolution allows researchers to improve enzymes without understanding the structure-activity relationship. Here, we present a transition path sampling study of a key chemical transformation in the tryptophan synthase catalytic cycle. We observed that while directed evolution does mimic the natural allosteric effect from a stability perspective, fast protein dynamics associated with chemistry has been dramatically altered. This work provides further evidence of the role of protein dynamics in catalysis and clearly demonstrates the multifaceted complexity of mutations associated with protein engineering. This study also demonstrates a fascinating contrast between allosteric and stand-alone functions at the femtosecond time scale.

Experimental mapping of short-wavelength phonons in proteins

Phonons are quasi-particles, observed as lattice vibrations in periodic materials, that often dampen in the presence of structural perturbations. Nevertheless, phonon-like collective excitations exist in highly complex systems, such as proteins, although the origin of such collective motions has remained elusive. Here we present a picture of temperature and hydration dependence of collective excitations in green fluorescent protein (GFP) obtained by inelastic neutron scattering. Our results provide evidence that such excitations can be used as a measure of flexibility/softness and are possibly associated with the protein’s activity. Moreover, we show that the hydration water in GFP interferes with the phonon propagation pathway, enhancing the structural rigidity and stability of GFP.

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Quantum phenomena in biology have long fascinated people around the world

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This work presents a direct experimental observation of phonons, the quantum vibrations in a protein

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The collective excitations or phonons in proteins were detected by utilizing inelastic neutron scattering technique at Oak Ridge National Laboratory

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Our results illustrate the flexibility-activity relationship in proteins by mapping the temperature and hydration dependence of these collective excitations

Chemical Mapping Exposes the Importance of Active Site Interactions in Governing the Temperature Dependence of Enzyme Turnover

Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔC _P ^‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme-substrate interactions and the global dynamics of the protein. We find that changes in ΔC _P ^‡ and protein dynamics can be mapped to specific substrate-enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.

Exploring Dihydroflavonol-4-Reductase Reactivity and Selectivity by QM/MM-MD Simulations

Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.

Correlated Motions in Structural Biology

Correlated motions in proteins arising from the collective movements of residues have long been proposed to be fundamentally important to key properties of proteins, from allostery and catalysis to evolvability. Recent breakthroughs in structural biology have made it possible to capture proteins undergoing complex conformational changes, yet intrinsic correlated motions within a conformation remain one of the least understood facets of protein structure. For many decades, the analysis of total X-ray scattering held the promise of animating crystal structures with correlated motions. With recent advances in both X-ray detectors and data interpretation methods, this long-held promise can now be met. In this Perspective, we will introduce how correlated motions are captured in total scattering and provide guidelines for the collection, interpretation, and validation of data. As structural biology continues to push the boundaries, we see an opportunity to gain atomistic insight into correlated motions using total scattering as a bridge between theory and experiment.

Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology

To gain insight into the reaction mechanism of activated processes, we introduce an exact approach for quantifying the topology of high-dimensional probability surfaces of the underlying dynamic processes. Instead of Morse indexes, we study the homology groups of a sequence of superlevel sets of the probability surface over high-dimensional configuration spaces using persistent homology. For alanine-dipeptide isomerization, a prototype of activated processes, we identify locations of probability peaks and connecting ridges, along with measures of their global prominence. Instead of a saddle point, the transition state ensemble (TSE) of conformations is at the most prominent probability peak after reactants/products, when proper reaction coordinates are included. Intuition-based models, even those exhibiting a double-well, fail to capture the dynamics of the activated process. Peak occurrence, prominence, and locations can be distorted upon subspace projection. While principal component analysis accounts for conformational variance, it inflates the complexity of the surface topology and destroys the dynamic properties of the topological features. In contrast, TSE emerges naturally as the most prominent peak beyond the reactant/product basins, when projected to a subspace of minimum dimension containing the reaction coordinates. Our approach is general and can be applied to investigate the topology of high-dimensional probability surfaces of other activated processes.

Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations

Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.

Protein Mass-Modulated Effects in Alkaline Phosphatase

Recent experimental studies engaging isotopically substituted protein (heavy protein) have revealed that many, but not all, enzymatic systems exhibit altered chemical steps in response to an altered mass. The results have been interpreted as femtosecond protein dynamics at the active site being linked (or not) to transition-state barrier crossing. An altered enzyme mass can influence several kinetic parameters (kcat, Km, and kchem) in amounts of ≤30% relative to light enzymes. An early report on deuterium-labeled Escherichia coli alkaline phosphatase (AP) showed an unusually large enzyme kinetic isotope effect on kcat. We examined steady-state and chemical step properties of native AP, [2H]AP, and [2H,13C,15N]AP to characterize the role of heavy enzyme protein dynamics in reactions catalyzed by AP. Both [2H]- and [2H,13C,15N]APs showed unaltered steady-state and single-turnover rate constants. These findings characterize AP as one of the enzymes in which mass-dependent catalytic site dynamics is dominated by reactant-linked atomic motions. Two catalytic site zinc ions activate the oxygen nucleophiles in the catalytic site of AP. The mass of the zinc ions is unchanged in light and heavy APs. They are essentially linked to catalysis and provide a possible explanation for the loss of linkage between catalysis and protein mass in these enzymes.

Low-Frequency Protein Motions Coupled to Catalytic Sites

This review examines low-frequency vibrational modes of proteins and their coupling to enzyme catalytic sites. That protein motions are critical to enzyme function is clear, but the kinds of motions present in proteins and how they are involved in function remain unclear. Several models of enzyme-catalyzed reaction suggest that protein dynamics may be involved in the chemical step of the catalyzed reaction, but the evidence in support of such models is indirect. Spectroscopic studies of low-frequency protein vibrations consistently show that there are underdamped modes of the protein with frequencies in the tens of wavenumbers where overdamped behavior would be expected. Recent studies even show that such underdamped vibrations modulate enzyme active sites. These observations suggest that increasingly sophisticated spectroscopic methods will be able to unravel the link between low-frequency protein vibrations and enzyme function.

Dynamic Instability from Non-equilibrium Structural Transitions on the Energy Landscape of Microtubule

Microtubules are the backbone of the cytoskeleton and vital to numerous cellular processes. The central dogma of microtubules is that all their functions are driven by dynamic instability, but its mechanism has remained unresolved for over 30 years because of conceptual difficulties inherent in the dominant GTP-cap framework. We present a physically rigorous structural mechanochemical model: dynamic instability is driven by non-equilibrium transitions between the bent (B), straight (S), and curved (C) forms of tubulin monomers and longitudinal interfaces in the two-dimensional lattice of microtubule. All the different phenomena (growth, shortening, catastrophe, rescue, and pausing) are controlled by the kinetic pathways for B↔S↔C transitions and corresponding energy landscapes. Different kinetics at minus end are due to different B↔S↔C pathways imposed by the polarity of microtubule lattice. This model enables us to reproduce all the observed phenomena of dynamic instability of purified tubulins in kinetic simulations.

The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol

Terpene synthases generate terpenes employing diversified carbocation chemistry, including highly specific ring formations, proton and hydride transfers, and methyl as well as methylene migrations, followed by reaction quenching. In this enzyme family, the main catalytic challenge is not rate enhancement, but rather structural and reactive control of intrinsically unstable carbocations in order to guide the resulting product distribution. Here we employ multiscale modeling within classical and quantum dynamics frameworks to investigate the reaction mechanism in the diterpene synthase CotB2, commencing with the substrate geranyl geranyl diphosphate and terminating with the carbocation precursor to the final product cyclooctat-9-en-7-ol. The 11-step in-enzyme carbocation cascade is compared with the same reaction in the absence of the enzyme. Remarkably, the free energy profiles in gas phase and in CotB2 are surprisingly similar. This similarity contrasts the multitude of strong π-cation, dipole-cation, and ion-pair interactions between all intermediates in the reaction cascade and the enzyme, suggesting a remarkable balance of interactions in CotB2. We ascribe this balance to the similar magnitude of the interactions between the carbocations along the reaction coordinate and the enzyme environment. The effect of CotB2 mutations is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, pointing the way for future terpene synthase design.

Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis

Proteins are intrinsically flexible macromolecules that undergo internal motions with time scales spanning femtoseconds to milliseconds. These fluctuations are implicated in the optimization of reaction barriers for enzyme catalyzed reactions. Time, temperature, and mutation dependent hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has been previously employed to identify spatially resolved, catalysis-linked dynamical regions of enzymes. We now extend this technique to pursue the correlation of protein flexibility and chemical reactivity within the diverse and widespread TIM barrel proteins, targeting murine adenosine deaminase (mADA) that catalyzes the irreversible deamination of adenosine to inosine and ammonia. Following a structure-function analysis of rate and activation energy for a series of mutations at a second sphere phenylalanine positioned in proximity to the bound substrate, the catalytically impaired Phe61Ala with an elevated activation energy (Ea = 7.5 kcal/mol) and the wild type (WT) mADA (Ea = 5.0 kcal/mol) were selected for HDX-MS experiments. The rate constants and activation energies of HDX for peptide segments are quantified and used to assess mutation-dependent changes in local and distal motions. Analyses reveal that approximately 50% of the protein sequence of Phe61Ala displays significant changes in the temperature dependence of HDX behaviors, with the dominant change being an increase in protein flexibility. Utilizing Phe61Ile, which displays the same activation energy for k_cat as WT, as a control, we were able to further refine the HDX analysis, highlighting the regions of mADA that are altered in a functionally relevant manner. A map is constructed that illustrates the regions of protein that are proposed to be essential for the thermal optimization of active site configurations that dominate reaction barrier crossings in the native enzyme.

Catalytic Effect of Electric Fields on the Kemp Elimination Reactions with Neutral Bases

The effect of solvent reaction fields and oriented electric fields on the Kemp elimination reaction between methylamine or imidazole and 5-nitrobenzisoxazole has been theoretically studied. The Kemp reaction is the most widely used for the design of new enzymes. Our results, using the SMD continuous model for solvents, are in quite good agreement with the experimental fact that the rate of the analogous reaction with butylamine is one order of magnitude smaller in water than in acetonitrile. In the case of external electric fields, our results show that they can increase or decrease the energy barrier depending on the magnitude and orientation of the field. A duly oriented electric field may have a notable catalytic effect on the reaction. So, external electric fields and reaction fields due to the medium can contribute to the design of new enzymes. Several factors that must be taken into account to increase the catalytic effect are discussed.

Nano-second protein dynamics of key residue at Position 38 in catechol-O-methyltransferase system: a time-resolved fluorescence study

Human catechol-O-methyltransferase, a key enzyme related to neurotransmitter metabolism, catalyses a methyl transfer from S-adenosylmethionine to catechol. Although extensive studies aim to understand the enzyme mechanisms, the connection of protein dynamics and enzyme catalysis is still not clear. Here, W38in (Trp143Phe) and W38in/Y68A (Trp143Phe with Tyr68Ala) mutants were carried out to study the relationship of dynamics and catalysis in nano-second timescale using time-resolved fluorescence lifetimes and Stokes shifts in various solvents. The comprehensive data implied the mutant W38in/Y68A with lower activity is more rigid than the ‘WT’−W38in, suggesting the importance of flexibility at residue 38 to maintain the optimal catalysis.

Directed Evolution's Influence on Rapid Density Fluctuations Illustrates How Protein Dynamics Can Become Coupled to Chemistry

Protein engineering is a growing field with a variety of experimental techniques available for altering protein function. However, creating an enzyme de novo is still in its infancy, so far yielding enzymes of modest catalytic efficiency. In this study, a system of artificial retro-aldolase enzymes found to have chemistry coupled to protein dynamics was examined. The original design was created computationally, and this protein was then subjected to directed evolution to improve the initial low catalytic efficiency. We found that this re-engineering of the enzyme resulted in rapid density fluctuations throughout the enzyme being reshaped via alterations in the hydrogen bonding network. This work also led to the discovery of a second important motion which aids in the release of an intermediate product. These results provide compelling evidence that to engineer efficient protein catalysts, fast protein dynamics need to be considered in the design.

Selectins-The Two Dr. Jekyll and Mr. Hyde Faces of Adhesion Molecules-A Review

Selectins belong to a group of adhesion molecules that fulfill an essential role in immune and inflammatory responses and tissue healing. Selectins are glycoproteins that decode the information carried by glycan structures, and non-covalent interactions of selectins with these glycan structures mediate biological processes. The sialylated and fucosylated tetrasaccharide sLe^x is an essential glycan recognized by selectins. Several glycosyltransferases are responsible for the biosynthesis of the sLe^x tetrasaccharide. Selectins are involved in a sequence of interactions of circulated leukocytes with endothelial cells in the blood called the adhesion cascade. Recently, it has become evident that cancer cells utilize a similar adhesion cascade to promote metastases. However, like Dr. Jekyll and Mr. Hyde’s two faces, selectins also contribute to tissue destruction during some infections and inflammatory diseases. The most prominent function of selectins is associated with the initial stage of the leukocyte adhesion cascade, in which selectin binding enables tethering and rolling. The first adhesive event occurs through specific non-covalent interactions between selectins and their ligands, with glycans functioning as an interface between leukocytes or cancer cells and the endothelium. Targeting these interactions remains a principal strategy aimed at developing new therapies for the treatment of immune and inflammatory disorders and cancer. In this review, we will survey the significant contributions to and the current status of the understanding of the structure of selectins and the role of selectins in various biological processes. The potential of selectins and their ligands as therapeutic targets in chronic and acute inflammatory diseases and cancer will also be discussed. We will emphasize the structural characteristic of selectins and the catalytic mechanisms of glycosyltransferases involved in the biosynthesis of glycan recognition determinants. Furthermore, recent achievements in the synthesis of selectin inhibitors will be reviewed with a focus on the various strategies used for the development of glycosyltransferase inhibitors, including substrate analog inhibitors and transition state analog inhibitors, which are based on knowledge of the catalytic mechanism.

Hydrogen deuterium exchange defines catalytically linked regions of protein flexibility in the catechol O-methyltransferase reaction

Human catechol O-methyltransferase (COMT) has emerged as a model for understanding enzyme-catalyzed methyl transfer from S-adenosylmethionine (AdoMet) to small-molecule catecholate acceptors. Mutation of a single residue (tyrosine 68) behind the methyl-bearing sulfonium of AdoMet was previously shown to impair COMT activity by interfering with methyl donor-acceptor compaction within the activated ground state of the wild type enzyme [J. Zhang, H. J. Kulik, T. J. Martinez, J. P. Klinman, Proc. Natl. Acad. Sci. U.S.A. 112, 7954-7959 (2015)]. This predicts the involvement of spatially defined protein dynamical effects that further tune the donor/acceptor distance and geometry as well as the electrostatics of the reactants. Here, we present a hydrogen/deuterium exchange (HDX)-mass spectrometric study of wild type and mutant COMT, comparing temperature dependences of HDX against corresponding kinetic and cofactor binding parameters. The data show that the impaired Tyr68Ala mutant displays similar breaks in Arrhenius plots of both kinetic and HDX properties that are absent in the wild type enzyme. The spatial resolution of HDX below a break point of 15-20 °C indicates changes in flexibility across ∼40% of the protein structure that is confined primarily to the periphery of the AdoMet binding site. Above 20 °C, Tyr68Ala behaves more like WT in HDX, but its rate and enthalpic barrier remain significantly altered. The impairment of catalysis by Tyr68Ala can be understood in the context of a mutationally induced alteration in protein motions that becomes manifest along and perpendicular to the primary group transfer coordinate.

Dissecting the Dynamics during Enzyme Catalysis: A Case Study of Pin1 Peptidyl-Prolyl Isomerase

Free energy surfaces have played a central role in studying protein conformational changes and enzymatic reactions over decades. Yet, free energy barriers and kinetics are highly dependent on the coordinates chosen to define the surface, and furthermore, the dynamics during the reactions are often overlooked. Our recent study on the Pin1-catalyzed isomerization reaction has indicated that the isomerization transition events remarkably deviate from the free energy path, highlighting the need to understand the reaction dynamics in more detail. To this end, here we investigate the reaction coordinates that describe the transition states of the free energy and transition pathways by minimizing the cross-entropy function. We show that the isomerization transition events can be expressed by the concerted changes in the improper torsion angle ζ and nearby backbone torsional angles of the ligand, whereas the transition state of the free energy surface involves changes in a broad range of coordinates including multiple protein-ligand interactions. The current result supports the previous finding that the isomerization transitions occur quickly from the conformational excited states, which is in sharp contrast to the slow and collective changes suggested from the free energy path. Our results further indicate that the coordinates derived from the transition trajectories are not sufficient for finding the transition states on the free energy surfaces due to the lack of information from conformational excited states.

Oscillatory Active-site Motions Correlate with Kinetic Isotope Effects in Formate Dehydrogenase

Thermal motions of enzymes have been invoked to explain the temperature dependence of kinetic isotope effects (KIE) in enzyme-catalyzed hydride transfers. Formate dehydrogenase (FDH) from Candida boidinii exhibits a temperature independent KIE that becomes temperature dependent upon mutation of hydrophobic residues in the active site. Ternary complexes of FDH that mimic the transition state structure allow investigation of how these mutations influence active-site dynamics. A combination of X-ray crystallography, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamic simulations characterize the structure and dynamics of the active site. FDH exhibits oscillatory frequency fluctuations on the picosecond timescale, and the amplitude of these fluctuations correlates with the temperature dependence of the KIE. Both the kinetic and dynamic phenomena can be reproduced computationally. These results provide experimental evidence for a connection between the temperature dependence of KIEs and motions of the active site in an enzyme-catalyzed reaction consistent with activated tunneling models of the hydride transfer reaction.

Heavy Enzymes and the Rational Redesign of Protein Catalysts

An unsolved mystery in biology concerns the link between enzyme catalysis and protein motions. Comparison between isotopically labelled "heavy" dihydrofolate reductases and their natural-abundance counterparts has suggested that the coupling of protein motions to the chemistry of the catalysed reaction is minimised in the case of hydride transfer. In alcohol dehydrogenases, unnatural, bulky substrates that induce additional electrostatic rearrangements of the active site enhance coupled motions. This finding could provide a new route to engineering enzymes with altered substrate specificity, because amino acid residues responsible for dynamic coupling with a given substrate present as hotspots for mutagenesis. Detailed understanding of the biophysics of enzyme catalysis based on insights gained from analysis of "heavy" enzymes might eventually allow routine engineering of enzymes to catalyse reactions of choice.

Effect of Protein Isotope Labeling on the Catalytic Mechanism of Lactate Dehydrogenase

We investigate how isotopic labeling of the enzyme lactate dehydrogenase (LDH) affects its function. LDH is of special interest because there exists a line of residues spanning the protein that are involved in the transition state (TS) of the chemical reaction coordinate (so-called promoting vibration). Hence, studies have been carried out on this protein (as well as others) using labeled protein (so-called heavy protein) along with measurements of single turnover k_cat yielding a KIE (=k_cat^light/k_cat^heavy) aimed at understanding the effect of labeling generally and more specifically this line of residues. Here, it is shown that ¹³C, ¹⁵N, and ²H atom labeling of hhLDH (human heart) affects its internal structure which in turn affects its dynamics and catalytic mechanism. Spectral studies employing advanced FTIR difference spectroscopy show that the height of the electronic potential surface of the TS is lowered (probably by ground state destabilization) by labeling. Moreover, laser-induced T-jump relaxation kinetic spectroscopy shows that the microsecond to millisecond nuclear motions internal to the protein are affected by labeling. While the effects are small, they are sufficient to contribute to the observed KIE values as well or even more than promoting vibration effects.

Detecting and Characterizing the Kinetic Activation of Thermal Networks in Proteins: Thermal Transfer from a Distal, Solvent-Exposed Loop to the Active Site in Soybean Lipoxygenase

The rate-limiting chemical reaction catalyzed by soybean lipoxygenase (SLO) involves quantum mechanical tunneling of a hydrogen atom from substrate to its active site ferric-hydroxide cofactor. SLO has emerged as a prototypical system for linking the thermal activation of a protein scaffold to the efficiency of active site chemistry. Significantly, hydrogen-deuterium exchange-mass spectrometry (HDX-MS) experiments on wild type and mutant forms of SLO have uncovered trends in the enthalpic barriers for HDX within a solvent-exposed loop (positions 317-334) that correlate well with trends in the corresponding enthalpic barriers for kcat. A model for this behavior posits that collisions between water and loop 317-334 initiate thermal activation at the protein surface that is then propagated 15-34 Å inward toward the reactive carbon of substrate in proximity to the iron catalyst. In this study, we have prepared protein samples containing cysteine residues either at the tip of the loop 317-334 (Q322C) or on a control loop, 586-603 (S596C). Chemical modification of cysteines with the fluorophore 6-bromoacetyl-2-dimethylaminonaphthalene (Badan, BD) provides site-specific probes for the measurement of fluorescence relaxation lifetimes and Stokes shift decays as a function of temperature. Computational studies indicate that surface water structure is likely to be largely preserved in each sample. While both loops exhibit temperature-independent fluorescence relaxation lifetimes as do the Stokes shifts for S596C-BD, the activation enthalpy for the nanosecond solvent reorganization at Q322C-BD (Ea(ksolv) = 2.8(0.9) kcal/mol)) approximates the enthalpy of activation for catalytic C-H activation (Ea(kcat) = 2.3(0.4) kcal/mol). This study establishes and validates the methodology for measuring rates of rapid local motions at the protein/solvent interface of SLO. These new findings, when combined with previously published correlations between protein motions and the rate-limiting hydride transfer in a thermophilic alcohol dehydrogenase, provide experimental evidence for thermally induced "protein quakes" as the origin of enthalpic barriers in catalysis.

Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods

Yersinia Protein Tyrosine Phosphatase (YopH) is the most efficient enzyme among all known PTPases and relies on its catalytic loop movements for substrate binding and catalysis. Fluorescence, NMR, and UV resonance Raman (UVRR) techniques have been used to study the thermodynamic and dynamic properties of the loop motions. In this study, a computational approach based on the pathway refinement methods nudged elastic band (NEB) and harmonic Fourier beads (HFB) has been developed to provide structural interpretations for the experimentally observed kinetic processes. In this approach, the minimum potential energy pathways for the loop open/closure conformational changes were determined by NEB using a one-dimensional global coordinate. Two dimensional data analyses of the NEB results were performed as an efficient method to qualitatively evaluate the energetics of transitions along several specific physical coordinates. The free energy barriers for these transitions were then determined more precisely using the HFB method. Kinetic parameters were estimated from the energy barriers using transition state theory and compared against experimentally determined kinetic parameters. When the calculated energy barriers are calibrated by a simple "scaling factor", as have been done in our previous vibrational frequency calculations to explain the ligand frequency shift upon its binding to protein, it is possible to make structural interpretations of several observed enzyme dynamic rates. For example, the nanosecond kinetics observed by fluorescence anisotropy may be assigned to the translational motion of the catalytic loop and microsecond kinetics observed in fluorescence T-jump can be assigned to the loop backbone dihedral angle flipping. Furthermore, we can predict that a Trp354 conformational conversion associated with the loop movements would occur on the tens of nanoseconds time scale, to be verified by future UVRR T-jump studies.

Universality of fold-encoded localized vibrations in enzymes

Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive. In this work, we use a powerful mathematical approach to show that rate-promoting vibrations in the picosecond range, specifically encoded in the 3D protein structure, are localized vibrations optimally coupled to the chemical reaction coordinates at the active site. Remarkably, our theory also exposes an hithertho unknown deep connection between the unique localization fingerprint and a distinct partition of the 3D fold into independent, foldspanning subdomains that govern long-range communication. The universality of these features is demonstrated on a pool of more than 900 enzyme structures, comprising a total of more than 10,000 experimentally annotated catalytic sites. Our theory provides a unified microscopic rationale for the subtle structure-dynamics-function link in proteins.

Interaction vs Preorganization in Enzyme Catalysis. A Dispute That Calls for Resolution

This essay focuses on the debate between Warshel et al. (proponents of preorganization) and Menger and Nome (proponents of spatiotemporal effects) over the source of fast enzyme catalysis. The Warshel model proposes that the main function of enzymes is to push the solvent coordinate toward the transition state. Other physical-organic factors (e.g., desolvation, entropic effects, ground state destabilization, etc.) do not, ostensibly, contribute substantially to the rate. Indeed, physical organic chemistry in its entirety was claimed to be "irrelevant to an enzyme's active site". Preorganization had been applied by Warshel to his "flagship" enzyme, ketosteroid isomerase, but we discuss troubling issues with their ensuing analysis. For example, the concepts of "general acid" and "general base", known to play a role in this enzyme's mechanism, are ignored in the text. In contrast, the spatiotemporal theory postulates that enzyme-like rates (i.e., accelerations >10⁸) occur when two functionalities are held rigidly at contact distances less than ca. 3 Å. Numerous diverse organic systems are shown to bear this out experimentally. Many of these are intramolecular systems where distances between functionalities are known. Among them are fast intramolecular systems where strain is actually generated during the reaction, thereby excluding steric compression as a source of the observed enzyme-like rates. Finally, the account ends with structural data from four active sites of enzymes, obtained by others, all showing contact distances between substrate analogues and enzyme. To our knowledge, contact distances less than the diameter of water are found universally among enzymes, and it is to this fact that we attribute their extremely fast rates given the assumption that enzymes, whatever their particular mechanism, obey elementary chemical principles.