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Biomedical subjects

M L Klein

Publications and source records attributed to M L Klein.

At least 37 records · Page 2Linked to original sources
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↗
PubMed1998

Computer simulation study of synthetic 4-helix bundle that binds halothane.

1. The synthetic peptide H10A24 self-assembles in aqueous solution into a 4-helix bundle, which exhibits saturable binding of halothane. 2. Molecular dynamics simulation techniques have been used to study the vacuum structure of this bundle. 3. The simulation, initiated as four ideal parallel alpha-helices, resulted in a compact bundle, whose secondary structure remains predominantly alpha-helical. 4. The hydrophobic core has no apparent pocket large enough to accomodate halothane.

Algorithms↗
PubMed1998

The M2 channel of influenza A virus: a molecular dynamics study.

Molecular dynamics simulations have been performed on a tetramer of the 25-residue (SSDPLVVAASIIGILHLILWILDRL) synthetic peptide [1] which contains the transmembrane domain of the influenza A virus M2 coat protein. The peptide bundle was initially assembled as a parallel alpha-helix bundle in the octane portion of a phase separated water/octane system, which provided a membrane-mimetic environment. A 4-ns dynamics trajectory identified a left-handed coiled coil state of the neutral bundle, with a water filled funnel-like structural motif at the N-terminus involving the long hydrophobic sequence. The neck of the funnel begins at V27 and terminates at H37, which blocks the channel. The C-terminus is held together by inter-helix hydrogen bonds and contains water below H37. Solvation of the S23 and D24 residues, located at the rim of the funnel, appears to be important for stability of the structure. The calculated average tilt of the helices in the neutral bundle is 27 +/- 5 degrees, which agrees well with recent NMR data.

Amino Acid Sequence↗
PubMed1998

Simulation of the HIV-1 Vpu transmembrane domain as a pentameric bundle.

The transmembrane domain of oligomeric protein Vpu encoded by HIV-1 has been studied by means of a molecular dynamics simulation. A pentameric bundle of unconstrained helices (residues 6-28 of Vpu) with a water filled pore was initially assembled in a membrane mimetic octane/water system. This system was simulated, using the CHARMm19 and OPLS united atom force fields with no constraints at a temperature of 300 K and a pressure of 1 atm. For these forcefields and the initial conditions tested, the oligomeric bundle expelled most of the pore water molecules. The resulting bundle and residual waters adopt a conical structural motif with some resemblance to a potassium channel.

Amino Acid Sequence↗
PubMed1998

Molecular dynamics study of the LS3 voltage-gated ion channel.

Molecular dynamics calculations have been carried out on a model of the LS3 synthetic ion channel in a membrane mimetic environment. In the absence of an external electrostatic field, the LS3 channel, which consists of a bundle of six alpha-helices with sequence Ac-(LSSLLSL)3-CONH2, exhibits large structural fluctuations. However, in the presence of the field, the bundle adopts a well defined coiled-coil structure with an inner pore of water. The observed structural changes induced by the applied field are consistent with the proposed gating mechanism of the ion channel.

Computer Simulation↗
PubMed1998

Age-related macular degeneration. Clinical features in a large family and linkage to chromosome 1q.

OBJECTIVES: To identify the chromosomal location of a disease-causing gene and to describe the clinical characteristics of a large family with age-related macular degeneration (ARMD). METHODS: An ARMD pedigree was identified, and the disease state of family members was documented by stereoscopic fundus photography and was classified using a modified version of the Wisconsin Age-Related Maculopathy Grading System. A genome-wide screen at approximately 6-centimorgan spacing using a DNA-pooling strategy combined with shared-segment analysis was used to identify likely chromosomal regions. The entire family was then screened at each likely locus, and 1 positive locus was refined by screening with markers at an average density of 0.5 centimorgan and subjected to parametric linkage analysis. RESULTS: In the 10 affected family members, ARMD was manifest by the presence of large, soft, confluent drusen accompanied by varying degrees of retinal pigment epithelial degeneration and/or geographic atrophy. Age-related macular degeneration segregated as an autosomal-dominant trait, with the disease locus mapping to chromosome 1q25-q31 between markers D1S466 and D1S413, with a multipoint lod score of 3.00. CONCLUSION: Age-related macular degeneration localized to chromosome 1q25-q31 (gene symbol, ARMD1) as a dominant trait in a large family with a predominantly dry phenotype. CLINICAL RELEVANCE: Identification of ARMD genes will facilitate early diagnosis and aid in understanding the molecular pathophysiological mechanisms of ARMD. This knowledge will contribute to the development of preventive and improved treatment strategies.

Aged↗
PubMed1998

Malattia leventinese: refinement of the genetic locus and phenotypic variability in autosomal dominant macular drusen.

PURPOSE: To study the phenotypic variability in patients inheriting the disease gene for malattia leventinese (dominant macular drusen) and refine the localization of the gene. METHODS: A family with dominant radial drusen was ascertained and studied with clinical examination and DNA linkage analysis. Inheritance of the disease gene was determined by DNA analysis and used to document the variability in phenotypic expression. RESULTS: Fifty family members were studied with fundus photography and genotyping. Linkage analysis showed that the disease in this family was linked to chromosome 2p16-21 with a maximum lod score of 3.72 at D2S2153. An affected patient with obligate recombinations allowed refinement of the disease interval to a 6.2-cM region between D2S2227 and D2S378. The phenotype of older affected patients varied from severe geographic atrophy or subretinal fibrosis to a single druse adjacent to the optic disk. Small and medium-sized, nonradial, and soft macular drusen seen in four older individuals in the family were not specifically associated with the disease haplotype. CONCLUSIONS: Refinement of the localization of the gene for malattia leventinese will facilitate its positional cloning. Genotypic documentation of the variable expression of the disease shows that a single, large, subretinal druse adjacent to the optic disk is consistent with inheritance of the disease gene. Soft macular drusen in low abundance were not specifically associated with inheritance of the disease gene. These results will facilitate the genetic counseling of patients with malattia leventinese. It is unknown what proportion of age-related macular degeneration arises from mutations in disease genes for dominant drusen.

Adolescent↗
PubMed1998

Effects of anesthetics on the structure of a phospholipid bilayer: molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine.

We report the results of constant temperature and pressure molecular dynamics calculations carried out on the liquid crystal (Lalpha) phase of dipalmitoylphosphatidylcholine with a mole fraction of 6.5% halothane (2-3 MAC). The present results are compared with previous simulations for pure dipalmitoylphosphatidylcholine under the same conditions (Tu et al., 1995. Biophys. J. 69:2558-2562) and with various experimental data. We have found subtle structural changes in the lipid bilayer in the presence of the anesthetic compared with the pure lipid bilayer: a small lateral expansion is accompanied by a modest contraction in the bilayer thickness. However, the overall increase in the system volume is found to be comparable to the molecular volume of the added anesthetic molecules. No significant change in the hydrocarbon chain conformations is apparent. The observed structural changes are in fair agreement with NMR data corresponding to low anesthetic concentrations. We have found that halothane exhibits no specific binding to the lipid headgroup or to the acyl chains. No evidence is obtained for preferential orientation of halothane molecules with respect to the lipid/water interface. The overall dynamics of the lipid-bound halothane molecules appears to be reminiscent of that of other small solutes (Bassolino-Klimas et al., 1995. J. Am. Chem. Soc. 117:4118-4129).

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1998

Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer.

We report a 1.4-ns constant-pressure molecular dynamics simulation of cholesterol at 12.5 mol% in a dipalmitoylphosphatidylcholine (DPPC) bilayer at 50 degrees C and compare the results to our previous simulation of a pure DPPC bilayer. The interlamellar spacing was increased by 2.5 A in the cholesterol-containing bilayer, consistent with x-ray diffraction results, whereas the bilayer thickness was increased by only 1 A. The bilayer/water interface was more abrupt because the lipid headgroups lie flatter to fill spaces left by the cholesterol molecules. This leads to less compensation by the lipid headgroups of the oriented water contribution to the membrane dipole potential and could explain the experimentally observed increase in the magnitude of the dipole potential by cholesterol. Our calculations suggested that 12.5 mol% cholesterol does not significantly affect the conformations and packing of the hydrocarbon chains and produces only a slight reduction in the empty free volume. However, cholesterol has a significant influence on the subnanosecond time scale lipid dynamics: the diffusion constant for the center-of-mass "rattling" motion was reduced by a factor of 3, and the reorientational motion of the methylene groups was slowed along the entire length of the hydrocarbon chains.

1,2-Dipalmitoylphosphatidylcholine↗
PubMed1998

Molecular dynamics simulation of a synthetic ion channel.

A molecular dynamics simulation has been performed on a synthetic membrane-spanning ion channel, consisting of four alpha-helical peptides, each of which is composed of the amino acids leucine (L) and serine (S), with the sequence Ac-(LSLLLSL)3-CONH2. This four-helix bundle has been shown experimentally to act as a proton-conducting channel in a membrane environment. In the present simulation, the channel was initially assembled as a parallel bundle in the octane portion of a phase-separated water/octane system, which provided a membrane-mimetic environment. An explicit reversible multiple-time-step integrator was used to generate a dynamical trajectory, a few nanoseconds in duration for this composite system on a parallel computer, under ambient conditions. After more than 1 ns, the four helices were found to adopt an associated dimer state with twofold symmetry, which evolved into a coiled-coil tetrameric structure with a left-handed twist. In the coiled-coil state, the polar serine side chains interact to form a layered structure with the core of the bundle filled with H2O. The dipoles of these H2O molecules tended to align opposite the net dipole of the peptide bundle. The calculated dipole relaxation function of the pore H2O molecules exhibits two reorientation times. One is approximately 3.2 ps, and the other is approximately 100 times longer. The diffusion coefficient of the pore H2O is about one-third of the bulk H2O value. The total dipole moment and the inertia tensor of the peptide bundle have been calculated and reveal slow (300 ps) collective oscillatory motions. Our results, which are based on a simple united atom force-field model, suggest that the function of this synthetic ion channel is likely inextricably coupled to its dynamical behavior.

Amino Acid Sequence↗
PubMed1998

Molecular dynamics simulation of a hydrated diphytanol phosphatidylcholine lipid bilayer containing an alpha-helical bundle of four transmembrane domains of the influenza A virus M2 protein.

An alpha-helical bundle composed of four transmembrane portions of the M2 protein from the Influenza A virus has been studied in a hydrated diphytanol phosphatidylcholine bilayer using molecular dynamics (MD) calculations. Experimentally, the sequence utilized is known to aggregate as a four-helix bundle and act as a pH-gated proton-selective ion channel, which is blocked by the drug amantadine hydrochloride. In the presented simulation, the ion channel was initially set up as a parallel four-helix bundle. The all-atom simulation consisted of almost 16,000 atoms, described classically, using a forcefield from the CHARMM22 database. Bilayers with and without the bundle were shown to be stable throughout the nanosecond timescale of the MD simulation. Structural and dynamical properties of the bilayer both with and without the transmembrane protein are reported.

Computer Simulation↗
PubMed1998

Indirect glutamate neurotoxicity.

Indirect glutamate toxicity can be demonstrated by exposing dissociated rat hippocampal cultures to the media of the same culture transiently exposed (1 min) to glutamate (0.5 mM). The toxicity was maximum when the media was collected 5 min after the glutamate exposure. While the primary glutamate toxicity was attenuated by ionotropic glutamate receptor antagonists, the transferred, indirect toxicity was unaffected by the same antagonists. The changes in nuclear morphology indicated chromatin condensation and nuclear fragmentation in both primary and transferred toxicity. The stain for DNA damage by TUNEL method also revealed cells staining positive in both primary and transferred glutamate toxicity. These observations demonstrate that glutamate-induced neurotoxicity can be propagated to the uninjured cells by an unknown toxin released into the extracellular space. This neurotoxin induced both apoptosis and necrosis in cultured rat hippocampal cells.

6-Cyano-7-nitroquinoxaline-2,3-dione↗
PubMed1998

Bone and cartilage formation in an experimental model of distraction osteogenesis.

OBJECTIVES: (a) To develop a reliable and reproducible system for distraction osteogenesis in the rat to establish a model for future investigations of bone repair and regeneration. (b) To describe and characterize the histological events in distraction osteogenesis in the rat and to determine whether cartilage development is a normal component of the process. STUDY DESIGN: Species-specific, longitudinal time study. METHODS: Twenty rats underwent production of a middiaphyseal femoral osteotomy and application of a monolateral external fixator specifically designed for distraction. Animals were divided into five groups based on the time and extent of lengthening. RESULTS: During distraction, gap tissue showed collagen bundles and fibroblasts that were oriented longitudinally to the direction of the distraction force. Woven bone appeared to be laid down on these collagen scaffolds, and the newly formed vascular sinuses appeared to be the sites from which bone formation was initiated within the distraction gap. All groups undergoing active distraction showed intramembranous ossification in the distraction gap and endochondral ossification peripherally. However, when distraction was discontinued, endochondral ossification was observed in the gap. CONCLUSION: Distraction produces an environment in the distraction gap that suppresses the formation of cartilage. The formation of cartilage by injured periosteum, however, is obligatory and does not appear to be influenced by distraction. Bone formation within the distraction gap occurs where angiogenesis develops.

Animals↗
PubMed1998

Histoplasmosis-like choroiditis in a nonendemic area: the northwest United States.

PURPOSE: Histoplasmosis is not endemic in the U.S. northwest, but a type of multifocal choroiditis resembling ocular histoplasmosis occurs there. This study was designed to find a group of affected patients and study their clinical characteristics and immunologic responses to Histoplasma antigens. METHOD: Ten patients were found in the authors' files whose geographic histories made it unlikely that they had ever been exposed to Histoplasma capsulatum and yet they had features of ocular histoplasmosis. They were recalled for examination and testing by lymphocyte-stimulation assay for previous exposure to histoplasmosis. RESULTS: The clinical features of these patients resembled those of patients with ocular histoplasmosis, but their histories and the results of the assay did not support H. capsulatum as the cause of the ocular disease. CONCLUSION: This study confirmed that there is a type of choroiditis that resembles ocular histoplasmosis but is due to another agent or agents.

Adolescent↗
PubMed1997

Sorsby fundus dystrophy: reevaluation of variable expressivity in patients carrying a TIMP3 founder mutation.

Interfamilial phenotypic variations in Sorsby fundus dystrophy (SFD) have given rise to controversy as to whether SFD constitutes more than 1 nosologic entity. The recent identification of the tissue inhibitor of metalloproteinases-3 (TIMP3) as the gene causing SFD has made it possible to readdress the question of genetic and clinical heterogeneity. In this study, we have extended previous findings on a Ser181Cys founder mutation in SFD families from the British Isles and show that carriers of this mutation residing in Canada, the United States, and South Africa likewise are descendants of the British ancestor. In addition, we have reevaluated the question of variable SFD phenotypes by analyzing the available clinical data on carriers of the Ser181Cys mutation.

Adolescent↗
PubMed1997

Discrete expression and distribution pattern of TIMP-3 in the human retina and choroid.

PURPOSE: Extracellular matrix homeostasis is dependent in part upon a family of matrix metalloproteinases and their specific inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Recently, gene defects in TIMP-3 have been identified in the affected individuals of several families with Sorsby's fundus dystrophy (SFD). Very little information is available regarding TIMP-3 function or even its existence in the retina or choroid. METHODS: We used reverse transcription-polymerase chain reaction and Northern analysis to evaluate the expression of TIMP mRNA and Western immunoblots to evaluate TIMP protein produced by select cells of the human retina and choroid. We also used these methods and immunohistochemistry to localize the TIMPs in the retina and choroid. RESULTS: TIMP-3 transcripts are found in cultured human retinal pigment epithelium (RPE), choroidal microcapillary endothelium and pericytes. RPE cells also express and secrete TIMP-3 protein, which is localized to the extracellular matrix and is not found in culture medium; TIMP-1 and -2 are found almost exclusively in the medium. Immunohistochemistry of human retina/choroid sections shows pronounced TIMP-3 immunostaining in Bruch's membrane, particularly near the surface of the RPE and endothelial cells, presumably in their basement membranes, with minimal staining in other portions of the retina. Immunostaining for TIMP-1 is absent and for TIMP-2 is much less prevalent, but detectable in Bruch's membrane. CONCLUSIONS: TIMP-1, -2 and -3 exhibit distinctive expression patterns in the retina and choroid. This distribution and expression pattern partially explains why TIMP-3 mutations result in SFD, rather than other retinal pathologies, such as those associated with proliferative diabetic retinopathy.

Cells, Cultured↗