Low-Frequency Protein Motions Coupled to Catalytic Sites

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the λ-exchange of free energy perturbation (FEP). Two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/λ-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

Identification of the Thermal Activation Network in Human 15-Lipoxygenase-2: Divergence from Plant Orthologs and Its Relationship to Hydrogen Tunneling Activation Barriers

The oxidation of polyunsaturated fatty acids by lipoxygenases (LOXs) is initiated by a C-H cleavage step in which the hydrogen atom is transferred quantum mechanically (i.e., via tunneling). In these reactions, protein thermal motions facilitate the conversion of ground-state enzyme-substrate complexes to tunneling-ready configurations and are thus important for transferring energy from the solvent to the active site for the activation of catalysis. In this report, we employed temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX-MS) to identify catalytically linked, thermally activated peptides in a representative animal LOX, human epithelial 15-LOX-2. TDHDX-MS of wild-type 15-LOX-2 was compared to two active site mutations that retain structural stability but have increased activation energies (Ea) of catalysis. The Ea value of one variant, V427L, is implicated to arise from suboptimal substrate positioning by increased active-site side chain rotamer dynamics, as determined by X-ray crystallography and ensemble refinement. The resolved thermal network from the comparative Eas of TDHDX-MS between wild-type and V426A is localized along the front face of the 15-LOX-2 catalytic domain. The network contains a clustering of isoleucine, leucine, and valine side chains within the helical peptides. This thermal network of 15-LOX-2 is different in location, area, and backbone structure compared to a model plant lipoxygenase from soybean that exhibits a low Ea value of catalysis compared to the human ortholog. The presented data provide insights into the divergence of thermally activated protein motions in plant and animal LOXs and their relationships to the enthalpic barriers for facilitating hydrogen tunneling.

Iminothioindoxyl Donors with Exceptionally High Cross Section for Protein Vibrational Energy Transfer

Various protein functions are related to vibrational energy transfer (VET) as an important mechanism. The underlying transfer pathways can be experimentally followed by ultrafast Vis-pump/IR-probe spectroscopy with a donor-sensor pair of non-canonical amino acids (ncAAs) incorporated in a protein. However, so far only one donor ncAA, azulenylalanine (AzAla), exists, which suffers from a comparably low Vis extinction coefficient. Here, we introduce two novel donor ncAAs based on an iminothioindoxyl (ITI) chromophore. The dimethylamino-ITI (DMA-ITI) and julolidine-ITI (J-ITI) moieties overcome the limitation of AzAla with a 50 times higher Vis extinction coefficient. While ITI moieties are known for ultrafast photoswitching, DMA-ITI and J-ITI exclusively form a hot ground state on the sub-ps timescale instead, which is essential for their usage as vibrational energy donor. In VET measurements of donor-sensor dipeptides we investigate the performance of the new donors. We observe 20 times larger signals compared to the established AzAla donor, which opens unprecedented possibilities for the study of VET in proteins.

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.

Anisotropic dynamics of an interfacial enzyme active site observed using tethered substrate analogs and ultrafast 2D IR spectroscopy

Enzymes accelerate the rates of biomolecular reactions by many orders of magnitude compared to bulk solution, and it is widely understood that this catalytic effect arises from a combination of polar pre-organization and electrostatic transition state stabilization. A number of recent reports have also implicated ultrafast (femtosecond-picosecond) timescale motions in enzymatic activity. However, complications arising from spatially-distributed disorder, the occurrence of multiple substrate binding modes, and the influence of hydration dynamics on solvent-exposed active sites still confound many experimental studies. Here we use ultrafast two-dimensional infrared (2D IR) spectroscopy and covalently-tethered substrate analogs to examine dynamical properties of the promiscuous Pyrococcus horikoshii ene-reductase (PhENR) active site in two binding configurations mimicking proposed "inactive" and "reactive" Michaelis complexes. Spectral diffusion measurements of aryl-nitrile substrate analogs reveal an end-to-end tradeoff between fast (sub-ps) and slow (>5 ps) motions. Fermi resonant aryl-azide analogs that sense interactions of coupled oscillators are described. Lineshape and quantum beat analyses of these probes reveal characteristics that correlate with aryl-nitrile frequency fluctuation correlation functions parameters, demonstrating that this anisotropy is an intrinsic property of the water-exposed active site, where countervailing gradients of fast dynamics and disorder in the reactant ground state are maintained near the hydration interface. Our results suggest several plausible factors leading to state-selective rate enhancement and promiscuity in PhENR. This study also highlights a strategy to detect perturbations to vibrational modes outside the transparent window of the mid-IR spectrum, which may be extended to other macromolecular systems.

Intra-protein interacting collective modes in the terahertz frequency region

Understanding how proteins work requires a thorough understanding of their internal dynamics. Proteins support a wide range of motions, from the femtoseconds to seconds time scale, relevant to crucial biological functions. In this context, the term "protein collective dynamics" refers to the complex patterns of coordinated motions of numerous atoms throughout the protein in the sub-picosecond time scale (terahertz frequency region). It is hypothesized that these dynamics have a substantial impact on the regulation of functional dynamical mechanisms, including ligand binding and allosteric signalling, charge transport direction, and the regulation of thermodynamic and thermal transport properties. Using the theoretical framework of hydrodynamics, the collective dynamics of proteins had previously been described in a manner akin to that of simple liquids, i.e. in terms of a single acoustic-like excitation, related to intra-protein vibrational motions. Here, we employ an interacting-mode model to analyse the results from molecular dynamics simulations and we unveil that the vibrational landscape of proteins is populated by multiple acoustic-like and low-frequency optic-like modes, with mixed symmetry and interfering with each other. We propose an interpretation at the molecular level of the observed scenario that we relate to the side-chains and the hydrogen-bonded networks dynamics. The present insights provide a perspective for understanding the molecular mechanisms underlying the energy redistribution processes in the interior of proteins.

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.

Enzyme dynamics-a brief review

Debate has been simmering for some years regarding the importance of internal thermal motions of enzymes to catalysis. Recent developments in protein design may bring resolution of the more contentious points a little closer.

Statistical Learning of Protein Elastic Network from Positional Covariance Matrix

Positional fluctuation and covariance during protein dynamics are key observables for understanding the molecular origin of biological functions. A frequently employed potential energy function for describing protein structural variation at the coarse-gained level is elastic network model (ENM). A long-standing issue in biomolecular simulation is thus the parametrization of ENM spring constants from the components of positional covariance matrix (PCM). Based on sensitivity analysis of PCM, the direct-coupling statistics of each spring, which is a specific combination of position fluctuation and covariance, is found to exhibit prominent signal of parameter dependence. This finding provides the basis for devising the objective function and the scheme of running through the effective one-dimensional optimization of every spring by self-consistent iteration. Formal derivation of the positional covariance statistical learning (PCSL) method also motivates the necessary data regularization for stable calculations. Robust convergence of PCSL is achieved in taking an all-atom molecular dynamics trajectory or an ensemble of homologous structures as input data. The PCSL framework can also be generalized with mixed objective functions to capture specific property such as the residue flexibility profile. Such physical chemistry-based statistical learning thus provides a useful platform for integrating the mechanical information encoded in various experimental or computational data.

Hydride Transfer Mechanism of Enzymatic Sugar Nucleotide C2 Epimerization Probed with a Loose-Fit CDP-Glucose Substrate

Transient oxidation–reduction through hydride transfer with tightly bound NAD coenzyme is used by a large class of sugar nucleotide epimerases to promote configurational inversion of carbon stereocenters in carbohydrate substrates. A requirement for the epimerases to coordinate hydride abstraction and re-addition with substrate rotation in the binding pocket poses a challenge for dynamical protein conformational selection linked to enzyme catalysis. Here, we studied the thermophilic C2 epimerase from Thermodesulfatator atlanticus (TaCPa2E) in combination with a slow CDP-glucose substrate (k_cat ≈ 1.0 min^–1; 60 °C) to explore the sensitivity of the enzymatic hydride transfer toward environmental fluctuations affected by temperature (20–80 °C). We determined noncompetitive primary kinetic isotope effects (KIE) due to ²H at the glucose C2 and showed that a normal KIE on the k_cat (^Dk_cat) reflects isotope sensitivity of the hydrogen abstraction to enzyme-NAD⁺ in a rate-limiting transient oxidation. The ^Dk_cat peaked at 40 °C was 6.1 and decreased to 2.1 at low (20 °C) and 3.3 at high temperature (80 °C). The temperature profiles for k_cat with the ¹H and ²H substrate showed a decrease in the rate below a dynamically important breakpoint (∼40 °C), suggesting an equilibrium shift to an impaired conformational landscape relevant for catalysis in the low-temperature region. Full Marcus-like model fits of the rate and KIE profiles provided evidence for a high-temperature reaction via low-frequency conformational sampling associated with a broad distribution of hydride donor–acceptor distances (long-distance population centered at 3.31 ± 0.02 Å), only poorly suitable for quantum mechanical tunneling. Collectively, dynamical characteristics of TaCPa2E-catalyzed hydride transfer during transient oxidation of CDP-glucose reveal important analogies to mechanistically simpler enzymes such as alcohol dehydrogenase and dihydrofolate reductase. A loose-fit substrate (in TaCPa2E) resembles structural variants of these enzymes by extensive dynamical sampling to balance conformational flexibility and catalytic efficiency.

Response of Terahertz Protein Vibrations to Ligand Binding: Calmodulin-Peptide Complexes as a Case Study

Terahertz vibrations are sensitive reporters of the structure and interactions of proteins. Ligand binding alters the nature and distribution of these collective vibrations. The ligand-induced changes in the terahertz protein vibrations contribute to the binding entropy and to the overall thermodynamic stability of the resultant protein-ligand complexes. Here, we have examined the response of the low-frequency (below 6 terahertz) collective vibrations of the calcium-loaded calmodulin (CaM) to binding to five different ligands, both in the presence and absence of water, using normal-mode analysis and molecular dynamics simulations. A comparison of the vibrational spectra of hydrated and dry systems reveals that protein-solvent interactions stiffen the terahertz protein vibrations and that these solvent-coupled collective vibrations contribute significantly to the hydration-sensitive variation in the vibrational entropy of CaM. In the absence of water, the low-frequency vibrations of CaM are stiffened by ligand binding. On the contrary, the number and the cumulative vibrational entropy of low-frequency vibrational modes (ω < 200 cm^-1) of the hydrated CaM are increased noticeably after binding to the peptides, indicating binding-induced softening of collective vibrations of the protein. Although the calculated and experimental binding affinities of the chosen complexes correlated reasonably well, no systematic correlation was observed between the protein vibrational entropy and the binding affinity. The results underscored the importance of the interplay of protein-ligand and solvent interactions in modulating the low-frequency vibrations of proteins.

Probing Ligand Effects on the Ultrafast Dynamics of Copper Complexes via Midinfrared Pump-Probe and 2DIR Spectroscopies

The effects of ligand structural variation on the ultrafast dynamics of a series of copper coordination complexes were investigated using polarization-dependent mid-IR pump-probe spectroscopy and two-dimensional infrared (2DIR) spectroscopy. The series consists of three copper complexes [(^R3P₃tren)Cu^IIN₃]BAr₄^F (1^PR3, ^R3P₃tren = tris[2-(phosphiniminato)ethyl]amine, BAr₄^F = tetrakis(pentafluorophenyl)borate) where the number of methyl and phenyl groups in the PR₃ ligand are systematically varied across the series (PR₃ = PMe₃, PMe₂Ph, PMePh₂). The asymmetric stretching mode of azide in the 1^PR3 series is used as a vibrational probe of the small-molecule binding site. The results of the pump-probe measurements indicate that the vibrational energy of azide dissipates through intramolecular pathways and that the bulkier phenyl groups lead to an increase in the spatial restriction of the diffusive reorientation of bound azide. From 2DIR experiments, we characterize the spectral diffusion of the azide group and find that an increase in the number of phenyl groups maps to a broader inhomogeneous frequency distribution (Δ₂). This indicates that an increase in the steric bulk of the secondary coordination sphere acts to create more distinct configurations in the local environment that are accessible to the azide group. This work demonstrates how ligand structural variation affects the ultrafast dynamics of a small molecular group bound to the metal center, which could provide insight into the structure-function relationship of the copper coordination complexes and transition-metal coordination complexes in general.

Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions

Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.

Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids

Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.

Diffusivelike Motions in a Solvent-Free Protein-Polymer Hybrid

The interaction between proteins and hydration water stabilizes protein structure and promotes functional dynamics, with water translational motions enabling protein flexibility. Engineered solvent-free protein-polymer hybrids have been shown to preserve protein structure, function, and dynamics. Here, we used neutron scattering, protein and polymer perdeuteration, and molecular dynamics simulations to explore how a polymer dynamically replaces water. Even though relaxation rates and vibrational properties are strongly modified in polymer coated compared to hydrated proteins, liquidlike polymer dynamics appear to plasticize the conjugated protein in a qualitatively similar way as do hydration-water translational motions.

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.