Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10 ps

Binding and docking interactions of NO, CO and O₂in heme proteins as probed by density functional theory

Dynamics and reactivity in heme proteins include direct and indirect interactions of the ligands/substrates like CO, NO and O(2) with the environment. Direct electrostatic interactions result from amino acid side chains in the inner cavities and/or metal coordination in the active site, whereas indirect interactions result by ligands in the same coordination sphere. Interactions play a crucial role in stabilizing transition states in catalysis or altering ligation chemistry. We have probed, by Density Functional Theory (DFT), the perturbation degree in the stretching vibrational frequencies of CO, NO and O(2) molecules in the presence of electrostatic interactions or hydrogen bonds, under conditions simulating the inner cavities. Moreover, we have studied the vibrational characteristics of the heme bound form of the CO and NO ligands by altering the chemistry of the proximal to the heme ligand. CO, NO and O(2) molecules are highly polarizable exerting vibrational shifts up to 80, 200 and 120 cm(-1), respectively, compared to the non-interacting ligand. The importance of Density Functional Theory (DFT) methodology in the investigation of the heme-ligand-protein interactions is also addressed.

Structural assignment of spectra by characterization of conformational substates in bound MbCO

Residue motions of the distal heme pocket and bound CO ligand of carbonmonoxy Myoglobin are studied using a combination of molecular dynamics simulations and quantum chemical methods. Using mixed quantum mechanics/molecular mechanics calculations together with sampling from molecular dynamics simulations (QM/MM(MD)), the experimentally observed spectroscopic A(0) and A(1) substates of the bound CO ligand are assigned to the open and closed conformation of His(64) and the His(epsilon)(64) tautomer, respectively. Several previously proposed origins of the A(3) substate, including rotamers of the doubly protonated His(64)H(+) side chain, His(64)H(+) inside the distal pocket, and cooperative motions with Arg(45), are investigated with QM/MM(MD). However, the signatures of the calculated infrared spectra do not agree with the experimentally observed ones. For additional insight on this, extensive molecular dynamics simulations are used together with improved electrostatics for the bound ligand. A CO fluctuating charge model is developed to describe the ab initio dipole and quadrupole moments of the bound ligand. CO absorption spectra are then obtained directly from the dynamics simulations. Finally, the electrostatics of the heme pocket is examined in detail in an attempt to determine the structural origins of the observed spectroscopic A-states from MD simulations. However, contrary to related simulations for unbound CO in myoglobin, the shifts and splittings for carbonmonoxy Myoglobin are generally small and difficult to relate to structural change. This suggests that coupling of the CO motion to other degrees of freedom, such as the Fe-CO stretching and bending, is important to correctly describe the dynamics of bound CO in myoglobin.

Diversity of solvent dependent energy transfer pathways in heme proteins

The time scales and pathways of heme cooling in both reduced cytochrome c and oxidized cytochrome c following heme photoexcitation were studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol, and a nonpolar solvent, were used in the simulation. Single exponential decay of the excess kinetic energy of the heme following photoexcitation was observed in all systems studied. The simulated time scale for heme cooling in normal water agrees with recent experimental results. In contrast to heme cooling in myoglobin, no solvent dependence was observed for the time scale for heme cooling in cytochrome c. The diversity of solvent dependence results from the different local heme environments in the two proteins. In myoglobin, it has been established that the dominant mechanism for heme cooling is direct energy transfer from the heme to the solvent. In cytochrome c, direct interaction between heme and protein residues forms the dominant energy transfer pathway. This distinction is dictated by protein topology and linked to function.

The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations

By using multiple molecular dynamics trajectories of photolyzed carbon monoxide (CO) within crystallized myoglobin, a quantitative description of CO diffusion and corresponding kinetics was obtained. Molecular dynamics results allowed us to construct a detailed kinetic model of the migration process, shedding light on the kinetic mechanism and relevant steps of CO migration and remarkably-well reproducing the available experimental data as provided by time-resolved Laue x-ray diffraction.

The role of higher CO-multipole moments in understanding the dynamics of photodissociated carbonmonoxide in myoglobin

The influence of electrostatic multipole moments up to hexadecapole on the dynamics of photodissociated carbon monoxide (CO) in myoglobin is investigated. The CO electrostatic potential is expressed as an expansion into atomic multipole moments of increasing order up to octopole which are obtained from a distributed multipole analysis. Three models with increasingly accurate molecular multipoles (accurate quadrupole, octopole, and hexadecapole moments, respectively) are developed and used in molecular dynamics simulations. All models with a fluctuating quadrupole moment correctly describe the location of the B-state whereas the sign of the octopole moment differentiates between the Fe...CO and Fe...OC orientation. For the infrared spectrum of photodissociated CO, considerable differences between the three electrostatic models are found. The most detailed electrostatic model correctly reproduces the splitting, shift, and width of the CO spectrum in the B-state. From an analysis of the trajectories, the spectroscopic B(1) and B(2) states are assigned to the Fe...CO and Fe...OC substates, respectively.

Molecular dynamics simulation of deoxy and carboxy murine neuroglobin in water

Globins are respiratory proteins that reversibly bind dioxygen and other small ligands at the iron of a heme prosthetic group. Hemoglobin and myoglobin are the most prominent members of this protein family. Unexpectedly a few years ago a new member was discovered and called neuroglobin (Ngb), being predominantly expressed in the brain. Ngb is a single polypeptide of 151 amino acids and despite the small sequence similarity with other globins, it displays the typical globin fold. Oxygen, nitric oxide, or carbon monoxide can displace the distal histidine which, in ferrous Ngb as well as in ferric Ngb, is bound to the iron, yielding a reversible adduct. Recent crystallographic data on carboxy Ngb show that binding of an exogenous ligand is associated to structural changes involving heme sliding and a topological reorganization of the internal cavities; in particular, the huge internal tunnel that connects the bulk with the active site, peculiar to Ngb, is heavily reorganized. We report the results of extended (90 ns) molecular dynamics simulations in water of ferrous deoxy and carboxy murine neuroglobin, which are both coordinated on the distal site, in the latter case by CO and in the former one by the distal His(64)(E7). The long timescale of the simulations allowed us to characterize the equilibrated protein dynamics and to compare protein structure and dynamical behavior coupled to the binding of an exogenous ligand. We have characterized the heme sliding motion, the topological reorganization of the internal cavities, the dynamics of the distal histidine, and particularly the conformational change of the CD loop, whose flexibility depends ligand binding.

Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations

Ultrafast protein dynamics of the CO adduct of a myoglobin mutant with the polar distal histidine replaced by a nonpolar valine (H64V) have been investigated by spectrally resolved infrared stimulated vibrational echo experiments and molecular dynamics (MD) simulations. In aqueous solution at room temperature, the vibrational dephasing rate of CO in the mutant is reduced by approximately 50% relative to the native protein. This finding confirms that the dephasing of the CO vibration in the native protein is sensitive to the interaction between the ligand and the distal histidine. The stimulated vibrational echo observable is calculated from MD simulations of H64V within a model in which vibrational dephasing is driven by electrostatic forces. In agreement with experiment, calculated vibrational echoes show slower dephasing for the mutant than for the native protein. However, vibrational echoes calculated for H64V do not show the quantitative agreement with measurements demonstrated previously for the native protein.

Free-energy barriers in MbCO rebinding

The rebinding of CO to myoglobin (Mb) from locations around the active site is studied using a combination of molecular dynamics and stochastic simulations for native and L29F mutant Mb. The interaction between the dissociated ligand and the protein environment is described by the recently developed fluctuating three-point charge model for the CO molecule. Umbrella sampling along trajectories, previously found to sample the binding site (B) and the Xe4 pocket, is used to construct free-energy profiles for the ligand escape. On the basis of the Smoluchowski equation, the relaxation of different initial population distributions is followed in space and time. For native Mb at room temperature, the calculated rebinding times are in good agreement with experimental values and give an inner barrier of 4.3 kcal/mol between the docking site B (Mb...CO) and the A state (bound MbCO), compared to an effective barrier, Heff, of 4.5 kcal/mol and barriers into the majority conformation A1 and the minority conformation A3 of 2.4 and 4.3 kcal/mol, respectively. In the case of the L29F mutant, the free-energy surface is flatter and the dynamics is much more rapid. As was found in experiment, escape to the Xe4 pocket is facile for L29F whereas, for native Mb, the barriers to this site are larger. At lower temperatures, the rebinding dynamics is delayed by orders of magnitude also due to increased barriers between the docking sites.

Molecular Dynamics Simulations of CN− Dynamics and Spectroscopy in Myoglobin

The vibrational dynamics of the cyanide anion and the heme group in MbCN (CN complexed to Myoglobin) are investigated using molecular dynamics simulations. A previously calculated quantum-chemical heme-ligand potential-energy surface together with a three-center charge model for the iron-ligand center that captures both polarization and ligand-to-metal charge transfer allows for a detailed description of the interactions around the active site. It is found that the CN binding orientation (Fe--CN or Fe--NC) to the heme affects the stretching frequency of the ligand, with a 25 cm-1 difference in the fundamental wavenumber between the two orientations as well as a change in bond length. The charge model also captures such crucial interactions as the possible hydrogen bond between the ligand and the His64 residue. This interaction is weakened when the ligand binds in the Fe--NC conformation but is also sensitive to the protonation state of His64. The structural changes around the active site, the observation of water penetration for the Fe--NC conformation, the computed IR spectrum, and the energetics suggest that the Fe--CN conformation with Hisepsilon64 is the most likely one. The water accessibility of the active site is also found to be related to the protonation state of His64. The presence of water in the active site could also affect the IR band of the C--N stretch mode. Thus, IR spectroscopy of the C--N stretch is a potentially useful reporter of ligand isomers and active-site structure.

Molecular dynamics study on the solvent dependent heme cooling following ligand photolysis in carbonmonoxy myoglobin

The time scale and mechanism of vibrational energy relaxation of the heme moiety in myoglobin was studied using molecular dynamics simulation. Five different solvent models, including normal water, heavy water, normal glycerol, deuterated glycerol and a nonpolar solvent, and two forms of the heme, one native and one lacking acidic side chains, were studied. Structural alteration of the protein was observed in native myoglobin glycerol solution and native myoglobin water solution. The single-exponential decay of the excess kinetic energy of the heme following ligand photolysis was observed in all systems studied. The relaxation rate depends on the solvent used. However, this dependence cannot be explained using bulk transport properties of the solvent including macroscopic thermal diffusion. The rate and mechanism of heme cooling depends upon the detailed microscopic interaction between the heme and solvent. Three intermolecular energy transfer mechanisms were considered: (i) energy transfer mediated by hydrogen bonds, (ii) direct vibration-vibration energy transfer via resonant interaction, and (iii) energy transfer via vibration-translation or vibration-rotation interaction, or in other words, thermal collision. The hydrogen bond interaction and vibration-vibration interaction between the heme and solvent molecules dominates the energy transfer in native myoglobin aqueous solution and native myoglobin glycerol solutions. For modified myoglobin, the vibration-vibration interaction is also effective in glycerol solution, different from aqueous solution. Thermal collisions form the dominant energy transfer pathway for modified myoglobin in water solution, and for both native myoglobin and modified myoglobin in a nonpolar environment. For native myoglobin in a nonpolar solvent solution, hydrogen bonds between heme isopropionate side chains and nearby protein residues, absent in the modified myoglobin nonpolar solvent solution, are key interactions influencing the relaxation pathways.

Angular momentum dependent friction slows down rotational relaxation under nonequilibrium conditions

It has recently been shown that relaxation of the rotational energy of hot nonequilibrium photofragments (i) slows down significantly with the increase of their initial rotational temperature and (ii) differs dramatically from the relaxation of the equilibrium rotational energy correlation function, manifesting thereby the breakdown of the linear response description [A. C. Moskun et al., Science 311, 1907 (2006)]. We demonstrate that this phenomenon may be caused by the angular momentum dependence of rotational friction. We have developed the generalized Fokker-Planck equation whose rotational friction depends upon angular momentum algebraically. The calculated rotational correlation functions correspond well to their counterparts obtained via molecular dynamics simulations in a broad range of initial nonequilibrium conditions. It is suggested that the angular momentum dependence of friction should be taken into account while describing rotational relaxation far from equilibrium.

Theoretical characterization of carbon monoxide vibrational spectrum in sperm whale myoglobin distal pocket

In this article we use the perturbed matrix method and an extended molecular dynamics sampling of the carbon monoxide (CO) in the myoglobin distal pocket to characterize the CO vibrational spectrum and hence to relate its spectroscopic features with the atomic-molecular behavior. Results show the accuracy of the method employed and confirm the assignment of the spectroscopic B1 and B2 states proposed by Lim et al.

Anisotropic Structural Relaxation and Its Correlation with the Excess Energy Diffusion in the Incipient Process of Photodissociated MbCO: High-Resolution Analysis via Ensemble Perturbation Method

The effectiveness of the ensemble perturbation method, in which many pairs of perturbed and unperturbed molecular dynamics simulations are executed for the ensemble average, has been demonstrated by calculating the subtle anisotropic structural change of carbonmonoxy myoglobin (MbCO) triggered by ligand photolysis. The results show that Mb largely expands in the direction perpendicular to the heme plane and slightly contracts in the horizontal one. This agrees well with the report in the transient grating experiment. In addition, it is suggested that the expansion contributes strongly to the fast energy-transfer process to the water solvent because it is undergone almost within several picoseconds. The mechanical work done on the solvent by the expansion within 1 ps was thermodynamically estimated to be 4.8 kcal/mol.

Energetics and Dynamics in MbCN: CN--Vibrational Relaxation from Molecular Dynamics Simulations

The dynamics of the cyanide anion bound to sperm-whale myoglobin is investigated using atomistic simulations. With density-functional theory, a 2D potential energy surface for the cyanide-heme complex is calculated. Two deep minima with a stabilization energy of approximately 50 kcal/mol corresponding to two different binding orientations (Fe-CN and Fe-NC) of the ligand are found. The Fe-CN conformation is favored over Fe-NC by several kcal/mol. Mixed quantum mechanics/molecular mechanics calculations show that the binding orientation affects the bond strength of the ligand, with a significantly different bond length and a 25 cm-1 shift in the fundamental CN-frequency. For the molecular dynamics (MD) simulations, a 3-center fluctuating charge model for the Fe-CN unit is developed that captures polarization and ligand-metal charge transfer. Stability arguments based on the energetics around the active site and the CN- frequency shifts suggest that the Fe-CN conformation with epsilon-protonation of His epsilon 64 are most likely, which is in agreement with experiment. Both equilibrium and nonequilibrium MD simulations are carried out to investigate the relaxation time scale and possible relaxation pathways in bound MbCN. The nonequilibrium MD simulations with a vibrationally excited ligand reveal that vibrational relaxation takes place on a time scale of hundreds of picoseconds within the active site. This finding supports the hypothesis that the experimentally observed relaxation rate (3.6 ps) reflects the repopulation of the electronic ground state.

Two ligand-binding sites in the O2-sensing signal transducer HemAT: implications for ligand recognition/discrimination and signaling

We have identified a ligand (CO) accommodation cavity in the signal transducer sensor protein HemAT (heme-based aerotactic transducer) that allows us to gain single-molecule insights into the mechanism of gas sensor proteins. Specific mutations that are distal and proximal to the heme were designed to perturb the electrostatic field near the ligand that is bound to the heme and near the accommodated ligand in the cavity. We report the detection of a second site in heme proteins in which the exogenous ligand is accommodated in an internal cavity. The conformational gate that directs the ligand-migration pathway from the distal to the proximal site of the heme, where the ligand is trapped, has been identified. The data provide evidence that the heme pocket is the specific ligand trap and suggest that the regulatory mechanism may be tackled starting from more than one position in the protein. Based on the results, we propose a dynamic coupling between the two distinct binding sites as the underlying allosteric mechanism for gas recognition/discrimination that triggers a conformational switch for signaling by the oxygen sensor protein HemAT.

Induction model for molecular electrostatics: Application to the infrared spectroscopy of CO liquid

Far-infrared intermolecular and midinfrared vibrational spectra of CO liquid have been calculated by Fourier transforming the quantum-corrected classical dipole correlation. The time dependence of the coordinates is determined from a standard nonpolarizable force field, and the dipole is determined from the coordinates with a "spectroscopic model" proposed herein. The model includes intramolecular induction and atomic charges, polarizabilities, and permanent dipoles. A good agreement with available experimental spectra is achieved. Our results demonstrate that the use of an anharmonic potential is necessary to reproduce the experimentally observed shift upon going from gas to liquid. The behavior of the simulated dipole time correlation functions suggests that CO liquid at 80 K exhibits aspects of both free rotation and solidlike caging. The proposition of some free rotation present in CO liquid supports Ewing's experimental hypothesis.

Restricted rotational motion of CO in a protein internal cavity: evidence for nonseparating correlation functions from IR pump-probe spectroscopy

The strongly restricted orientational motion of CO molecules trapped in the Xe4 internal cavity of myoglobin mutant L29W-S108L is investigated by polarization-dependent mid-infrared pump-probe spectroscopy at cryogenic temperatures. Following an ultrafast initial decay, the signal anisotropy reaches an asymptotic value that is significantly larger than the prediction from the well-known relation [see text], based on previously established potential parameters. This discrepancy is explained by showing that the full four-point correlation function describing third-order spectroscopy [see text] does not factorize in systems where its fast decay is dominated by restricted reorientation of the transition dipole moments.

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mus of total simulation time) for the rebinding of NO to myoglobin. The unbound surface (Fe...NO) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities

The results of extended (80-ns) molecular dynamics simulations of wild-type and YQR triple mutant of sperm whale deoxy myoglobin in water are reported and compared with the results of the simulation of the intermediate(s) obtained by photodissociation of CO in the wild-type protein. The opening/closure of pathways between preexistent cavities is different in the three systems. For the photodissociated state, we previously reported a clear-cut correlation between the opening probability and the presence of the photolyzed CO in the proximity of the passage; here we show that in wild-type deoxy myoglobin, opening is almost random. In wild-type deoxy myoglobin, the passage between the distal pocket and the solvent is strictly correlated to the presence/absence of a water molecule that simultaneously interacts with the distal histidine side chain and the heme iron; conversely, in the photodissociated myoglobin, the connection with the bulk solvent is always open when CO is in the vicinity of the A pyrrole ring. In YQR deoxy myoglobin, the mutated Gln(E7)64 is stably H-bonded with the mutated Tyr(B10)29. The essential dynamics analysis unveils a different behavior for the three systems. The motion amplitude is progressively restricted in going from wild-type to YQR deoxy myoglobin and to wild-type myoglobin photoproduct. In all cases, the principal motions involve mainly the same regions, but their directions are different. Analysis of the dynamics of the preexisting cavities indicates large fluctuations and frequent connections with the solvent, in agreement with the earlier hypothesis that some of the ligand may escape from the protein through these pathways.

Solubility of CO2, CO, and H2 in the Ionic Liquid [bmim][PF6] from Monte Carlo Simulations

This work reports predictions from molecular simulation results for the solubility of the single gases carbon dioxide, carbon monoxide, and hydrogen in the ionic liquid 1-N-butyl-3-methyl-imidazolium hexafluorophosphate ([bmim][PF6]) at temperatures from 293 to 393 K and at pressures up to 9 MPa. The predictions are achieved by Gibbs ensemble Monte Carlo simulations at constant pressure and temperature (NpT-GEMC). The intermolecular forces are approximated by effective pair potentials for the pure gases and by a quantum-chemistry-based pair potential for [bmim][PF6]. The interactions between unlike groups are described using common mixing rules without any adjustable binary interaction parameter. The simulation results for the solubility of hydrogen agree within their statistical uncertainty with experimental data, whereas the results for carbon monoxide and carbon dioxide reveal somewhat larger deviations.

Nonlinear optical studies of heme protein dynamics: Implications for proteins as hybrid states of matter

Protein structure is fundamentally related to function. However, static structures alone are insufficient to understand how a protein works. Dynamics play an equally important role. Given that proteins are highly associated aperiodic systems, it may be expected that protein dynamics would follow glass-like dynamics. However, protein functions occur on time scales orders of magnitude faster than the time scales typically associated with glassy systems. It is becoming clear that the reaction forces driving functions do not sample entirely the large number of configurations available to a protein but are highly directed along an optimized pathway. Could there be any correlation between specific topological features in protein structures and dynamics that leads to strongly correlated atomic displacements in the dynamical response to a perturbation? This review will try to provide an answer by focusing upon recent nonlinear optical studies with the aim of directly observing functionally important protein motions over the entire dynamic range of the protein response function. The specific system chosen is photoinduced dynamics of ligand dissociation at the active site in heme proteins, with myoglobin serving as the simplest model system. The energetics and nuclear motions from the very earliest events involved in bond breaking on the femtosecond time scale all the way out to ligand escape and bimolecular rebinding on the microsecond and millisecond time scale have been mapped out. The picture that is emerging is that the system consists of strongly coupled motions from the very instant the bond breaks at the active site that cascade into low frequency collective modes specific to the protein structure. It is this coupling that imparts the ability of a protein to function on time scales more commensurate with liquids while simultaneously conserving structural integrity akin to solids.

Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid

WIN antiviral compounds bind human rhinovirus, as well as enterovirus and parechovirus, in an internal cavity located within the viral protein capsid. Access to the buried pocket necessitates deviation from the average viral protein structure identified by crystallography. We investigated the dissociation of WIN 52084 from the pocket in human rhinovirus 14 by using an adiabatic, biased molecular dynamics simulation method. Multiple dissociation trajectories are used to characterize the pathway. WIN 52084 exits between the polypeptide chain near the ends of betaC and betaH in a series of steps. Small, transient packing defects in the protein are sufficient for dissociation. A number of torsion-angle transitions of the antiviral compound are involved, which suggests that flexibility in antiviral compounds is important for binding. It is interesting to note that dissociation is associated with an increase in the conformational fluctuations of residues never in direct contact with WIN 52084 over the course of dissociation. These residues are N-terminal residues in the viral proteins VP3 and VP4 and are located in the interior of the capsid near the icosahedral 5-fold axis. The observed changes in dynamics may be relevant to structural changes associated with virion uncoating and its inhibition by antiviral compounds.

Picosecond Dynamics of Ligand Interconversion in the Primary Docking Site of Heme Proteins

We have used femtosecond IR spectroscopy to probe interconversion dynamics of ligand in the primary docking site of heme proteins under physiological conditions. The docking site, fashioned with highly conserved amino acid residues, modulates ligand-binding activity by mediating the passage of ligand to and from the active binding site. Ligands in two states of the docking site interconvert on the picosecond time scale, and the rates are about 4 times slower in hemoglobin than that in myoglobin. The accurate interconversion rates on the time scale readily accessible by MD simulations can be used to refine computer simulations, which could in turn provide a detailed mechanistic picture of ligand binding in heme proteins.

Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case

In this paper we extend the perturbed matrix method by explicitly including the nuclear degrees of freedom, in order to treat quantum vibrational states in a perturbed molecule. In a previous paper we showed how to include, in a simple way, nuclear degrees of freedom for the calculation of molecular polarizability. In the present work we extend and generalize this approach to model vibroelectronic transitions, requiring a more sophisticated treatment.

Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin

We performed a room temperature molecular dynamics (MD) simulation on a system containing 1 carboxy-myoglobin (MbCO) molecule in a sucrose-water matrix of identical composition (89% [sucrose/(sucrose + water)] w/w) as for a previous trehalose-water-MbCO simulation (Cottone et al., Biophys J 2001;80:931-938). Results show that, as for trehalose, the amplitude of protein atomic mean-square fluctuations, on the nanosecond timescale, is reduced with respect to aqueous solutions also in sucrose. A detailed comparison as a function of residue number evidences mobility differences along the protein backbone, which can be related to a different efficacy in bioprotection. Different heme pocket structures are observed in the 2 systems. The joint distribution of the magnitude of the electric field at the CO oxygen atom and of the angle between the field and the CO unit vector shows a secondary maximum in sucrose, absent in trehalose. This can explain the CO stretching band profile (A substates distribution) differences evidenced by infrared spectroscopy in sucrose- and trehalose-coated MbCO (Giuffrida et al., J Phys Chem B 2004;108:15415-15421), and in particular the appearance of a further substate in sucrose. Analysis of hydrogen bonds at the protein-solvent interface shows that the fraction of water molecules shared between the protein and the sugar is lower in sucrose than in trehalose, in spite of a larger number of water molecules bound to the protein in the former system, thus indicating a lower protein-matrix coupling, as recently observed by Fourier transform infrared (FTIR) experiments (Giuffrida et al., J Phys Chem B 2004;108:15415-15421).

Quantum Chemical Evaluation of Protein Control over Heme Ligation: CO/O2 Discrimination in Myoglobin

Control of O2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8 degrees ) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O2 decreased by 0.8 and 4.1 kcal/mol for MbCO and MbO2, in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO2 that may play a key role in MbO2 photodynamics.

Ligand Dynamics in Myoglobin: Calculation of Infrared Spectra for Photodissociated NO

We present molecular dynamics simulations of the photodissociated state of MbNO performed at 300 K using a fluctuating charge model for the nitric oxide (NO) ligand. After dissociation, NO is observed to remain mainly in the centre of the distal haem pocket, although some movement towards the primary docking site and the xenon-4 pocket can be seen. We calculate the NO infrared spectrum for the photodissociated ligand within the haem pocket and find a narrow peak in the range 1915-1922 cm(-1). The resulting blue shift of 1 to 8 cm(-1) compared to gas-phase NO is much smaller than the red shifts calculated and observed for carbon monoxide (CO) in Mb. A small splitting, due to NO in the xenon-4 pocket, is also observed. At lower temperatures, the spectra and conformational space explored by the ligand remain largely unchanged, but the electrostatic interactions with residue His64 become increasingly significant in determining the details of the ligand orientation within the distal haem pocket. The investigation of the effect of the L29F mutation reveals significant differences between the behaviour of NO and that of CO, and suggests a coupling between the ligand and the protein dynamics due to the different ligand dipole moments.

Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations

A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved x-ray structures was performed to gain single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin after ligand dissociation reproduce the direction, amplitude, and time scales of crystallographically determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories. From 1,700 single-molecule trajectories, we identified and structurally characterized a conformational switch that directs dissociated ligands to one of two nearby protein cavities. Subsequent ligand migration proceeds through a network of transiently interconnected internal cavities, with passage between them involving correlated protein-ligand motions. The simulations also suggest how picosecond protein motions modulate the functional dissociation of oxygen and suppress the geminate recombination of toxic carbon monoxide.

Orientational distribution of CO before and after photolysis of MbCO and HbCO: a determination using time-resolved polarized Mid-IR spectroscopy

The technique of time-resolved polarized mid-IR spectroscopy was used to probe the orientational distribution of carbon monoxide (CO) bound to and docked within horse myoglobin, sperm whale myoglobin, and human hemoglobin A in neutral pH solution at 283 K. An accurate determination of the orientation required that the experimentally measured polarization anisotropy be corrected for the effects of fractional photolysis in an optically thick sample. The experimental method measures the direction of the transition dipole, which is parallel to the CO bond axis when docked and nearly parallel when bound to the heme. The polarization anisotropy of bound CO is virtually the same for all protein systems investigated and is unchanging across its inhomogeneously broadened mid-IR absorption spectrum. From these results, it was concluded that the transition dipole moment of bound CO is oriented </=7 degrees from the heme plane normal. The polarized absorbance spectra of docked CO are similar for all protein systems investigated, but in stark contrast to bound CO, the polarization anisotropy is strongly correlated with vibrational frequency. The frequency-dependent anisotropy imposes severe constraints on the orientational probability distribution function of the transition dipole, which is well described as a dipole bathed in a Stark field whose out-of-plane motion is constrained by a simple double-well potential. The orientational and spatial constraints imposed on docked CO by the surrounding highly conserved amino acids serve to mediate ligand transport to and from the binding site and thereby control the rates and pathways for geminate ligand rebinding and ligand escape.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3-7 cm(-1) (compared to the experimental value of 10 cm(-1)) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe...CO and Fe...OC) is 0.3 kcal mol(-1) and agrees well with the experimentally estimated value of 0.29 kcal mol(-1). A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin

We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins.

CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment.

Conformational fluctuations and electronic properties in myoglobin

In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics simulation and unperturbed Configuration Interaction (CISD) calculations in PMM, we reproduced the main spectroscopic features of deoxy-Myoglobin. Moreover, in line with our previous results on a photosensitive protein, this study reveals a clear dynamical coupling between electronic properties and conformational fluctuations, suggesting that this correlation could be a general feature of proteins.

Theoretical study of the discrimination between O(2) and CO by myoglobin

Combined quantum chemical and molecular mechanics geometry optimisations have been performed on myoglobin without or with O(2) or CO bound to the haem group. The results show that the distal histidine residue is protonated on the N(epsilon 2) atom and forms a hydrogen bond to the haem ligand both in the O(2) and the CO complexes. We have also re-refined the crystal structure of CO[bond]myoglobin by a combined quantum chemical and crystallographic refinement. Thereby, we probably obtain the most accurate available structure of the active site of this complex, showing a Fe[bond]C[bond]O angle of 171 degrees, and Fe[bond]C and C[bond]O bond lengths of 170-171 and 116-117 pm. The resulting structures have been used to calculate the strength of the hydrogen bond between the distal histidine residue and O(2) or CO in the protein. This amounts to 31-33 kJ/mol for O(2) and 2-3 kJ/mol for CO. The difference in hydrogen-bond strength is 21-22 kJ/mol when corrected for entropy effects. This is slightly larger than the observed discrimination between O(2) or CO by myoglobin, 17 kJ/mol. We have also estimated the strain of the active site inside the protein. It is 2-4 kJ/mol larger for the O(2) complex than for the CO complex, independent of which crystal structure the calculations are based on. Together, these results clearly show that myoglobin discriminates between O(2) and CO mainly by electrostatic interactions, rather than by steric strain.

NO rebinding to myoglobin: a reactive molecular dynamics study

The rebinding of NO to myoglobin after photolysis is studied using the 'reactive molecular dynamics' method. In this approach the energy of the system is evaluated on two potential energy surfaces that include the heme-ligand interactions which change between liganded and unliganded myoglobin. This makes it possible to take into account in a simple way, the high dimensionality of the transition seam connecting the reactant and product states. The dynamics of the dissociated NO molecules are examined, and the geometrical and energetic properties of the transition seam are studied. Analysis of the frequency of recrossing shows that the height of the effective rebinding barrier is dependent on the time after photodissociation. This effect is due mainly to protein relaxation and may contribute to the experimentally observed non-exponential rebinding rate of NO, as has been suggested previously.

Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy

Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described.