C. Mark Maupin

Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II

Human carbonic anhydrase II (HCA II) is one of the fastest known enzymes, which utilizes a rate-limiting proton transport (PT) step in its enzymatic reaction. To evaluate the PT event at an atomistic level, the multistate empirical valence bond (MS-EVB) method has been utilized in this work. It is observed that the PT event in HCA II exploits a transient active site water cluster to transport the excess proton between the catalytic zinc-bound water/hydroxide and the proton shuttling residue, His64. This PT event is found to be dependent on the enzymes ability to form and stabilize the active site water cluster in addition to its ability to orient His64 in a favorable conformation. Evaluation of the PT free energy barrier for different orientations of His64 reveals this residues vital role as a proton transporter and elucidates its direct effect on the barrier to PT through the active site water. It is suggested that the rate-limiting step oscillates between the active site water PT event to His64 and the de/protonation of His64 depending on the exogenous buffer concentration and the orientation of His64. In the absence of a PT acceptor/donor at position 64, it is found that the excess proton will utilize one of three distinct paths to enter/leave the active site. This latter result not only allows for an increased understanding of how enzymes capitalize on the protein/solvent interface to guide excess protons to/from areas of interest, it also provides valuable insight into the chemical rescue experiments on HCA II mutants.

The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations.

The self-consistent charge density functional tight binding (SCC-DFTB) method is a relatively new approximate electronic structure method that is increasingly used to study biologically relevant systems in aqueous environments. There have been several gas phase cluster calculations that indicate, in some instances, an ability to predict geometries, energies, and vibrational frequencies in reasonable agreement with high level ab initio calculations. However, to date, there has been little validation of the method for bulk water properties, and no validation for the properties of the hydrated excess proton in water. Presented here is a detailed SCC-DFTB analysis of the latter two systems. This work focuses on the ability of the original SCC-DFTB method, and a modified version that includes a hydrogen bonding damping function (HBD-SCC-DFTB), to describe the structural, energetic, and dynamical nature of these aqueous systems. The SCC-DFTB and HBD-SCC-DFTB results are compared to experimental data and Car-Parrinello molecular dynamics (CPMD) simulations using the HCTH/120 gradient-corrected exchange-correlation energy functional. All simulations for these systems contained 128 water molecules, plus one additional proton in the case of the excess proton system, and were carried out in a periodic simulation box with Ewald long-range electrostatics. The liquid water structure for the original SCC-DFTB is shown to poorly reproduce bulk water properties, while the HBD-SCC-DFTB somewhat more closely represents bulk water due to an improved ability to describe hydrogen bonding energies. Both SCC-DFTB methods are found to underestimate the water dimer interaction energy, resulting in a low heat of vaporization and a significantly elevated water oxygen diffusion coefficient as compared to experiment. The addition of an excess hydrated proton to the bulk water resulted in the Zundel cation (H(5)O(2)(+)) stabilized species being the stable form of the charge defect, which diffuses at a rate similar to the underlying water diffusion. These SCC-DFTB results differ significantly from other existing computational descriptions of the hydrated excess proton in water, as well as from the available experimental data.

Chemical Rescue of Enzymes: Proton Transfer in Mutants of Human Carbonic Anhydrase II

In human carbonic anhydrase II (HCA II), the mutation of position 64 from histidine to alanine (H64A) disrupts the rate limiting proton transfer (PT) event, resulting in a reduction of the catalytic activity of the enzyme as compared to the wild-type. Potential of mean force (PMF) calculations utilizing the multistate empirical valence bond (MS-EVB) methodology for H64A HCA II yields a PT free energy barrier significantly higher than that found in the wild-type enzyme. This high barrier, determined in the absence of exogenous buffer and assuming no additional ionizable residues in the PT pathway, indicates the likelihood of alternate enzyme pathways that utilize either ionizable enzyme residues (self-rescue) and/or exogenous buffers (chemical rescue). It has been shown experimentally that the catalytic activity of H64A HCA II can be chemically rescued to near wild-type levels by the addition of the exogenous buffer 4-methylimidazole (4MI). Crystallographic studies have identified two 4MI binding sites, yet site-specific mutations intended to disrupt 4MI binding have demonstrated these sites to be nonproductive. In the present work, MS-EVB simulations show that binding of 4MI near Thr199 in the H64A HCA II mutant, a binding site determined by NMR spectroscopy, results in a viable chemical rescue pathway. Additional viable rescue pathways are also identified where 4MI acts as a proton transport intermediary from the active site to ionizable residues on the rim of the active site, revealing a probable mode of action for the chemical rescue pathway.

Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions.

The self-consistent charge density functional tight binding (SCC-DFTB) method has been applied to hydroxide water clusters and a hydroxide ion in bulk water. To determine the impact of various implementations of SCC-DFTB on the energetics and dynamics of a hydroxide ion in gas phase and condensed phase, the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus, and DFTB3-3OB implementations have been tested. Energetic stabilities for small hydroxide clusters, OH(-)(H2O)n, where n = 4-7, are inconsistent with the results calculated with the B3LYP and second order Møller-Plesset (MP2) levels of ab initio theory. The condensed phase simulations, OH(-)(H2O)127, using the DFTB2, DFTB2-γ(h), DFTB2-γ(h)+gaus, DFTB3-diag, DFTB3-diag+gaus, DFTB3-Full+gaus and DFTB3-3OB methods are compared to Car-Parrinello molecular dynamics (CPMD) simulations using the BLYP functional. The SCC-DFTB method including a modified O-H repulsive potential and the third order correction (DFTB3-diag/Full+gaus) is shown to poorly reproduce the CPMD computational results, while the DFTB2 and DFTB2-γ(h) method somewhat more closely describe the structural and dynamical nature of the hydroxide ion in condensed phase. The DFTB3-3OB outperforms the MIO parameter set but is no more accurate than DFTB2. It is also shown that the overcoordinated water molecules lead to an incorrect bulk water density and result in unphysical water void formation. The results presented in this paper point to serious drawbacks for various DFTB extensions and corrections for a hydroxide ion in aqueous environments.

Origins of enhanced proton transport in the Y7F mutant of human carbonic anhydrase II.

Human carbonic anhydrase II (HCA II), among the fastest enzymes known, catalyzes the reversible hydration of CO 2 to HCO 3 (-). The rate-limiting step of this reaction is believed to be the formation of an intramolecular water wire and transfer of a proton across the active site cavity from a zinc-bound solvent to a proton shuttling residue (His64). X-ray crystallographic studies have shown this intramolecular water wire to be directly stabilized through hydrogen bonds via a small well-defined set of amino acids, namely, Tyr7, Asn62, Asn67, Thr199, and Thr200. Furthermore, X-ray crystallographic and kinetic studies have shown that the mutation of tyrosine 7 to phenylalanine, Y7F HCA II, has the effect of increasing the proton transfer rate by 7-fold in the dehydration direction of the enzyme reaction compared to wild-type (WT). This increase in the proton transfer rate is postulated to be linked to the formation of a more directional, less branched, water wire. To evaluate this proposal, molecular dynamics simulations have been employed to study water wire formation in both the WT and Y7F HCA II mutant. These studies reveal that the Y7F mutant enhances the probability of forming small water wires and significantly extends the water wire lifetime, which may account for the elevated proton transfer seen in the Y7F mutant. Correlation analysis of the enzyme and intramolecular water wire indicates that the Y7F mutant significantly alters the interaction of the active site waters with the enzyme while occupancy data of the water oxygens reveals that the Y7F mutant stabilizes the intramolecular water wire in a manner that maximizes smaller water wire formation. This increase in the number of smaller water wires is likely to elevate the catalytic turnover of an already very efficient enzyme.

Electronic structure and spectroscopic analysis of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ion pair.

Electronic and structural properties of the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulonyl)imide are studied using density functional theory (DFT) methods in addition to infrared and UV-vis spectroscopy. The DFT methods were conducted for both gas phase and solution phase using the integral equation formalism polarizable continuum model, while optical absorption experiments were conducted using neat and dilute methanol solutions. Three energetically similar conformers were obtained for each of the gas phase and solution phase DFT calculations. These multiple configurations were considered when analyzing the molecular interactions between the ion pair and for a molecular-level interpretation of the experimental IR and UV-vis spectroscopy data. Excitation energies of low-lying singlet excited states of the conformers were calculated with time-dependent DFT and experimentally with UV-vis absorption spectra. Difference density plots and excited-state calculations in the gas phase are found to be in good agreement with the experimental findings, while the implicit solvation model calculations adversely impacted the accuracy of the predicted spectra.

Proton transport in carbonic anhydrase: Insights from molecular simulation.

This article reviews the insights gained from molecular simulations of human carbonic anhydrase II (HCA II) utilizing non-reactive and reactive force fields. The simulations with a reactive force field explore protein transfer and transport via Grotthuss shuttling, while the non-reactive simulations probe the larger conformational dynamics that underpin the various contributions to the rate-limiting proton transfer event. Specific attention is given to the orientational stability of the His64 group and the characteristics of the active site water cluster, in an effort to determine both of their impact on the maximal catalytic rate. The explicit proton transfer and transport events are described by the multistate empirical valence bond (MS-EVB) method, as are alternative pathways for the excess proton charge defect to enter/leave the active site. The simulation results are interpreted in light of experimental results on the wild-type enzyme and various site-specific mutations of HCA II in order to better elucidate the key factors that contribute to its exceptional efficiency.

Overview: Nucleation of clathrate hydrates

Molecular level knowledge of nucleation and growth of clathrate hydrates is of importance for advancing fundamental understanding on the nature of water and hydrophobic hydrate formers, and their interactions that result in the formation of ice-like solids at temperatures higher than the ice-point. The stochastic nature and the inability to probe the small length and time scales associated with the nucleation process make it very difficult to experimentally determine the molecular level changes that lead to the nucleation event. Conversely, for this reason, there have been increasing efforts to obtain this information using molecular simulations. Accurate knowledge of how and when hydrate structures nucleate will be tremendously beneficial for the development of sustainable hydrate management strategies in oil and gas flowlines, as well as for their application in energy storage and recovery, gas separation, carbon sequestration, seawater desalination, and refrigeration. This article reviews various aspects of hydrate nucleation. First, properties of supercooled water and ice nucleation are reviewed briefly due to their apparent similarity to hydrates. Hydrate nucleation is then reviewed starting from macroscopic observations as obtained from experiments in laboratories and operations in industries, followed by various hydrate nucleation hypotheses and hydrate nucleation driving force calculations based on the classical nucleation theory. Finally, molecular simulations on hydrate nucleation are discussed in detail followed by potential future research directions.

pKa determination of histidine residues in α-conotoxin MII peptides by 1H NMR and constant pH molecular dynamics simulation.

α-Conotoxin MII (α-CTxMII) is a potent and selective peptide antagonist of neuronal nicotinic acetylcholine receptors (nAChRs). Studies have shown that His9 and His12 are significant determinants of toxin binding affinity for nAChR, while Glu11 may dictate differential toxin affinity between nAChR isoforms. The protonation state of these histidine residues and therefore the charge on the α-CTx may contribute to the observed differences in binding affinity and selectivity. In this study, we assess the pH dependence of the protonation state of His9 and His12 by (1)H NMR spectroscopy and constant pH molecular dynamics (CpHMD) in α-CTxMII, α-CTxMII[E11A], and the triple mutant, α-CTxMII[N5R:E11A:H12K]. The E11A mutation does not significantly perturb the pKa of His9 or His12, while N5R:E11A:H12K results in a significant decrease in the pKa value of His9. The pKa values predicted by CpHMD simulations are in good agreement with (1)H NMR spectroscopy, with a mean absolute deviation from experiment of 0.3 pKa units. These results support the use of CpHMD as an efficient and inexpensive predictive tool to determine pKa values and structural features of small peptides critical to their function.

Impact of water dilution and cation tail length on ionic liquid characteristics: Interplay between polar and non-polar interactions

The recalcitrance of lignocellulosic biomass poses a major challenge that hinders the economical utilization of biomass for the production of biofuel, plastics, and chemicals. Ionic liquids have become a promising solvent that addresses many issues in both the pretreatment process and the hydrolysis of the glycosidic bond for the deconstruction of cellulosic materials. However, to make the use of ionic liquids economically viable, either the cost of ionic liquids must be reduced, or a less expensive solvent (e.g., water) may be added to reduce the overall amount of ionic liquid used in addition to reducing the viscosity of the binary liquid mixture. In this work, we employ atomistic molecular dynamics simulations to investigate the impact of water dilution on the overall liquid structure and properties of three imidazolium based ionic liquids. It is found that ionic liquid-water mixtures exhibit characteristics that can be grouped into two distinct regions, which are a function of the ionic liquid concent...