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M L Klein

Publications and source records attributed to M L Klein.

At least 19 recordsLinked to original sources
PubMed2002

Molecular dynamics simulations of a hydrated protein vectorially oriented on polar and nonpolar soft surfaces.

We present a collection of molecular dynamics computer simulation studies on a model protein-membrane system, namely a cytochrome c monolayer attached to an organic self-assembled monolayer (SAM). Modifications of the system are explored, including the polarity of the SAM endgroups, the amount of water present for hydration, and the coordination number of the heme iron atom. Various structural parameters are measured, e.g., the protein radius of gyration and eccentricity, the deviation of the protein backbone from the x-ray crystal structure, the orientation of the protein relative to the SAM surface, and the profile structures of the SAM, protein, and water. The polar SAM appears to interact more strongly with the protein than does the nonpolar SAM. Increased hydration of the system tends to reduce the effects of other parameters. The choice of iron coordination model has a significant effect on the protein structure and the heme orientation. The overall protein structure is largely conserved, except at each end of the sequence and in one loop region. The SAM structure is only perturbed in the region of its direct contact with the protein. Our calculations are in reasonably good agreement with experimental measurements (polarized optical absorption/emission spectroscopy, x-ray interferometry, and neutron interferometry).

Binding Sites↗
PubMed2001

Short wavelength collective dynamics in phospholipid bilayers: a molecular dynamics study.

Short wavelength density fluctuations of hydrated multilamellar phospholipid bilayers have been studied by molecular dynamics simulations in both the gel and liquid crystalline phases, and the results compared to recent inelastic x-ray scattering data [Phys. Rev. Lett. 86, 740 (2001)]. We confirm the existence of a highly dispersive sound mode, whose frequency and damping depend on the lipid phase, that the scattering arises mainly from in-plane motion of hydrocarbon chains, and we also identify a nondispersive mode attributed to motions of the chain terminal carbons.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2001

Influence of highly polyunsaturated lipid acyl chains of biomembranes on the NMR order parameters.

We investigate the effect of specific conformations of double-bond segments in highly polyunsaturated acyl chains on the deuterium (2)H NMR order parameters of a fully hydrated 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer. The system is analyzed by performing a molecular dynamics simulation study at ambient conditions in the fluid lamellar phase. By separately calculating the different partial contributions to the total order parameter profiles measurable experimentally, we are able to get insights into the molecular origin of earlier experimental and theoretical observations. The effect of the position of the different conformations of double-bond segments along the polyunsaturated acyl chain is also examined. As in experiments performed in a series of lipid bilayers with an increasing number of cis double bonds per lipid molecule [Holte, L. L., et al. Biophys. J. 1995, 68, 2396], we find that unsaturations influence mainly the order of the bottom half of the saturated chain. Specific conformations of the polyunsaturated chain close to the lipid headgroups have a distinct effect on the order of the bottom half of the saturated chain and on the top half of the polyunsaturated chain. Our results indicate that for SDPC the conformation of the region of the polyunsaturated chain located between the first three cis double bonds is responsible for the major effects on the orientational order of both the saturated and the polyunsaturated chains.

Fatty Acids, Unsaturated↗
PubMed2001

Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations.

The structure of a fully hydrated mixed (saturated/polyunsaturated) chain lipid bilayer in the biologically relevant liquid crystalline phase has been examined by performing a molecular dynamics study. The model membrane, a 1-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine (SDPC, 18:0/22:6 PC) lipid bilayer, was investigated at constant (room) temperature and (ambient) pressure, and the results obtained in the nanosecond time scale reproduced quite well the available experimental data. Polyunsaturated fatty acids are found in high concentrations in neuronal and retinal tissues and are essential for the development of human brain function. The docosahexaenoic fatty acid, in particular, is fundamental for the proper function of the visual receptor rhodopsin. The lipid bilayer order has been investigated through the orientational order parameters. The water-lipid interface has been explored thoroughly in terms of its dimensions and the organization of the different components. Several types of interactions occurring in the system have been analyzed, specifically, the water-hydrocarbon chain, lipid-lipid and lipid-water interactions. The distribution of dihedral angles along the chains and the molecular conformations of the polyunsaturated chain of the lipids have also been studied. Special attention has been focused on the microscopic (molecular) origin of the effects of polyunsaturations on the different physical properties of membranes.

Computer Simulation↗
PubMed2001

Dynamical properties of a hydrated lipid bilayer from a multinanosecond molecular dynamics simulation.

A fully hydrated dimiristoylphosphatidylcholine (DMPC) bilayer has been studied by a molecular dynamics simulation. The system, which consisted of 64 DMPC molecules and 1792 water molecules, was run in the NVE ensemble at a temperature of 333 K for a total of 10 ns. The resulting trajectory was used to analyze structural and dynamical quantities. The electron density, bilayer spacing, and order parameters (S(CD)), based on the AMBER forcefield and SPCE water model are in good agreement with previous calculations and experimental data. The simulation reveals evidence for two types of lateral diffusive behavior: cage hopping and that of a two-dimensional liquid. The lateral diffusion coefficient is 8 x 10(-8) cm(2)/s. We characterize the rotational motion, and find that the lipid tail rotation (D(rot_tail) = -0.04 rad(2)/ns) is slower then the head group rotation (D(rot_hg) = 2.2 rad(2)/ns), which is slower than the overall in plane (D(rot) = 3.2 rad(2)/ns) for the lipid molecule.

Computer Simulation↗
PubMed2001

Membrane structural perturbations caused by anesthetics and nonimmobilizers: a molecular dynamics investigation.

The structural perturbations of the fully hydrated dimyristoyl-phosphatidylcholine bilayer induced by the presence of hexafluoroethane C(2F6), a "nonimmobilizer," have been examined by molecular dynamics simulations and compared with the effects produced by halothane CF3CHBrCl, an "anesthetic," on a similar bilayer (DPPC) (Koubi et al., Biophys. J. 2000. 78:800). We find that the overall structure of the lipid bilayer and the zwitterionic head-group dipole orientation undergo only a slight modification compared with the pure lipid bilayer, with virtually no change in the potential across the interface. This is in contrast to the anesthetic case in which the presence of the molecule led to a large perturbation of the electrostatic potential across to the membrane interface. Similarly, the analysis of the structural and dynamical properties of the lipid core are unchanged in the presence of the nonimmobilizer although there is a substantial increase in the microscopic viscosity for the system containing the anesthetic. These contrasting perturbations of the lipid membrane caused by those quite similarly sized molecules may explain the difference in their physiological effects as anesthetics and nonimmobilizers, respectively.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2001

Molecular genetic heterogeneity in autosomal dominant drusen.

OBJECTIVE: Autosomal dominant drusen is of particular interest because of its phenotypic similarity to age related macular degeneration. Currently, mutation R345W of EFEMP1 and, in a single pedigree, linkage to chromosome 6q14 have been causally related to the disease. We proposed to investigate and quantify the roles of EFEMP1 and the 6q14 locus in dominant drusen patients from the UK and USA. DESIGN: Molecular genetic analysis. PARTICIPANTS: Ten unrelated families and 17 young drusen patients. MAIN OUTCOME MEASURES: Exons 1 and 2 of EFEMP1 were characterised by 5' rapid amplification of cDNA ends and direct sequencing. Exons 1-12 of EFEMP1 were then investigated for mutation by direct sequencing. A HpaII restriction digest test was constructed to detect the EFEMP1 R345W mutation. Marker loci spanning the two dominant drusen linked loci were used to generate haplotype data. RESULTS: Only seven of the 10 families (70%) and one of the 17 sporadic patients (6%) had the R345W mutation. The HpaII restriction digest test was found to be a reliable and quick method for detecting this. No other exonic or splice site mutation was identified. Of the three families without EFEMP1 mutation, two were linked to the 2p16 region. CONCLUSIONS: EFEMP1 R345W accounts for only a proportion of the dominant drusen phenotype. Importantly, other families linked to chromosome 2p16 raise the possibility of EFEMP1 promoter sequence mutation or a second dominant drusen gene at this locus. Preliminary haplotype data suggest that the disease gene at the 6q14 locus is responsible for only a minority of dominant drusen cases.

Adult↗
PubMed2000

Molecular dynamics simulation of four-alpha-helix bundles that bind the anesthetic halothane.

The mutation of a single leucine residue (L38) to methionine (M) is known experimentally to significantly increase the affinity of the synthetic four-alpha-helix bundle (Aalpha(2))(2) for the anesthetic halothane. We present a molecular dynamics study of the mutant (Aalpha(2)-L38M)(2) peptide, which consists of a dimer of 62-residue U-shaped di-alpha-helical monomers assembled in an anti topology. A comparison between the simulation results and those obtained for the native (Aalpha(2))(2) peptide indicates that the overall secondary structure of the bundle is not affected by the mutation, but that the side chains within the monomers are better packed in the mutant structure. Unlike the native peptide, binding of a single halothane molecule to the hydrophobic core of (Aalpha(2)-L38M)(2) deforms the helical nature of one monomer in a region close to the mutation site. Increased exposure of the cysteine side chain to the hydrophobic core in the mutant structure leads to the enhancement of the attractive interaction between halothane and this specific residue. Since the mutated residues are located outside the hydrophobic core the observed increased affinity for halothane appears to be an indirect effect of the mutation.

Amino Acid Sequence↗
PubMed2000

Two possible conducting states of the influenza A virus M2 ion channel.

Molecular dynamics simulations have been performed on protonated four-helix bundles based on the 25-residue Duff-Ashley transmembrane sequence of the M2 channel of the influenza A virus. Well-equilibrated tetrameric channels, with one, two and four of the H37 residues protonated, were investigated. The protonated peptide bundles were immersed in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. The simulations suggest that there could be two conducting states of the M2 channel corresponding to tetramers containing one or two protonated histidines. The more open structure of the doubly protonated state suggests it would have the higher conductance.

Amino Acid Sequence↗
PubMed2000

Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations.

We report a 2-ns constant pressure molecular dynamics simulation of halothane, at a mol fraction of 50%, in the hydrated liquid crystal bilayer phase of dipalmitoylphosphatidylcholine. Halothane molecules are found to preferentially segregate to the upper part of the lipid acyl chains, with a maximum probability near the C(5) methylene groups. However, a finite probability is also observed along the tail region and across the methyl trough. Over 95% of the halothane molecules are located below the lipid carbonyl carbons, in agreement with photolabeling experiments. Halothane induces lateral expansion and a concomitant contraction in the bilayer thickness. A decrease in the acyl chain segment order parameters, S(CD), for the tail portion, and a slight increase for the upper portion compared to neat bilayers, are in agreement with several NMR studies on related systems. The decrease in S(CD) is attributed to a larger accessible volume per lipid in the tail region. Significant changes in the electric properties of the lipid bilayer result from the structural changes, which include a shift and broadening of the choline headgroup dipole (P-N) orientation distribution. Our findings reconcile apparent controversial conclusions from experiments on diverse lipid systems.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed2000

A comparison of stereoscopic fluorescein angiography with indocyanine green videoangiography in age-related macular degeneration.

PURPOSE: To correlate features of indocyanine green (ICG) videoangiography with stereo film fluorescein angiography (FA) in the analysis of age-related macular degeneration (AMD). DESIGN: A retrospective study with concurrent comparison of two methods of assessment on one set of patients with AMD undergoing sequential FA-ICG videoangiography. METHODS: One hundred four patients with AMD who had undergone immediately sequential FA-ICG videoangiography were selected in a consecutive fashion from the photographic files of the Casey Eye Institute. Three interpreters independently graded in an unbiased fashion the FA features of AMD. These were compared with ICG videoangiography features of hypocyanescence (ICG videoangiography hypofluorescence), moderate or intense hypercyanescence (ICG videoangiography hyperfluorescence), or absence of fluorescence over background (ICG videoangiography isocyanescence). We also assessed ICG videoangiography features in the opposite eye of those with choroidal neovascularization (CNV) by FA in one eye by examining an additional 96 FA-ICG videoangiography scans. MAIN OUTCOME MEASURES: Outcomes were the ICG videoangiography characteristics of classic and occult CNV, serous pigment epithelial detachments (SPEDs) both with and without CNV, macular hemorrhage, and the comparative size of these features. RESULTS: There were 25 eyes that had significant macular hemorrhage by FA. Of these, the FA revealed CNV in its entirety under or near the hemorrhage in 11. The ICG examination revealed all 11 plus an additional 12 hypercyanescent features that were not visible by FA. Although 26 of 32 SPEDs had CNV by FA analysis, 31 of 32 had well-defined hypercyanescence under or at the SPED edge by ICG videoangiography. Eighty-seven percent of eyes with classic choroidal neovascular membranes (CCNV; 20 of 23) and 93% of eyes with fibrovascular pigment epithelial detachments (FVPED; 66 of 71) were hypercyanescent with distinct edges. Fifty percent of eyes with only late leakage of undetermined source (LLUS) were hypercyanescent, whereas 50% were isocyanescent on ICG videoangiography. There were four of 104 eyes in which ICG videoangiography revealed poorly defined hypercyanescent areas when, by FA, there were only drusen or elevated blocked fluorescence. Indocyanine green videoangiography revealed only three eyes with poorly defined hypercyanescence of 200 fellow eyes in patients with unilateral AMD. CONCLUSIONS: Indocyanine green videoangiography correlated fairly well with stereoscopic FA for the presence of CCNV or FVPED, but correlated poorly when LLUS was present. In certain cases where CNV was associated with SPED or macular hemorrhage, ICG videoangiography demonstrated features not apparent on FA.

Aged↗
PubMed2000

Clinicopathologic correlation of fluorescein and indocyanine green angiography in exudative age-related macular degeneration.

PURPOSE: To correlate the clinical and histopathologic features of an eye with age-related macular degeneration studied with fluorescein (FA) and indocyanine green (ICG) angiography 4.5 months before the patient's death. METHODS: Histopathologic features from serial sections through the macula of a 76-year-old man with occult choroidal neovascularization (CNV) were reconstructed in a scaled two-dimensional map and compared with FA and ICG angiogram images obtained 4.5 months before his death. RESULTS: The region of prior laser photocoagulation was identified as a well-demarcated hypofluorescent region in the early frames of the FA and the early and late phases of the ICG angiogram. This corresponded histopathologically to a well-circumscribed area of absence of the choriocapillaris, loss of the outer retina and retinal pigment epithelium, and scarring of the choroid. Occult CNV characterized by elevated late hyperfluorescence on the FA and intense well-defined hyperfluorescence on the ICG angiogram corresponded to a thick fibrovascular membrane in the subretinal space and within Bruch's membrane. Thin extensions of both the subretinal and intra-Bruch's membrane fibrovascular membrane components corresponded to nonelevated stippled late hyperfluorescence on the FA and mild late hyperfluorescence on the ICG angiogram. CONCLUSION: Histopathologic mapping revealed a large fibrovascular complex located subretinally and within Bruch's membrane with thin and thick components that correlate well with findings of occult CNV on FA and ICG angiography.

Aged↗
PubMed1999

Molecular dynamics simulation of a synthetic four-alpha-helix bundle that binds the anesthetic halothane.

The structural features of binding sites for volatile anesthetics are examined by performing a molecular dynamics simulation study of the synthetic four-alpha-helix bundles (Aalpha2)2, which are formed by association of two 62-residue di-alpha-helical peptides. The peptide bundle (Aalpha2)2 was designed by Johansson et al. [Biochemistry 37 (1998) 1421-1429] and was shown experimentally to have a high affinity for the binding of the anesthetic halothane (CF3CBrCIH) in a hydrophobic cavity. Since (Aalpha2)2 can exhibit either the anti or syn topologies, the two distinct bundles are simulated both in the presence and in the absence of halothane. Nanosecond length molecular dynamics trajectories were generated for each system at room temperature (T = 298 K). The structural and dynamic effects of the inclusion of halothane are compared, illustrating that the structures are stable over the course of the simulation; that the (Aalpha2)2 bundles have suitable pockets that can accommodate halothane; that the halothane remains in the designed hydrophobic cavity in close proximity to the Trp residues with a preferred orientation; and that the dimensions of the peptide are perturbed by the inclusion of an anesthetic molecule.

Amino Acid Sequence↗
PubMed1999

Influence of a knot on the strength of a polymer strand.

Many experiments have been done to determine the relative strengths of different knots, and these show that the break in a knotted rope almost invariably occurs at the point just outside the 'entrance' to the knot. The influence of knots on the properties of polymers has become of great interest, in part because of their effect on mechanical properties. Knot theory applied to the topology of macromolecules indicates that the simple trefoil or 'overhand' knot is likely to be present in any long polymer strand. Fragments of DNA have been observed to contain such knots in experiments and computer simulations. Here we use ab initio computational methods to investigate the effect of a trefoil knot on the breaking strength of a polymer strand. We find that the knot weakens the strand significantly, and that, like a knotted rope, it breaks under tension at the entrance to the knot.

Alkanes↗
PubMed1999

Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface.

Molecular dynamics simulations have been used to investigate the structure of hybrid bilayers (HB) formed by dipalmitoylphosphatidylcholine (DPPC) lipid monolayers adsorbed on a hydrophobic alkanethiol self-assembled monolayer (SAM). The HB system was studied at 20 degrees C and 60 degrees C, and the results were compared with recent neutron reflectivity measurements (Meuse, C. W., S. Krueger, C. F. Majkrzak, J. A. Dura, J. Fu, J. T. Connor, and A. L. Plant. 1998. Biophys. J. 74:1388) and previous simulations of hydrated multilamellar bilayers (MLB) of DPPC (Tu, K., D. J. Tobias, and M. L. Klein. 1995. Biophys. J. 69:2558; and 1996. 70:595). The overall structures of the HBs are in very good agreement with experiment. The structure of the SAM monolayer is hardly perturbed by the presence of the DPPC overlayer. The DPPC layer presents characteristics very similar to the MLB gel phase at low temperature and to the liquid crystal phase at high temperature. Subtle changes have been found for the lipid/water interface of the HBs compared to the MLBs. The average phosphatidylcholine headgroup orientation is less disordered, and this produces changes in the electric properties of the HB lipid/water interface. These changes are attributed to the fact that the aqueous environment of the lipids in these unilamellar films is different from that of MLB stacks. Finally, examination of the intramolecular and whole-molecule dynamics of the DPPC molecules in the fluid phase HB and MLB membranes revealed that the reorientations of the upper part of the acyl chains (near the acyl ester linkage) are slower, the single molecule protrusions are slightly damped, and the lateral rattling motions are significantly reduced in the HB compared with the MLB.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1999

Exploration of the structural features defining the conduction properties of a synthetic ion channel.

The finite-difference Poisson-Boltzmann methodology was applied to a series of parallel, alpha-helical bundle models of the designed ion channel peptide Ac-(LSSLLSL)3-CONH2. This method is able to fully describe the current-voltage curves for this channel and quantitatively explains their cation selectivity and rectification. We examined a series of energy-minimized models representing different aggregation states, side-chain rotamers, and helical rotations, as well as an ensemble of structures from a molecular dynamics trajectory. Potential energies were computed for single, permeating K+ and Cl- ions at a series of positions along a central pathway through the models. A variable-electric-field Nernst-Planck electrodiffusion model was used, with two adjustable parameters representing the diffusion coefficients of K+ and Cl- to scale the individual ion current magnitudes. The ability of a given DelPhi potential profile to fit the experimental data depended strongly on the magnitude of the desolvation of the permeating ion. Below a pore radius of 3.8 A, the predicted profiles showed large energy barriers, and the experimental data could be fit only with unrealistically high values for the K+ and Cl- diffusion coefficients. For pore radii above 3.8 A, the desolvation energies were 2kT or less. The electrostatic calculations were sensitive to positioning of the Ser side chains, with the best fits associated with maximum exposure of the Ser side-chain hydroxyls to the pore. The backbone component was shown to be the major source of asymmetry in the DelPhi potential profiles. Only two of the energy-minimized structures were able to explain the experimental data, whereas an average of the dynamics structures gave excellent agreement with experimental results. Thus this method provides a promising approach to prediction of current-voltage curves from three-dimensional structures of ion channel proteins.

Cations↗