Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent

A Strategy for Modeling Nonstatistical Reactivity Effects: Combining Chemical Activation Estimates with a Vibrational Relaxation Model

The kinetics of many chemical reactions can be readily explained with a statistical approach, for example, using a form of transition state theory and comparing calculated Gibbs energies along the reaction coordinate(s). However, there are cases where this approach fails, notably when the vibrational relaxation of the molecule to its statistical equilibrium occurs on the same time scale as the reaction dynamics, whether it is caused by slow relaxation, a fast reaction, or both. These nonstatistical phenomena are then often explored computationally using (quasi)classical ab initio molecular dynamics by calculating a large number of trajectories while being prone to issues such as zero-point energy leakage. On the other side of the field, we see resource-intensive quantum dynamics simulations, which significantly limit the size of explorable systems. We find that using a Fermi's golden rule type of model for vibrational relaxation, based on anharmonic coupling constants, we can extract the same qualitative information while giving insights into how to enhance (or destroy) the bottlenecks causing the phenomena. We present this model as a middle ground for exploring complex nonstatistical behavior, capable of treating medium-sized organic molecules or biologically relevant fragments. We also cover the challenges involved, in particular quantifying the excess energy in terms of vibrational modes. Relying on readily available electronic structure methods and providing results in a simple master equation form, this model shows promise as a screening tool for opportunities in mode-selective chemistry without external control.

Energy Transport and Its Function in Heptahelical Transmembrane Proteins

Photoproteins such as bacteriorhodopsin (bR) and rhodopsin (Rho) need to effectively dissipate photoinduced excess energy to prevent themselves from damage. Another well-studied seven transmembrane (TM) helices protein is the β₂ adrenergic receptor (β₂AR), a G protein-coupled receptor for which energy dissipation paths have been linked with allosteric communication. To study the vibrational energy transport in the active and inactive states of these proteins, a master equation approach [J. Chem. Phys.2020, 152, 045103] is employed, which uses scaling rules that allow us to calculate energy transport rates solely based on the protein structure. Despite their overall structural similarity, the three 7TM proteins reveal quite different strategies to redistribute excess energy. While bR quickly removes the energy using the TM7 helix as a "lightning rod", Rho exhibits a rather poor energy dissipation, which might eventually require the hydrolysis of the Schiff base between the protein and the retinal chromophore to prevent overheating. Heating the ligand adrenaline of β₂AR, the resulting energy transport network of the protein is found to change significantly upon switching from the active state to the inactive state. While the energy flow may highlight aspects of the inter-residue couplings of β₂AR, it seems not particularly suited to explain allosteric phenomena.

A Plausible Mechanism of Uracil Photohydration Involves an Unusual Intermediate

It is well-known that photolysis of pyrimidine nucleobases, such as uracil, in an aqueous environment results in the formation of hydrate as one of the main products. Although several hypotheses regarding photohydration have been proposed in the past, e.g., the zwitterionic and "hot" ground-state mechanisms, its detailed mechanism remains elusive. Here, theoretical nonadiabatic simulations of the uracil photodynamics reveal the formation of a highly energetic but kinetically stable intermediate that features a half-chair puckered pyrimidine ring and a strongly twisted intracyclic double bond. The existence and the kinetic stability of the intermediate are confirmed by a variety of computational chemistry methods. According to the simulations, the unusual intermediate is mainly formed almost immediately (∼50-200 fs) upon photoabsorption and survives long enough to engage in a hydration reaction with a neighboring water. A plausible mechanism of uracil photohydration is proposed on the basis of the modeling of nucleophilic insertion of water into the twisted double bond of the intermediate.

Learning the Hydrophobic, Hydrophilic, and Aromatic Character of Amino Acids from Thermal Relaxation and Interfacial Thermal Conductance

In this study, the thermal relaxation of the 20 naturally occurring amino acids in water and in the protein lysozyme is investigated using transient nonequilibrium molecular dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the amino acids in water occurs over a time scale covering 2-5 ps. For the hydrophobic amino acids, the relaxation time is controlled by the size of the hydrocarbon side chain, while for hydrophilic amino acids, the number of hydrogen bonds does not significantly affect the time scales of the heat dissipation. Our results show that the interfacial thermal conductance at the amino acid-water interface is in the range of 40-80 MW m^-2 K^-1. Hydrophobic and aromatic amino acids tend to have a lower interfacial thermal conductance. Notably, we show that amino acids can be correlated with their thermal relaxation times and molar masses, into simply connected phases with the same hydrophilicity, hydrophobicity, and aromaticity. The thermal relaxation slows down by a factor of up to five in the protein relative to that in water. In the case of the hydrophobic amino acids in the protein lysozyme, the slow down in the thermal relaxation relative to that in water appears to be controlled primarily by the size of the side chain.

do Casal M, Pinheiro M, Toldo JM, Barbatti M. Modeling the heating and cooling of a chromophore after photoexcitation

The heating of a chromophore due to internal conversion and its cooling down due to energy dissipation to the solvent are crucial phenomena to characterize molecular photoprocesses. In this work, we simulated the ab initio nonadiabatic dynamics of cytosine, a prototypical chromophore undergoing ultrafast internal conversion, in three solvents—argon matrix, benzene, and water—spanning an extensive range of interactions. We implemented an analytical energy-transfer model to analyze these data and extract heating and cooling times. The model accounts for nonadiabatic effects, and excited- and ground-state energy transfer, and can analyze data from any dataset containing kinetic energy as a function of time. Cytosine heats up in the subpicosecond scale and cools down within 25, 4, and 1.3 ps in argon, benzene, and water, respectively. The time constants reveal that a significant fraction of the benzene and water heating occurs while cytosine is still electronically excited.

An analytical energy-transfer model is implemented to obtain a chromophore's heating and cooling times in a given solvent by using quantities available in nonadiabatic dynamics simulations.

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.

Asymmetric dynamics of dimeric SARS-CoV-2 and SARS-CoV main proteases in an apo form: Molecular dynamics study on fluctuations of active site, catalytic dyad, and hydration water

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world. It is necessary to examine the viral proteins that play a notorious role in the invasion of our body. The main protease (3CL^pro) facilitates the maturation of the coronavirus. It is thought that the dimerization of 3CL^pro leads to its catalytic activity; the detailed mechanism has, however, not been suggested. Furthermore, the structural differences between the predecessor SARS-CoV 3CL^pro and SARS-CoV-2 3CL^pro have not been fully understood. Here, we show the structural and dynamical differences between the two main proteases, and demonstrate the relationship between the dimerization and the activity via atomistic molecular dynamics simulations. Simulating monomeric and dimeric 3CL^pro systems for each protease, we show that (i) global dynamics between the two different proteases are not conserved, (ii) the dimerization stabilizes the catalytic dyad and hydration water molecules behind the dyad, and (iii) the substrate-binding site (active site) and hydration water molecules in each protomer fluctuate asymmetrically. We then speculate the roles of hydration water molecules in their catalytic activity.

Nonequilibrium molecular dynamics simulations of infrared laser-induced dissociation of a tetrameric Aβ42 β-barrel in a neuronal membrane model

Experimental studies have reported that the amyloid-β proteins can form pores in cell membranes, and this could be one possible source of toxicity in Alzheimer's disease. Dissociation of these pores could therefore be a potential therapeutic approach. It is known that high photon density free-electron laser experiments and laser-induced nonequilibrium molecular dynamics simulations (NEMD) can dissociate amyloid fibrils at specific frequencies in vitro. Our question is whether NEMD simulations can dissociate amyloid pores in a bilayer mimicking a neuronal membrane, and as an example, we select a tetrameric Aβ42 β-barrel. Our simulations shows that the resonance between the laser field and the amide I vibrational mode of the barrel destabilises all intramolecular and intermolecular hydrogen bonds of Aβ42 and converts the β-barrel to a random/coil disordered oligomer. Starting from this disordered oligomer, extensive standard MD simulations shows sampling of disordered Aβ42 states without any increase of β-sheet and reports that the orientational order of lipids is minimally disturbed. Interestingly, the frequency to be employed to dissociate this beta-barrel is specific to the amino acid sequence. Taken together with our previous simulation results, this study indicates that infrared laser irradiation can dissociate amyloid fibrils and oligomers in bulk solution and in a membrane environment without affecting the surrounding molecules, offering therefore a promising way to retard the progression of AD.

Infrared Laser-Induced Amyloid Fibril Dissociation: A Joint Experimental/Theoretical Study on the GNNQQNY Peptide

Neurodegenerative diseases are usually characterized by plaques made of well-ordered aggregates of distinct amyloid proteins. Dissociating these very stable amyloid plaques is a critical clinical issue. In this study, we present a joint mid-infrared free electron laser experiment/nonequilibrium molecular dynamics simulation to understand the dissociation process of a representative example GNNQQNY fibril. By tuning the laser frequency to the amide I band of the fibril, the resonance takes place and dissociation is occurred. With the calculated and observed wide-angle X-ray scattering profiles and secondary structures before and after laser irradiation being identical, we can propose a dissociation mechanism with high confidence from our simulations. We find that dissociation starts in the core of the fibrils by fragmenting the intermolecular hydrogen bonds and separating the peptides and then propagates to the fibril extremities leading to the formation of unstructured expanded oligomers. We suggest that this should be a generic mechanism of the laser-induced dissociation of amyloid fibrils.

Role of atomic contacts in vibrational energy transfer in myoglobin

Heme proteins are ideal systems to investigate vibrational energy flow at the atomic level. Upon photoexcitation, a large amount of excess vibrational energy is selectively deposited on heme due to extremely fast internal conversion. This excess energy is redistributed to the surrounding protein moiety and then to water. Vibrational energy flow in myoglobin (Mb) was examined using picosecond time-resolved anti-Stokes ultraviolet resonance Raman (UVRR) spectroscopy. We used the Trp residue directly contacting the heme group as a selective probe for vibrationally excited populations. Trp residues were placed at different position close to the heme by site-directed mutagenesis. This technique allows us to monitor the excess energy on residue-to-residue basis. Anti-Stokes UVRR measurements for Mb mutants suggest that the dominant channel for energy transfer in Mb is the pathway through atomic contacts between heme and nearby amino acid residues as well as that between the protein and solvent water. It is found that energy flow through proteins is analogous to collisional exchange processes in solutions.

Energy Transport Pathways in Proteins: A Non-equilibrium Molecular Dynamics Simulation Study

To facilitate the observation of biomolecular energy transport in real time and with single-residue resolution, recent experiments by Baumann et al. ( Angew. Chem. Int. Ed. 2019 , 58 , 2899 , DOI: 10.1002/anie.201812995 ) have used unnatural amino acids β-(1-azulenyl)alanine (Azu) and azidohomoalanine (Aha) to site-specifically inject and probe vibrational energy in proteins. To aid the interpretation of such experiments, non-equilibrium molecular dynamics simulations of the anisotropic energy flow in proteins TrpZip2 and PDZ3 domains are presented. On this account, an efficient simulation protocol is established that accurately mimics the excitation and probing steps of Azu and Aha. The simulations quantitatively reproduce the experimentally found cooling times of the solvated proteins at room temperature and predict that the cooling slows by a factor 2 below the glass temperature of water. In PDZ3, vibrational energy is shown to travel from the initially excited peptide ligand via a complex network of inter-residue contacts and backbone transport to distal regions of the protein. The supposed connection of these energy transport pathways with pathways of allosteric communication is discussed.

The full dynamics of energy relaxation in large organic molecules: from photo-excitation to solvent heating

In some molecular systems, such as nucleobases, polyenes or sunscreens, substantial amounts of photo-excitation energy are dissipated on a sub-picosecond time scale. Where does this energy go or among which degrees of freedom it is being distributed at such early times?

In some molecular systems, such as nucleobases, polyenes or the active ingredients of sunscreens, substantial amounts of photo-excitation energy are dissipated on a sub-picosecond time scale, raising questions such as: where does this energy go or among which degrees of freedom it is being distributed at such early times? Here we use transient absorption spectroscopy to track excitation energy dispersing from the optically accessible vibronic subsystem into the remaining vibrational subsystem of the solute and solvent. Monitoring the flow of energy during vibrational redistribution enables quantification of local molecular heating. Subsequent heat dissipation away from the solute molecule is characterized by classical thermodynamics and molecular dynamics simulations. Hence, we present a holistic approach that tracks the internal temperature and vibronic distribution from the act of photo-excitation to the restoration of the global equilibrium. Within this framework internal vibrational redistribution and vibrational cooling are emergent phenomena. We demonstrate the validity of the framework by examining a highly controversial example, carotenoids. We show that correctly accounting for the local temperature unambiguously explains their energetically and temporally congested spectral dynamics without the ad hoc postulation of additional ‘dark’ states. An immediate further application of this approach would be to monitor the excitation and thermal dynamics of pigment–protein systems.

Extended Hamiltonian molecular dynamics: semiclassical trajectories with improved maintenance of zero point energy

It is well known that classical trajectories, even if they are initiated with zero point energy (ZPE) in each mode (trajectories initiated this way are commonly called quasiclassical trajectories), do not maintain ZPE in the final states. The energy of high-frequency modes will typically leak into low-frequency modes or relative translation of subsystems during the time evolution. This can lead to severe problems such as unphysical dissociation of a molecule, production of energetically disallowed reaction products, and unphysical product energy distributions. Here a new molecular dynamics method called extended Hamiltonian molecular dynamics (EHMD) is developed to improve the ZPE problem in classical molecular dynamics. In EHMD, two images of a trajectory are connected by one or more springs. The EHMD method is tested with the Henon-Heiles Hamiltonian in reduced and real units and with a Hamiltonian with quartic anharmonicity in real units, and the method is found to improve zero-point maintenance as intended.

A non-equilibrium approach to allosteric communication

While the theory of protein folding is well developed, including concepts such as rugged energy landscape, folding funnel, etc., the same degree of understanding has not been reached for the description of the dynamics of allosteric transitions in proteins. This is not only due to the small size of the structural change upon ligand binding to an allosteric site, but also due to challenges in designing experiments that directly observe such an allosteric transition. On the basis of recent pump-probe-type experiments (Buchli et al. 2013 Proc. Natl Acad. Sci. USA110, 11 725-11 730. (doi:10.1073/pnas.1306323110)) and non-equilibrium molecular dynamics simulations (Buchenberg et al. 2017 Proc. Natl Acad. Sci. USA114, E6804-E6811. (doi:10.1073/pnas.1707694114)) studying an photoswitchable PDZ2 domain as model for an allosteric transition, we outline in this perspective how such a description of allosteric communication might look. That is, calculating the dynamical content of both experiment and simulation (which agree remarkably well with each other), we find that allosteric communication shares some properties with downhill folding, except that it is an 'order-order' transition. Discussing the multiscale and hierarchical features of the dynamics, the validity of linear response theory as well as the meaning of 'allosteric pathways', we conclude that non-equilibrium experiments and simulations are a promising way to study dynamical aspects of allostery.This article is part of a discussion meeting issue 'Allostery and molecular machines'.

Time-resolved observation of protein allosteric communication

Allostery represents a fundamental mechanism of biological regulation that is mediated via long-range communication between distant protein sites. Although little is known about the underlying dynamical process, recent time-resolved infrared spectroscopy experiments on a photoswitchable PDZ domain (PDZ2S) have indicated that the allosteric transition occurs on multiple timescales. Here, using extensive nonequilibrium molecular dynamics simulations, a time-dependent picture of the allosteric communication in PDZ2S is developed. The simulations reveal that allostery amounts to the propagation of structural and dynamical changes that are genuinely nonlinear and can occur in a nonlocal fashion. A dynamic network model is constructed that illustrates the hierarchy and exceeding structural heterogeneity of the process. In compelling agreement with experiment, three physically distinct phases of the time evolution are identified, describing elastic response ([Formula: see text] ns), inelastic reorganization ([Formula: see text] ns), and structural relaxation ([Formula: see text]s). Issues such as the similarity to downhill folding as well as the interpretation of allosteric pathways are discussed.

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study

Recently, mid-infrared free-electron laser technology has been developed to dissociate amyloid fibrils. Here, we present a theoretical framework for this type of experiment based on laser-induced nonequilibrium all-atom molecular dynamics simulations. We show that the fibril is destroyed due to the strong resonance between its amide I vibrational modes and the laser field. The effects of laser irradiation are determined by a balance between fibril formation and dissociation. While the overall rearrangements of the fibril finish over short time scales, the interaction between the peptides and the solvent continues over much longer times indicating that the waters play an important role in the dissociation process. Our results thus provide new insights into amyloid fibril dissociation by laser techniques and open up new venues to investigate the complex phenomena associated with amyloidogenesis.

Importance of Atomic Contacts in Vibrational Energy Flow in Proteins

Vibrational energy flow in proteins was studied by monitoring the time-resolved anti-Stokes ultraviolet resonance Raman scattering of three myoglobin mutants in which a Trp residue substitutes a different amino acid residue near heme. The anti-Stokes Raman intensities of the Trp residue in the three mutants increased with similar rates after depositing excess vibrational energy at heme, despite the difference in distance between heme and each substituted Trp residue along the main chain of the protein. This indicates that vibrational energy is not transferred through the main chain of the protein but rather through atomic contacts between heme and the Trp residue. Distinct differences were observed in the amplitude of the band intensity change between the Trp residues at different positions, and the amplitude of the band intensity change exhibits a correlation with the extent of exposure of the Trp residue to solvent water. This correlation indicates that atomic contacts between an amino acid residue and solvent water play an important role in vibrational energy flow in a protein.

Scaling Rules for Vibrational Energy Transport in Globular Proteins

Computational studies of vibrational energy flow in biomolecules have to date mapped out transport pathways on a case-by-case basis. To provide a more general approach, we derive scaling rules for vibrational energy transport in a globular protein, which are identified from extensive nonequilibrium molecular dynamics simulations of vibrational energy flow in the villin headpiece subdomain HP36. We parametrize a master equation based on inter-residue, residue-solvent, and heater-residue energy-transfer rates, which closely reproduces the results of the all-atom simulations. From that fit, two scaling rules emerge, one for energy transport along the protein backbone which relies on a diffusion model and another for energy transport between tertiary contacts, which is based on a harmonic model. Requiring only the calculation of mean and variance of relatively few atomic distances, the approach holds the potential to predict the pathways and time scales of vibrational energy flow in large proteins.

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

Laser-induced all-atom nonequilibrium molecular dynamics simulation of virus dissociation.

Effect of viscogens on the kinetic response of a photoperturbed allosteric protein

By covalently binding a photoswitchable linker across the binding groove of the PDZ2 domain, a small conformational change can be photo-initiated that mimics the allosteric transition of the protein. The response of its binding groove is investigated with the help of ultrafast pump-probe IR spectroscopy from picoseconds to tens of microseconds. The temperature dependence of that response is compatible with diffusive dynamics on a rugged energy landscape without any prominent energy barrier. Furthermore, the dependence of the kinetics on the concentration of certain viscogens, sucrose, and glycerol, has been investigated. A pronounced viscosity dependence is observed that can be best fit by a power law, i.e., a fractional viscosity dependence. The change of kinetics when comparing sucrose with glycerol as viscogen, however, provides strong evidence that direct interactions of the viscogen molecule with the protein do play a role as well. This conclusion is supported by accompanying molecular dynamics simulations.

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study

Resonance between carboxylate bond vibrations and laser frequency results in melting of nanotube.

Hybrid quantum/classical simulations of the vibrational relaxation of the amide I mode of N-methylacetamide in D2O solution

Hybrid quantum/classical molecular dynamics (MD) is applied to simulate the vibrational relaxation (VR) of the amide I mode of deuterated N-methylacetamide (NMAD) in aqueous (D(2)O) solution. A novel version of the vibrational molecular dynamics with quantum transitions (MDQT) treatment is developed in which the amide I mode is treated quantum mechanically while the remaining degrees of freedom are treated classically. The instantaneous normal modes of the initially excited NMAD molecule (INM(0)) are used as internal coordinates since they provide a proper initial partition of the system in quantum and classical subsystems. The evolution in time of the energy stored in each individual normal mode is subsequently quantified using the hybrid quantum-classical instantaneous normal modes (INM(t)). The identities of both the INM(0)s and the INM(t)s are tracked using the equilibrium normal modes (ENMs) as templates. The results extracted from the hybrid MDQT simulations show that the quantum treatment of the amide I mode accelerates the whole VR process versus pure classical simulations and gives better agreement with experiments. The relaxation of the amide I mode is found to be essentially an intramolecular vibrational redistribution (IVR) process with little contribution from the solvent, in agreement with previous theoretical and experimental studies. Two well-defined relaxation mechanisms are identified. The faster one accounts for ≈40% of the total vibrational energy that flows through the NMAD molecule and involves the participation of the lowest frequency vibrations as short-life intermediate modes. The second and slower mechanism accounts for the remaining ≈60% of the energy released and is associated to the energy flow through specific mid-range and high-frequency modes.

Understanding the dynamics behind the photoisomerization of a light-driven fluorene molecular rotary motor

Light-driven molecular rotary motors derived from chiral overcrowded alkenes represent a broad class of compounds for which photochemical rearrangements lead to large scale motion of one part of the molecule with respect to another. It is this motion/change in molecular shape that is employed in many of their applications. A key group in this class are the molecular rotary motors that undergo unidirectional light-driven rotation about a double bond through a series of photochemical and thermal steps. In the present contribution we report a combined quantum chemical and molecular dynamics study of the mechanism of the rotational cycle of the fluorene-based molecular rotary motor 9-(2,4,7-trimethyl-2,3-dihydro-1H-inden-1-ylidene)-9H-fluorene (1). The potential energy surfaces of the ground and excited singlet states of 1 were calculated, and it was found that conical intersections play a central role in the mechanism of photo conversion between the stable conformer of 1 and its metastable conformer. Molecular dynamics simulations indicate that the average lifetime of the fluorene motor in the excited state is 1.40 +/- 0.10 ps when starting from the stable conformer, which increases to 1.77 +/- 0.13 ps for the reverse photoisomerization. These simulations indicate that the quantum yield of photoisomerization of the stable conformer is 0.92, whereas it is only 0.40 for the reverse photoisomerization. For the first time, a theoretical understanding of the experimentally observed photostationary state of 1 is reported that provides a detailed picture of the photoisomerization dynamics in overcrowded alkene-based molecular motor 1. The analysis of the electronic structure of the fluorene molecular motor holds considerable implications for the design of molecular motors. Importantly, the role of pyramidalization and conical intersections offer new insight into the factors that dominate the photostationary state achieved in these systems.