Biomedical subjects

Michael L Klein

Publications and source records attributed to Michael L Klein.

At least 55 records · Page 3Linked to original sources

PubMed2005

Unfolding a linker between helical repeats.

In many multi-repeat proteins, linkers between repeats have little secondary structure and place few constraints on folding or unfolding. However, the large family of spectrin-like proteins, including alpha-actinin, spectrin, and dystrophin, share three-helix bundle, spectrin repeats that appear in crystal structures to be linked by long helices. All of these proteins are regularly subjected to mechanical stress. Recent single molecule atomic force microscopy (AFM) experiments demonstrate not only forced unfolding but also simultaneous unfolding of tandem repeats at finite frequency, which suggests that the contiguous helix between spectrin repeats can propagate a cooperative helix-to-coil transition. Here, we address what happens atomistically to the linker under stress by steered molecular dynamics simulations of tandem spectrin repeats in explicit water. The results for alpha-actinin repeats reveal rate-dependent pathways, with one pathway showing that the linker between repeats unfolds, which may explain the single-repeat unfolding pathway observed in AFM experiments. A second pathway preserves the structural integrity of the linker, which explains the tandem-repeat unfolding event. Unfolding of the linker begins with a splay distortion of proximal loops away from hydrophobic contacts with the linker. This is followed by linker destabilization and unwinding with increased hydration of the backbone. The end result is an unfolded helix that mechanically decouples tandem repeats. Molecularly detailed insights obtained here aid in understanding the mechanical coupling of domain stability in spectrin family proteins.

Animals↗

PubMed2005

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

The recently introduced hills method (Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562) is a powerful tool to compute the multidimensional free energy surface of intrinsically concerted reactions. We have extended this method by focusing our attention on localizing the lowest free energy path that connects the stable reactant and product states. This path represents the most probable reaction mechanism, similar to the zero temperature intrinsic reaction coordinate, but also includes finite temperature effects. The transformation of the multidimensional problem to a one-dimensional reaction coordinate allows for accurate convergence of the free energy profile along the lowest free energy path using standard free energy methods. Here we apply the hills method, our lowest free energy path search algorithm, and umbrella sampling to the prototype S(N)2 reaction. The hills method replaces the in many cases difficult problem of finding a good reaction coordinate with choosing relatively simple collective variables, such as the bond lengths of the broken and formed chemical bonds. The second part of the paper presents a guide to using the hills method, in which we test and fine-tune the method for optimal accuracy and efficiency using the umbrella sampling results as a reference.

Journal Article↗

PubMed2005

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

The existence of an ice Ih/XI proton-ordering transition to a low-temperature ferroelectric phase has sparked considerable debate in the literature. Electronic density functional theory calculations, extended using graph invariants, confirm that a transition to a low-temperature ferroelectric phase should occur. The predicted transition at 98 K is in qualitative agreement with the observed transition at 72 K, and the low-temperature phase is the ferroelectric phase determined in diffraction experiments. The theoretical methods used to predict the phase transition are validated by comparing their prediction to the well-characterized ice VII/VIII proton-ordering transition.

Journal Article↗

PubMed2005

Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamics.

We have used ab initio molecular dynamics (AIMD) to investigate the dynamical flexibility of the bridged binuclear structural motif in the active site of arginase. Dynamical transformations play a crucial role in catalysis. We have provided direct insight into the motions of the first-shell ligands with emphasis on the chelating and bridging carboxylates. In the case of the terminal Asp234 residue we observe changes in the binding mode (carboxylate shifts). AIMD dynamics of sufficient duration has allowed us to observe proton transfer from the bridging nucleophile to the catalytically essential Asp 128 residue and to map the underlying free energy surface in terms of simple reaction coordinates, such as the oxygen-oxygen distance Ro-o and the asymmetric stretch delta. This has provided valuable insight into the nature of the last step of the catalytic cycle. In addition, constrained molecular dynamics permitted us to compare the deprotonation free energy of the bridging nucleophile in the case of native versus metal-depleted arginase.

Arginase↗

PubMed2005

Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study.

The perturbations induced in a lipid bilayer by the presence of a transmembrane nanotube are investigated using coarse grained molecular dynamics. Meniscus formation by the lipids and tilting of the nanotube occur in response to hydrophobic mismatch, although these two effects do not compensate completely for the total mismatch. The lipid head-to-tail vector field is examined and shows strong ordering in the membrane plane regardless of the nanotube length. Molecular layering at the lipid-nanotube interface is reported. This study extends previous theoretical approaches to a more realistic setting.

Biophysical Phenomena↗

PubMed2005

Structure and dynamics of model pore insertion into a membrane.

A cylindrical transmembrane molecule is constructed by linking hydrophobic sites selected from a coarse grain model. The resulting hollow tube assembly serves as a representation of a transmembrane channel, pore, or a carbon nanotube. The interactions of a coarse grain di-myristoyl-phosphatidyl-choline hydrated bilayer with both a purely hydrophobic tube and a tube with hydrophilic caps are studied. The hydrophobic tube rotates in the membrane and becomes blocked by lipid tails after a few tens of nanoseconds. The hydrophilic sites of the capped tube stabilize it by anchoring the tube in the lipid headgroup/water interfacial region of each membrane leaflet. The capped tube remains free of lipid tails. The capped tube spontaneously conducts coarse grain water sites; the free-energy profile of this process is calculated using three different methods and is compared to the barrier for water permeation through the lipid bilayer. Spontaneous tube insertion into an undisturbed lipid bilayer is also studied, which we reported briefly in a previous publication. The hydrophobic tube submerges into the membrane core in a carpetlike manner. The capped tube laterally fuses with the closest leaflet, and then, after plunging into the membrane interior, rotates to assume a transbilayer orientation. Two lipids become trapped at the end of the tube as it penetrates the membrane. The hydrophilic headgroups of these lipids associate with the lower tube cap and assist the tube in crossing the interior of the membrane. When the rotation is complete these lipids detach from the tube caps and fuse with the lower leaflet lipids.

Binding Sites↗

PubMed2005

Simulating vapor-liquid nucleation of water: A combined histogram-reweighting and aggregation-volume-bias Monte Carlo investigation for fixed-charge and polarizable models.

The method of histogram-reweighting was integrated with a recently developed approach using aggregation-volume-bias Monte Carlo and self-adaptive umbrella sampling to develop the AVUS-HR algorithm that allows for exceedingly efficient calculations of nucleation properties over a wide range of thermodynamic conditions. Simulations were carried out for water using both fixed-charge and polarizable force fields belonging to the TIP4P family (namely, TIP4P, TIP4P-FQ, TIP4P-pol2, and TIP4P-pol3) to investigate the nucleation of water over a temperature range from 200 to 300 K and the concentration of water clusters in the atmosphere at elevations up to 15 km. It was found that the nucleation free energy barriers and atmospheric concentrations are extremely sensitive to the force field, albeit all of the models investigated in this study support the following general conclusions: (i) ice nucleation is not present under the thermodynamic conditions and cluster-size range investigated here, i.e., the critical nuclei possess liquidlike structures, and (ii) the atmospheric concentrations of water clusters under homogeneous conditions are very low with the mole fraction of hexamers being about 10(-10), a number probably too low to influence the solar radiation balance. Compared to the experimental data, the TIP4P-pol3 model yields the most accurate nucleation results, consistent with its excellent performance for the second virial coefficient and the minimum cluster energies.

Journal Article↗

PubMed2005

Protonated clathrate cages enclosing neutral water molecules: (H+)(H2O)21 and (H+)(H2O)28.

This paper describes a systematic study on the clathrate structure of (H+)(H2O)21 using tandem mass spectrometry, vibrational predissociation spectroscopy, Monte Carlo simulations, and density functional theory calculations. We produced (H+)(H2O)n from a continuous corona-discharged supersonic expansion and observed three anomalies simultaneously at the cluster temperature near 150 K, including (1) the peak at n=21 is more intense than its neighboring ions in the mass spectrum, (2) the size-dependent dissociation fractions show a distinct drop for the 21-mer, and (3) the infrared spectrum of (H+)(H2O)21 exhibits only a single feature at 3699 cm(-1), corresponding to the free-OH stretching of three-coordinated water molecules. Interestingly, the anomalies appear or disappear together with cluster temperature, indicating close correlation of these three observations. The observations, together with Monte Carlo simulations and density functional theory calculations, corroborate the notion for the formation of a distorted pentagonal dodecahedral (5(12)) cage with a H2O molecule in the cage and a H3O+ ion on the surface for this "magic number" water cluster ion. The dodecahedral cage melts at higher temperatures, as evidenced by the emergence of a free-OH stretching feature at 3717 cm(-1) for the two-coordinated water in (H+)(H2O)21 produced in a warmer molecular beam. Extension of this study to larger clusters strongly suggests that the experimentally observed isomer of (H+)(H2O)28 is most likely to consist of a distorted protonated pentakaidecahedral (5(12)6(3)) cage enclosing two neutral water molecules.

Journal Article↗

PubMed2005

Structure of protonated water clusters: low-energy structures and finite temperature behavior.

The structure of protonated water clusters H+(H2O)n (n=5-22) are examined by two Monte Carlo methods in conjunction with the OSS2 potential [L. Ojamae, I. Shavitt, and S. J. Singer J. Chem. Phys. 109, 5547 (1998)]. The basin-hopping method is employed to explore the OSS2 potential energy surface and to locate low-energy structures. The topology of the "global minimum," the most stable low-energy structure, changes from single ring to multiple ring to polyhedral cage as the cluster size grows. The temperature dependence of the cluster geometry is examined by carrying out parallel tempering Monte Carlo simulations. Over the temperature range we studied (25-330 K), all water clusters undergo significant structural changes. The trends are treelike structures dominating at high temperature and single-ring structures appearing in slightly lower temperatures. For n> or =7, an additional transition from single ring to multiple rings appears as the temperature decreases. Only for n> or =16 do polyhedral structures dominate the lowest temperature range. Our results indicate very dynamic structural changes at temperature range relevant to atmospheric chemistry and current experiments. The structures and properties of medium-sized protonated clusters in this temperature range are far from their global minimum cousins. The relevance of these findings to recent experiments and theoretical simulations is also discussed.

Journal Article↗

PubMed2005

Ab initio molecular dynamics simulation of a water-hydrogen fluoride equimolar mixture.

Hydrogen fluoride and water can be mixed in any proportion. The resulting solutions have unique acidic properties. In particular, hydrogen fluoride undergoes a weak-to-strong acidity transition with increasing concentration of HF To supplement the knowledge already obtained on dilute or moderately concentrated solutions and gas-phase aggregates, an equimolar mixture is studied here by Car-Parrinello molecular dynamics. The natures of the ions and of the complexes formed in the equimolar liquid were determined. Specifically, H3O+, H5O2+, FH-OH2, and HF2- were spontaneously obtained while only hydronium and fluoride ions pre-exist in the equimolar crystal. The behaviour of the proton in the equimolar liquid was compared with mixtures of other proportions simulated previously in an attempt to relate proton dynamics to acidity. In the same way, the behaviour of HF2- was also examined. In this case, proton localization and transfer appeared to be driven by the fluctuating environment of the solvated ion.

Journal Article↗

PubMed2005

Key roles for chain flexibility in block copolymer membranes that contain pores or make tubes.

Block copolymer amphiphiles that self-assemble into membranes present robust and functionalizable alternatives to biological assemblies. Coarse-grained molecular dynamics shows that thick bilayers of A-B copolymers accommodate protein-like channels and also tend to regulate transport. This occurs as flexible, hydrophilic A chains insert into the pore and obstruct water entry. A-B-A triblocks that exploit "hairpin" and "straight" conformations also show assembly into novel nanotubules and further highlight the key roles for chain flexibility in biomimetic block copolymer assemblies.

Computer Simulation↗

PubMed2005

HEMICENTIN-1 (FIBULIN-6) and the 1q31 AMD locus in the context of complex disease: review and perspective.

Age-related macular degeneration (AMD) is the most common blinding disorder in the Western world. Similar to other common diseases in which age is a risk factor (e.g., type II diabetes or Alzheimer's disease), AMD is thought to have a complex etiology. Previously, a Gln5345Arg mutation in HEMICENTIN-1 was found to segregate with AMD in a large family. However, the population frequency of this allele is inconsistent with the large proportion of families shown by linkage studies to map near this gene at 1q31. This review summarizes current knowledge regarding the role of HEMICENTIN-1 in AMD, the results of association studies for the Gln5345Arg mutation, and the linkage evidence for an AMD locus on 1q31. The data can be reconciled through proposing both additional variants in HEMICENTIN-1 and a second genetic risk factor for AMD in the region.

Aging↗

PubMed2005

Long-term juxtafoveal retinal telangiectasia.

PURPOSE: To determine the long-term natural history of idiopathic juxtafoveal telangiectasia (IJRT). METHODS: Record review in 2 university-based and 2 private vitreoretinal practices sought patients with IJRT documented by color photographs and fluorescein angiograms (FAs) during the period January 1, 1980, to December 31, 1993. Patients then had repeated examinations and FAs. RESULTS: Twenty patients with IJRT in 32 eyes had follow-up examinations. Fifteen patients had color photographs and FAs, and one had color photographs alone. Follow-up varied from 10 years to 21 years (average, 15 years). Six eyes were treated by laser photocoagulation at onset. Twenty-four of the 26 untreated eyes lost vision as measured by Snellen testing. Visual loss and morphologic progression depended on IJRT type. Six of 8 untreated eyes with type IA IJRT lost vision by >/ or = 3 lines (Snellen), 4 to 20/70 or worse. Vision loss was caused by progressive telangiectatic changes and intraretinal edema. Fifteen of 20 initially untreated eyes with type IIA IJRT developed either central retinal pigment epithelium membranes or subretinal neovascularization with loss of vision to 20/80 or less. CONCLUSION: IJRT prognosis depends on type and clinical features. Long-term prognosis for central vision is poor.

Adult↗

PubMed2004

Concentration effects of volatile anesthetics on the properties of model membranes: a coarse-grain approach.

To gain insights into the molecular level mechanism of drug action at the membrane site, we have carried out extensive molecular dynamics simulations of a model membrane in the presence of a volatile anesthetic using a coarse-grain model. Six different anesthetic (halothane)/lipid (dimyristoylphosphatidylcholine) ratios have been investigated, going beyond the low doses typical of medical applications. The volatile anesthetics were introduced into a preassembled fully hydrated 512-molecule lipid bilayer and each of the molecular dynamics simulations were carried out at ambient conditions, using the NPT ensemble. The area per lipid increases monotonically with the halothane concentration and the lamellar spacing decreases, whereas the lipid bilayer thickness shows no appreciable differences and only a slight increase upon addition of halothane. The density profiles of the anesthetic molecules display a bimodal distribution along the membrane normal with maxima located close to the lipid-water interface region. We have studied how halothane molecules fluctuate between the two maxima of the bimodal distribution and we observed a different mechanism at low and high anesthetic concentrations. Through the investigation of the reorientational motions of the lipid tails, we found that the anesthetic molecules increase the segmental order of the lipids close to the membrane surface.

Anesthetics, Inhalation↗

PubMed2004

The transmembrane domain of the acetylcholine receptor: insights from simulations on synthetic peptide models.

We have studied the structure and properties of a bundle of alpha-helical peptides embedded in a 1,2-dimyristoyl-3-phosphatidylcholine phospholipid bilayer by molecular dynamics simulations. The bundle of five transmembrane deltaM2 segments constitutes the model for the pore region of the nicotinic acetylcholine receptor, which is the neurotransmitter-gated ion-channel responsible for the fast propagation of electrical signals between cells at the nerve-muscle synapse. The deltaM2 segments were shown to oligomerize in biomembranes resulting in ion-channel activity with characteristics similar to the native protein, and the structure of the isolated peptides was studied in 1,2-dimyristoyl-3-phosphatidylcholine bilayers and micelles by NMR experiments (Opella, S. J., et al. 1999. Nat. Struct. Biol. 6:374-379). Our analyses indicate that the structure, helix tilt, and the overall shape of the channel are in good agreement with the NMR experiments and the proposed model for the channel, which we show is formed by rings of functional residues. The studied geometry resulted in a closed pore state, where the channel is partially dehydrated at the hydrophobic extracellular half and the extracellular mouth of the channel blocked by the hydrocarbon chains of Arg+ residues. The arginine amino acids form intermolecular salt-bridges with the C-terminus, which contribute as well to the bundle stabilization.

Binding Sites↗

PubMed2004

On the quantum nature of an excess proton in liquid hydrogen fluoride.

Liquid hydrogen fluoride consists of chains of hydrogen-bonded molecules. The nature of an excess proton in liquid HF, which is of interest not only for its own sake, but also in relation to super-acid chemistry and to its behavior in water, has been studied using computer simulations. The methodology employed is the density-functional-theory-based path-integral Car-Parrinello ab initio molecular dynamics. The excess proton, which formally exists as a H2F+ or a H2F2+ defect in an HF chain, is found to strongly perturb the chain to which it is attached. Moreover, due to large zero-point energy, the charge defect is largely delocalized over several HF molecules.

Journal Article↗

PubMed2004

Controlling the conformation of arylamides: computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers.

The role of an ortho-alkylthioether group in controlling the conformation around the ring-N bonds of meta-connected arylamide oligomers is studied. Density functional theory (DFT) geometries of model compounds, including acetanilide, an ether acetanilide, and a thioether acetanilide, and their corresponding diamides, show that for either monoamide or diamide the alkyl side chain of the thioether should be perpendicular to the aryl plane, whereas for the ether monoamide, the alkyl side chain is in the aryl plane. DFT ring-N torsional potentials and constrained geometries of the model compounds demonstrate that carbonyl-S repulsion leads to a high torsional barrier and that intramolecular N-H...S and C-H...O hydrogen bonds and ring-amide conjugation lead to N-H having a preferred orientation in the benzene plane pointing towards S. The N-H bond lengthens and the ortho-ring C-H bond shortens in a regular pattern in the approach to the preferred orientation. Calculated IR frequencies for the N-H stretch show a clear red shift between model compounds without and with the thioether side chain.

Amides↗

PubMed2004

A novel diagnostic test detects a low frequency of the hemicentin Gln5345Arg variant among Northern Irish age related macular degeneration patients.

PURPOSE: Age related macular degeneration (AMD) is a common cause of severe vision loss. Identification of genes involved in AMD will facilitate early detection and ultimately help to identify pathways for treatment for this disorder. The A16,263G mutation in the HEMICENTIN-1 gene produces a non-conservative substitution of arginine for glutamine at codon 5345 which has been implicated in familial AMD. The aim of this study is to develop a rapid diagnostic assay for the detection of this mutation and to evaluate its frequency in a sample of AMD patients. METHODS: A primer probe set was designed from exon 104 of the HEMICENTIN-1 gene to differentiate between mutant and wild type alleles. A region spanning the mutation was amplified by PCR using a LightCycler (Roche Diagnostic). The mutation was then detected by melt curve analysis of the hybrid formed between the PCR product and a specific fluorescent probe. The frequency of the mutation within the Northern Ireland population was evaluated by assaying 508 affected AMD patients, 25 possibly affected and 163 controls. RESULTS: This assay clearly discriminates between the A16,263G mutant and wild type HEMICENTIN-1 alleles. The wild type sequence has a single base mismatch with the probe which decreases the stability of the hybrid, resulting in a lower TM (TM=51.27 degrees C) than that observed for the perfectly matched mutant allele (TM=59.9 degrees C). The mutant allele was detected in only one of the 696 subjects, an affected AMD patient. CONCLUSIONS: We describe a rapid assay for the genotyping of the Gln5345Arg mutation using real-time fluorescence PCR to facilitate rapid processing of samples through combined amplification and detection steps. These characteristics are suitable for a clinical setting where high throughput diagnostic procedures are required. The frequency of this mutation within the Northern Ireland population has been estimated at 0.2%, concurring with previous findings that this mutation is a rare variant associated with AMD. A rapid diagnostic assay will facilitate a reliable and convenient evaluation of the frequency of the Gln5345Arg mutation and its association with AMD within other populations.

Aged↗