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Biomedical subjects

Michael L Klein

Publications and source records attributed to Michael L Klein.

At least 19 recordsLinked to original sources
PubMed2007

Proton shuttles and phosphatase activity in soluble epoxide hydrolase.

Recently, a novel metal Mg2+-dependent phosphatase activity has been discovered in the N-terminal domain of the soluble epoxide hydrolase (sEH), opening a new branch of fatty acid metabolism and providing an additional site for drug targeting. Importantly, the sEH N-terminal fold belongs to the haloacid dehalogenase (HAD) superfamily, which comprises a vast majority of phosphotransferases. Herein, we present the results of a computational study of the sEH phosphatase activity, which includes classical molecular dynamics (MD) simulations and mixed quantum mechanical/molecular mechanics (QM/MM) calculations. On the basis of experimental results, a two-step mechanism has been proposed and herein investigated: (1) phosphoenzyme intermediate formation and (2) phosphoenzyme intermediate hydrolysis. Building on our earlier work, we now provide a detailed description of the reaction mechanism for the whole catalytic cycle along with its free energy profile. The present computations suggest metaphosphate-like transition states for these phosphoryl transfers. They also reveal that the enzyme promotes water deprotonation and facilitates shuttling of protons via a metal-ligand connecting water bridge (WB). These WB-mediated proton shuttles are crucial for the activation of the solvent nucleophile and for the stabilization of the leaving group. Moreover, due to the conservation of structural features in the N-terminal catalytic site of sEH and other members of the HAD superfamily, we suggest a generalization of our findings to these other metal-dependent phosphatases.

Catalysis↗
PubMed2006

Gemini surfactants at the air/water interface: a fully atomistic molecular dynamics study.

Gemini surfactants typically consist of two single-chain surfactants chemically linked by a spacer molecule. We report herein the results of fully atomistic molecular dynamics (MD) simulations of a series of Gemini surfactants: CsH2s-alpha,omega-bis(C12H25N+(CH3)2Cl-), at the air/water interface with s = 3, 4, 6, 12, 14, and 16, at values of the initial surface area per surfactant AS = 70 A2, 77 A2, 95 A2, 151 A2, 133 A2, and 103 A2, respectively. The AS values employed were obtained from surface tension and neutron reflection experiments at the respective cmc of each surfactant. The Gemini surfactant corresponding to s = 3 was also simulated at AS = 105 A2, which is the experimentally derived value of surface area per surfactant at 1/10th of cmc. Only the surfactants with s = 12 and 14 and the surfactant with s = 3 at AS = 105 A2 gave a stable monolayer at the air/water interface. In other cases, we observe movement of some surfactant molecules from the air/water interface into the aqueous phase, resulting in a stable primary monolayer of surfactants at the air/water interface and a small concentration of surfactant molecules below it. The latter form aggregates, with their hydrophobic chains in the core. The density profiles along the normal to the interface are compared with the ones obtained from neutron reflection experiments. The MD simulations confirm the bending of the spacer toward the hydrophobic chains as the spacer length is increased and the spacer becomes more hydrophobic. The simulations have helped to shed light on the low-resolution picture which emerges from experimental analyses.

Air↗
PubMed2006

Structural and dynamical properties of manganese catalase and the synthetic protein DF1 and their implication for reactivity from classical molecular dynamics calculations.

There is a pressing need for accurate force fields to assist in metalloprotein analysis and design. Recent work on the design of mimics of dimetal proteins highlights the requirements for activity. DF1 is a de novo designed protein, which mimics the overall fold and active site geometry of a series of diiron and dimanganese proteins. Specifically, the dimanganese form of DF1 is a mimic of the natural enzyme manganese catalase, which catalyzes the dismutation reaction of hydrogen peroxide into water and oxygen. During catalytic turnover, the active site has to accommodate both the reduced and the oxidized state of the dimanganese core. The biomimetic protein DF1 is only stable in the reduced form and thus not active. Furthermore, the synthetic protein features an additional bridging glutamate sidechain, which occupies the substrate binding site. The goal of this study is to develop classical force fields appropriate for design of such important dimanganese proteins. To this aim, we use a nonbonded model to represent the metal-ligand interactions, which implicitly takes into account charge transfer and local polarization effects between the metal and its ligands. To calibrate this approach, we compare and contrast geometric and dynamical properties of manganese catalase and DF1. Having demonstrated a good correspondence with experimental structural data, we examine the effect of mutating the bridging glutamate to aspartate (M1) and serine (M2). Classical MD based on the refined forcefield shows that these point mutations affect not only the immediate coordination sphere of the manganese ions, but also the relative position of the helices, improving the similarity to Mn-catalase, especially in case of M2. On the basis of these findings, classical molecular dynamics calculations with the active site parameterization scheme introduced herein seem to be a promising addition to the protein design toolbox.

Binding Sites↗
PubMed2006

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations.

Almost half of the proteome of living organisms is constituted of metalloproteins. Unfortunately, the ability of the current generation of molecular dynamics pairwise-additive forcefields to properly describe metal pockets is severely lacking due to the intrinsic difficulty of handling polarization and charge transfer contributions. In order to improve the description of metalloproteins, a simple reparameterization strategy is proposed herein that does not involve artificial constraints. Specifically, a non-bonded quantum mechanical-based model is used to capture the mean polarization and charge transfer contributions to the interatomic forces within the metal site. The present approach is demonstrated to provide enough accuracy to maintain the integrity of the metal pocket for a variety of metalloproteins during extended (multi-nanosecond) molecular dynamics simulations. The method enables the sampling of small conformational changes and the relaxation of local frustrations in NMR structures.

Binding Sites↗
PubMed2006

Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein.

To explore the possibility of electron transport in a recently designed four-helix bundle protein (Cochran, F. V.; et al. J. Am. Chem. Soc. 2005, 127, 1346), we have computed the reorganization free energy for (i) oxidation of a single Ru-porphyrin cofactor and (ii) electron self-exchange between two Ru-porphyrin cofactors binding to the solvated protein. Sampling the classical electrostatic energy gap for 20 ns, we find that the fluctuations are well described by Gaussian statistics and obtain reorganization free energies of 0.90 +/- 0.04 eV for oxidation and 1.36 +/- 0.08 eV for self-exchange. The latter is 0.1-0.2 eV higher than the experimental estimate for interprotein electron self-exchange in cytochrome b5. As in natural electron carriers, inner-sphere reorganization is very small, 88 meV for self-exchange between two model cofactors computed at the density functional level of theory. Decomposing the outer-sphere reorganization free energy, we find that the solvent (aqueous ionic solution) is the primary outer-sphere medium for oxidation, contributing 0.60 eV (69%). The protein contributes only 0.27 eV (31%). For self-exchange, the solvent contribution, 0.68 eV (54%), and the protein contribution, 0.59 eV (46%), are almost equally important. The large solvent contribution is due to the slow decay of dipole reorientation of the solvent as a function of distance to the cofactor, implying that the change in the electric field upon electron transfer is not as effectively screened by the four-helix bundle protein. However, ranking the residues according to their free energy contributions, it is suggested that the reorganization free energy can be decreased by about 0.2 eV if two glutamine residues in the vicinity of the cofactor are mutated into less polar amino acids.

Amino Acid Sequence↗
PubMed2006

Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.

The self-assembly of cyclic D,L-alpha-peptides into hollow nanotubes is a crucial mechanistic step in their application as antibacterial and drug-delivery agents. To understand this process, molecular dynamics (MD) simulations were performed on dimers of cyclic peptides formed from cyclo [(-L-Trp-D-N-MeLeu-)4-]2 and cyclo [(-L-Trp-D-Leu-)4-]2 subunits in nonpolar (nonane) and polar (water) solvent. The dimers were observed to be stable only in nonpolar solvent over the full 10 ns length of the MD trajectory. The behavior of the dimers in different solvents is rationalized in terms of the intersubunit hydrogen bonding, hydrogen bonding with the solvent, and planarity of the rings. It is shown that the phi and psi dihedral angles of a single uncapped ring in nonane lie in the beta-sheet region of the Ramachandran plot, and the ring stays in a flat conformation. Steered MD (SMD) simulations based on Jarzynski's equality were performed to obtain the potential of mean force as a function of the distance between the two rings of the capped dimer in nonane. It is also shown that a single peptide subunit prefers to reside close to the nonane/water interface rather than in bulk solvent because of the amphiphilic character of the peptide ring. The present MD results build the foundation for using MD simulations to study the mechanism of the formation of cyclic peptide nanotubes in lipid bilayers.

Dimerization↗
PubMed2006

Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles.

Molecular dynamics simulations have been performed to investigate the partitioning of the volatile anesthetic halothane from an aqueous phase into a coexisting hydrated bilayer, composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipids, with embedded alpha-helical peptide bundles based on the membrane-bound portions of the alpha- and delta-subunits, respectively, of nicotinic acetylcholine receptor. In the molecular dynamics simulations halothane molecules spontaneously partitioned into the DOPC bilayer and then preferentially occupied regions close to lipid headgroups. A single halothane molecule was observed to bind to tyrosine (Tyr-277) residue in the alpha-subunit, an experimentally identified specific binding site. The binding of halothane attenuated the local loop dynamics of alpha-subunit and significantly influenced global concerted motions suggesting anesthetic action in modulating protein function. Steered molecular dynamics calculations on a single halothane molecule partitioned into a DOPC lipid bilayer were performed to probe the free energy profile of halothane across the lipid-water interface and rationalize the observed spontaneous partitioning. Partitioned halothane molecules affect the hydrocarbon chains of the DOPC lipid, by lowering of the hydrocarbon tilt angles. The anesthetic molecules also caused a decrease in the number of peptide-lipid contacts. The observed local and global effects of anesthetic binding on protein motions demonstrated in this study may underlie the mechanism of action of anesthetics at a molecular level.

Anesthetics, Inhalation↗
PubMed2006

Exploring the gating mechanism in the ClC chloride channel via metadynamics.

Computer simulations have been used to probe the gating mechanism in the Salmonella serovar typhimurium chloride channel (st-ClC). Specifically, the recently developed metadynamics methodology has been exploited to construct free energy surfaces as a function of the positions of either one or two chloride ions inside the pore, the position and protonation state of the key E148 residue, and the number of water molecules coordinating the translocating ions. The present calculations confirm the multi-ion mechanism in which an ion-push-ion effect lowers the main barriers to chloride ion translocation. When a second anion is taken into account, the barrier for chloride passage through the E148 narrow region is computed to be 6 kcal/mol in the wild-type channel, irrespective of the protonation state of the E148 residue, which is shown to only affect the entrance barrier. In the E148A mutant, this barrier is much lower, amounting to 3 kcal/mol. The metadynamics calculations reported herein also demonstrate that before reaching the periplasmic solution, chloride ions have to overcome an additional barrier arising from two different effects, namely the rearrangement of their solvation shell and a flip in the backbone angles of the residues E148 and G149, which reside at the end of the alphaF helix.

Chloride Channels↗
PubMed2006

CFH gene variant, Y402H, and smoking, body mass index, environmental associations with advanced age-related macular degeneration.

OBJECTIVES: We tested the hypothesis that modifiable lifestyle factors alter the genetic susceptibility associated with a common coding variant in the complement factor H (CFH) gene, Y402H, for the leading cause of blindness among the elderly, age-related macular degeneration (AMD). METHODS: In this case-control association analysis, Caucasian participants in the multicenter Age-Related Eye Disease Study with advanced AMD (n = 574 cases) or no AMD (n = 280 controls) were evaluated. AMD status was determined by grading of fundus photographs. Risk factors including cigarette smoking and body mass index (BMI) were assessed and DNA specimens were genotyped for the variant in the CFH gene. Unconditional logistic regression analyses were performed. Attributable risks and multivariable AMD risk scores were calculated. RESULTS: The number of risk alleles for Y402H was associated with advanced AMD, with odds ratios (OR) of 2.7 (95% confidence interval (CI) 1.8-3.8) for the CT heterozygous genotype and OR 7.4 (4.7-11.8) for the homozygous CC risk genotype, after controlling for demographic and behavioral risk factors. Current cigarette smoking (OR 5.1) and high BMI > or =30 (OR 2.1) were independently related to AMD, controlling for genotype. The association between AMD and BMI varied dependent on genotype (P interaction = 0.006 for the CT vs. TT genotype). The CC genotype plus higher BMI (OR 5.9) or smoking (OR 10.2) conferred the greatest risks. Gene plus environment risk scores provided an area under the receiver operating characteristic (ROC) curve of 0.70-0.75. CONCLUSIONS: Genetic and environmental factors are independently related to advanced AMD, and modifiable factors alter genetic susceptibility. The AMD risk score identifies a highly susceptible population.

Aged↗
PubMed2006

Hydrogen bond topology and the ice VII/VIII and Ih/XI proton ordering phase transitions.

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized. In order to shed some light on the ice Ih proton ordering transition, we present the results of periodic electronic density functional theory calculations and statistical simulations. We are able to describe the small energy differences among the innumerable H-bond configurations possible in a large simulation cell by using an analytic theory to extrapolate from electronic DFT calculations on small unit cells to cells large enough to approximate the thermodynamic limit. We first validate our methods by comparing our predictions to the well-characterized ice VII/VIII proton ordering transition, finding agreement with respect to both the transition temperature and structure of the low-temperature phase. For ice Ih, our results indicate that a proton-ordered phase is attainable at low temperatures, the structure of which is in agreement with the experimentally proposed ferroelectric structure. The predicted transition temperature of is in qualitative agreement with the observed transition at on KOH-doped ice samples.

Journal Article↗
PubMed2006

Ab initio calculations of intramolecular parameters for a class of arylamide polymers.

Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers.

Amides↗
PubMed2006

Polarization effects and charge transfer in the KcsA potassium channel.

The electronic structure of the selectivity filter of KcsA K(+) channel is investigated by density functional theory (DFT/BLYP) and QM/MM methods. The quantum part includes the selectivity filter, which is polarized by the electrostatic field of the environment treated with the Amber force field. The details of the electronic structure were investigated using the maximally localized Wannier function centers of charge and Bader's atoms in molecules charge analysis. Our results show that the channel backbone carbonyl groups are largely polarized and that there is a sizeable charge transfer from the backbone to the cations. These effects are expected to be important for an accurate description of the carbonyl groups and the ion-ion electrostatic repulsion, which have been proposed to play a central role for the selectivity mechanism of the channel [S.Y. Noskov, S. Berneche, B. Roux, Control of ion selectivity in potassium channels by electrostatic and dynamic properties of carbonyl ligands. Nature 431 (2004) 830-834].

Bacterial Proteins↗
PubMed2006

Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonation.

Accurate calculation of pK(a) values and free energies for acid/base reactions in the condensed phase has been a long-standing goal of theoretical chemistry. We present a novel application of the Car-Parrinello molecular dynamics method to the problem of relative pK(a) determination. As a particular example, we focus on the second stage in the dissociation of histidine, a process that holds special importance for biology. Using constrained molecular dynamics, we have analyzed the structural, electronic, and dynamical transformations taking place along a preselected, intuitive reaction coordinate. By integrating the potentials of mean force for the deprotonation of histidine and for a reference reaction, autodissociation of water, we obtain a pK(a) value of 6.8, which appears to be in good agreement with the experimental estimate of 6.1. Detailed analysis was undertaken to determine the value of the constraint, which transformed the N*-H* from a covalent to a hydrogen bond. This helped to identify a number of properties that could be successfully used in monitoring the dissociation process. Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction.

Histidine↗
PubMed2006

Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study.

Using quantum chemistry plus ab initio molecular dynamics and classical molecular dynamics methods, we address the relationship between molecular conformation and the biomedical function of arylamide polymers. Specifically, we have developed new torsional parameters for a class of these polymers and applied them in a study of the interaction between a representative arylamide and one of its biomedical targets, the anticoagulant drug heparin. Our main finding is that the torsional barrier of a C(aromatic)-C(carbonyl) bond increases significantly upon addition of an o-OCH2CH2NH3+ substituent on the benzene ring. Our molecular dynamics studies that are based on the original general AMBER force field (GAFF) and GAFF modified to include our newly developed torsional parameters show that the binding mechanism between the arylamide and heparin is very sensitive to the choice of torsional potentials. Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used.

Acetanilides↗
PubMed2006

Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics.

We have applied molecular dynamics to investigate the structural properties and activity of recently synthesized amphiphilic polymethacrylate derivatives, designed to mimic the antimicrobial activity of natural peptides. The composition, molecular weight, and hydrophobicity (ratio of hydrophobic and cationic units) of these short copolymers can be modulated to achieve structural diversity, which is crucial in controlling the antimicrobial activity. We have carried out all-atom molecular dynamics to systematically investigate the conformations adopted by these copolymers in water and at the water-lipid interface as a function of sequence and the chemical nature of the monomers. For two sequences, we observe partial insertion into the bilayer. Formation of strong interactions between the lipid headgroups and the amine groups of the polymers assists in the initial association with the lipids. However, the primary driving force for the observed partial insertion appears to be the hydrophobic effect. Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design.

Anti-Infective Agents↗
PubMed2006

Diabatic free energy curves and coordination fluctuations for the aqueous Ag+Ag2+ redox couple: a biased Born-Oppenheimer molecular dynamics investigation.

Biased Born-Oppenheimer molecular dynamics simulations are performed to compute redox potential and free energy curves for the redox half reaction Ag(+)-->Ag(2+)+e(-) in aqueous solution. The potential energy surfaces of reactant and product state are linearly coupled and the system transferred from the reduced state to the oxidized state by variation of the coupling parameter from 0 to 1. The redox potential is obtained by thermodynamic integration of the average ionization energy of Ag(+). Diabatic free energy curves of reduced (R) and oxidized (O) states are obtained to good statistical accuracy by reweighting and combining the set of biased distributions of the ionization energy. The diabatic free energy curves of Ag(+) and Ag(2+) are parabolic over a wide range of the reaction coordinate in agreement with the linear response assumption that underlies Marcus theory. However, we observe deviations from parabolic behavior in the equilibrium region of Ag(+) and find different values for the reorganization free energy of R (1.4 eV) and O (0.9 eV). The computed reorganization free energy of Ag(2+) is in good agreement with the experimental estimate of 0.9-1.2 eV obtained from photoelectron spectroscopy. As suggested by our calculations, the moderate deviation from linear response behavior found for Ag(+) is likely related to the highly fluxional solvation shell of this ion, which exhibits water exchange reactions on the picosecond time scale of the present molecular dynamics simulation.

Journal Article↗
PubMed2006

Molecular dynamics simulations of surfactant self-organization at a solid-liquid interface.

Self-organization of aqueous surfactants at a planar graphite-like surface is studied by means of coarse-grain molecular dynamics simulations. The nonionic surfactant, n-alkyl poly(ethylene oxide), and water are both represented by coarse-grain models while an implicit representation is used for the graphite surface. The observed morphology of the aggregated surfactants depends on the alkyl chain length. Surfactants with a short chain form a monolayer on the graphite surface with a thickness roughly equal to that of the alkane tail. On the other hand, longer-tail surfactants form continuous hemicylinders on the surface with diameter approximately 5.0 +/- 0.5 nm, in good agreement with experimental AFM data.

Adsorption↗