Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways.

The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 µs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.

Photoinduced transport in an H64Q neuroglobin antidote for carbon monoxide poisoning.

Carbon monoxide (CO) is a leading cause of poisoning deaths worldwide, without available antidotal therapy. Recently, a potential treatment for CO poisoning was introduced, based on binding of CO by neuroglobin (Ngb) with a mutated distal histidine (H64Q). Here, we present an atomistic mechanism of CO trapping by H64Q Ngb revealed by nonadiabatic molecular dynamics. We focused on CO photodissociation and recombination of CO to wild type (WT) and H64Q Ngb. Our results demonstrate that the distribution of CO within the proteins differs substantially due to rearrangement of amino acids surrounding the distal heme pocket. This leads to the decrease of the distal pocket volume in H64Q Ngb in comparison to WT Ngb, trapping migrating CO molecules in the distal pocket. We show that the mutation implicates the shortening of the time scale of CO geminate recombination, making H64Q Ngb 2.7 times more frequent binder than WT Ngb.

Thermodynamics of camphor migration in cytochrome P450cam by atomistic simulations.

Understanding the mechanisms of ligand binding to enzymes is of paramount importance for the design of new drugs. Here, we report on the use of a novel biased molecular dynamics (MD) methodology to study the mechanism of camphor binding to cytochrome P450cam. Microsecond-long MD simulations allowed us to observe reaction coordinates characterizing ligand diffusion from the active site of cytochrome P450cam to solvent via three egress routes. These atomistic simulations were used to estimate thermodynamic quantities along the reaction coordinates and indicate diverse binding configurations. The results suggest that the diffusion of camphor along the pathway near the substrate recognition site (SRS) is thermodynamically preferred. In addition, we show that the diffusion near the SRS is triggered by a transition from a heterogeneous collection of closed ligand-bound conformers to the basin comprising the open conformations of cytochrome P450cam. The conformational change accompanying this switch is characterized by the retraction of the F and G helices and the disorder of the B' helix. These results are corroborated by experimental studies and provide detailed insight into ligand binding and conformational behavior of the cytochrome family. The presented methodology is general and can be applied to other ligand-protein systems.

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

Machine Learning Based Dimensionality Reduction Facilitates Ligand Diffusion Paths Assessment: A Case of Cytochrome P450cam.

In this work we propose an application of a nonlinear dimensionality reduction method to represent the high-dimensional configuration space of the ligand-protein dissociation process in a manner facilitating interpretation. Rugged ligand expulsion paths are mapped into 2-dimensional space. The mapping retains the main structural changes occurring during the dissociation. The topological similarity of the reduced paths may be easily studied using the Fréchet distances, and we show that this measure facilitates machine learning classification of the diffusion pathways. Further, low-dimensional configuration space allows for identification of residues active in transport during the ligand diffusion from a protein. The utility of this approach is illustrated by examination of the configuration space of cytochrome P450cam involved in expulsing camphor by means of enhanced all-atom molecular dynamics simulations. The expulsion trajectories are sampled and constructed on-the-fly during molecular dynamics simulations using the recently developed memetic algorithms [ Rydzewski, J.; Nowak, W. J. Chem. Phys. 2015 , 143 ( 12 ), 124101 ]. We show that the memetic algorithms are effective for enforcing the ligand diffusion and cavity exploration in the P450cam-camphor complex. Furthermore, we demonstrate that machine learning techniques are helpful in inspecting ligand diffusion landscapes and provide useful tools to examine structural changes accompanying rare events.

Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations.

This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads to an increase of the main- and side-chain entropies in proteins. We show that such over-minimization may diverge the protein structures from the near-native attraction basin which possesses a minimum of free energy. We propose a measure based on the Pareto front of total entropy for quality assessment of minimized protein conformation. This measure may help in selection of adequate number of energy minimization steps in protein modelling and, thus, in preservation of the near-native protein conformation.

Memetic algorithms for ligand expulsion from protein cavities.

Ligand diffusion through a protein interior is a fundamental process governing biological signaling and enzymatic catalysis. A complex topology of channels in proteins leads often to difficulties in modeling ligand escape pathways by classical molecular dynamics simulations. In this paper, two novel memetic methods for searching the exit paths and cavity space exploration are proposed: Memory Enhanced Random Acceleration (MERA) Molecular Dynamics (MD) and Immune Algorithm (IA). In MERA, a pheromone concept is introduced to optimize an expulsion force. In IA, hybrid learning protocols are exploited to predict ligand exit paths. They are tested on three protein channels with increasing complexity: M2 muscarinic G-protein-coupled receptor, enzyme nitrile hydratase, and heme-protein cytochrome P450cam. In these cases, the memetic methods outperform simulated annealing and random acceleration molecular dynamics. The proposed algorithms are general and appropriate in all problems where an accelerated transport of an object through a network of channels is studied.

In vivo observation of lactate methyl proton magnetization transfer in rat C6 glioma.

Magnetic resonance spectroscopy (MRS) measurements of the lactate methyl proton in rat brain C6 glioma tissue acquired in the presence of an off-resonance irradiation field, analyzed using coupled Bloch equation formalism assuming two spin pools, demonstrated the occurrence of magnetization transfer. Quantitative analysis revealed that a very small fraction of lactate (f = 0.0012) is rotationally immobilized despite a large magnetization transfer effect. Off-resonance rotating frame spin-lattice relaxation studies demonstrated that deuterated lactate binds to bovine serum albumin and the proteins present in human plasma, thereby providing a possible physical basis for the observed magnetization transfer effect. These results demonstrate that partial or complete saturation of the motionally restricted lactate pool (as well as other metabolites) by the application of an off-resonance irradiation field, such as that used for water presaturation, can lead to a substantial decrease in resonance intensity by way of magnetization transfer effects, resulting in quantitation errors.

High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA.

The three-dimensional solution structure of duocarmycin SA in complex with d-(G1ACTAATTGAC11).d-(G12TCATTAGTC22) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1H NMR spectroscopy. The final input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 final structures, there were no distance constraint violations >0.06 A or torsion angle violations >0.8 degrees. The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A (average RMSD from the mean: 0.39 A). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles beta, epsilon, and zeta are distorted from standard values in the binding site region. The structure reveals site-specific bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.

The width of the minor groove affects the binding of the bisquaternary heterocycle SN-6999 to duplex DNA.

A complex between d(GGGAAAAACGG).d(CCGTTTTTCCC) and the minor groove binding drug SN-6999 has been studied by 1H nuclear magnetic resonance spectroscopy. The drug is found to bind in the d(A)5 tract, but with interactions extending one residue in the 3'-direction along each strand. Doubling of resonances in the complex indicates slow to intermediate exchange between two binding modes. An orientational preference (7:3) is found, the first such example in an SN-6999 complex. Furthermore, the upper limit of the lifetime for the major species is longer than was found for SN-6999 with other DNA duplexes. The preferred orientation of SN-6999 has the pyridinium ring near the 5'-end of the (+) strand; the minor binding mode has the reverse orientation. The orientational preference and slower exchange rate relative to other SN-6999 complexes is attributed to increased stabilization from van der Waals interactions due to better shape complementarity between the DNA duplex and ligand. The comparison of these results with studies of SN-6999 complexed to other DNA duplexes reveals the sensitivity of the binding properties to the delicate interplay between the molecular structure of the ligand and the specific characteristics of the DNA minor groove.

Deuterium off-resonance rotating frame spin-lattice relaxation of macromolecular bound ligands.

Deuterated 3-trimethylsilylpropionic acid binding to bovine serum albumin was used as a model system to examine the feasibility and limitations of using the deuterium off-resonance rotating frame spin-lattice relaxation experiment for the study of equilibrium ligand-binding behavior to proteins. The results of this study demonstrate that the rotational-diffusion behavior of the bound species can be monitored directly, i.e., the observed correlation time of the ligand in the presence of a protein is approximately equal to the correlation time of the ligand in the bound state, provided that the fraction of bound ligand is at least 0.20. The presence of local ligand motion and/or chemical exchange contributions to relaxation in the bound state was inferred from the observation that the correlation time of the bound ligand was somewhat smaller than the correlation time characterizing the overall tumbling of the protein. An approximate value for the fraction of bound ligand was obtained from off-resonance relaxation experiments when supplemental spin-lattice or transverse relaxation times were employed in the analysis. Incorporation of local motion effects for the bound species into the theoretical relaxation formalism enabled the evaluation of an order parameter and an effective correlation time, which in conjunction with a wobbling in a cone model, provided additional information about ligand motion in the bound state.

Off-resonance rotating-frame spin-lattice relaxation of quadrupolar (spin-1) nuclei.

The validity of the formalism for the off-resonance rotating-frame spin-lattice relaxation experiment applicable to spin-1 quadrupolar nuclei was experimentally examined by considering two model systems, deuterated glycerol and deuterated benzene in castor oil, at different temperatures. When appropriately implemented, the deuterium off-resonance rotating-frame spin-lattice relaxation experiment provides spectral-intensity-ratio-dispersion data which agree remarkably well with those predicted by the theoretical formalism. The assumption of quadrupolar relaxation as the dominant relaxation mechanism, and rigid-rotor isotropic tumbling, permits the assessment of rotational diffusion behavior, i.e., the determination of a rotational correlation time, of a variety of molecular systems. With the inclusion of an additional relaxation measurement, T1 or T2, the 2H off-resonance rotating-frame spin-lattice relaxation experiment becomes a convenient method for the estimation of the 2H quadrupolar coupling constant, provided that a realistic reorientational motional model is assumed in the theoretical relaxation expressions used in the analysis. Because the motional window of the 2H off-resonance rotating-frame spin-lattice relaxation experiment includes intermediate molecular motion with correlation times as short as 1 or 2 ns, this experiment is appropriate for the investigation of the rotational diffusion behavior of deuterated molecules varying in size from moderately small to macromolecular. The 2H off-resonance rotating-frame spin-lattice relaxation experiment is applicable to in vitro and in vivo experimental situations.

13C NMR studies of protein motional dynamics in bovine, human, rat, and chicken ocular lenses.

The motional dynamics of lens proteins were studied by two 13C nuclear magnetic resonance (NMR) techniques sensitive to molecular motion to define the effect of lens water content on the presence of solid-like protein domains in ocular lenses from bovine (juvenile and adult), human, rat, and chicken eyes. The solid state 13C NMR technique of proton dipolar decoupling was used to study slow (solid-like) motions (correlation time, tau o > or = 10 microseconds), whereas for intermediate (mobile) protein, rotational reorientational motion (tau o range of 1-500 nsec) the 13C off-resonance rotating frame spin-lattice relaxation technique was employed. 13C NMR studies of calf lens cortical and nuclear homogenates indicated a reversible loss of lens protein motional freedom with decreasing water content. Values of 6% and 63% solid-like protein contents were obtained for native cortical and nuclear calf lens homogenates, respectively. At equivalent total protein concentrations cortical and nuclear calf lens homogenates exhibited essentially the same solid-like (motionally restricted) protein content. Lens protein rotational correlation times determined by off-resonance rotating frame spin-lattice relaxation measurements were consistent with lens protein aggregation. The solid-like protein content of the bovine nuclear lens region was observed to increase with age, whereas no significant change was detected for the cortex. Across lens species an inverse correlation between the percentage of solid-like protein content and water content was observed. Very broad 13C NMR resonances, even in the presence of proton dipolar decoupling, were observed for the lens proteins present in the cataractous human lens, indicating the presence of highly aggregated protein species. The occurrence of solid-like protein domains in lens tissue has implications for the interpretation of proton nuclear magnetic resonance dispersion (NMRD) measurements of lens homogenates and for proton magnetization transfer contrast enhanced magnetic resonance imaging of lens. Solid-like protein domains may play a protective role in the maintenance of lens transparency by minimizing enhanced refractive index fluctuations created by protein packing defects resulting from post-translational modification.

Water self-diffusion in the calf lens.

Proton pulsed gradient spin echo (PGSE) nuclear magnetic resonance (NMR) spectroscopy was used to explore the free and restricted non-Brownian nature of lens water self-diffusion in calf lens tissue. At all temperatures investigated the water self-diffusion coefficient (Dw) of the cortical homogenate (25% protein) was 1.6-1.7 times greater than that for the nucleus (42% protein), and 0.3-0.5 times the value of Dw for pure water. The nuclear lens homogenate displayed anomalous temperature dependent water diffusion behavior, i.e. a departure from the smooth monotonic decrease in Dw with decreasing temperature, in the temperature range of 3-5 degrees C. By contrast, no such behavior was observed for cortical homogenate. Analysis of water proton echo attenuation data employing a parallel-plate model of restricted diffusion provided values for the parallel-plate barrier separation and self-diffusion coefficient in the limit of free diffusion. Nuclear material showed a smaller spatially average barrier separation and a significantly stronger barrier separation temperature dependence than cortical material.

Diameter distribution spectral of myelinated axons in the median and ulnar nerves of the Soay sheep.

An ulnar and a median nerve were taken from each of three Soay sheep, two aged 13 months and one aged 6 years. The axon diameter distribution spectra in these six nerves were determined by measurement of transverse sections stained by the Weigert-Pal technique. The histograms of myelinated axon diameters, between 1-17 micron, were unimodal in all the ulnar nerves. The mode lay between 4-5 micron in the nerves from the young sheep and between 6-7 micron in the old animal. The histograms of the median nerve axon diameters, between 1-18 micron, were all tri-modal. The nerves from the young sheep had modes between 2-3, 4-5 and 9-11 micron, and in the nerve from the old animal the modes were between 3-4, 6-7 and 12-13 micron. These findings are correlated with the conduction velocities recorded from these nerves in an earlier series of experiments.