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Michael L Klein

Publications and source records attributed to Michael L Klein.

At least 73 records · Page 4Linked to original sources
PubMed2004

A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.

The prototype binuclear elimination (E2) reaction illustrates the mechanism of a large number of biochemical and industrial applied processes but has received surprisingly little attention in theoretical studies compared to, for example, the substitution (SN2) reaction. This is due to its concerted mechanism, which requires an independent description of the three bonds that are being formed or broken. In this work, we have taken the advantage of a new and promising methodology to efficiently sample intrinsically multidimensional free-energy surfaces. We locate the lowest free-energy reaction path in the 3D configurational space and use this finite-temperature intrinsic reaction coordinate in an umbrella sampling scheme to access the temperature contributions to high accuracy. The small increase of the barrier and the decrease of the overall endothermicity for the E2 reaction due to entropic contributions is non-trivial. Moreover, our strategy to efficiently handle multiple reaction coordinates could be a great benefit to many chemistry-related fields, such as enzyme catalysis, reactions in solution, and nucleation processes.

Journal Article↗
PubMed2004

Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics.

Block-copolymer amphiphiles have been observed to assemble into vesicles and other morphologies long known for lipids but with remarkably different properties. Coarse-grain molecular dynamics (CG-MD) is used herein to elaborate the structures and properties of diblock copolymer assemblies in water. By varying the hydrophilic/hydrophobic ratio of the copolymer in line with experiment, bilayer, cylindrical and spherical micelle morphologies spontaneously assemble. Varying the molecular weight (MW) with hydrophilic/hydrophobic ratio appropriate to a bilayer yields a hydrophobic core thickness that scales for large MW as a random coil polymer, in agreement with experiment. The extent of hydrophobic-segment overlap in the core increases nonlinearly with MW, indicative of chain entanglements and consistent with the dramatic decrease reported for lateral mobility in polymer vesicles. Calculated trends with MW as well as hydrophilic/hydrophobic ratio thus agree with experiment, demonstrating that CG-MD simulations provide a rational design tool for diblock copolymer assemblies.

Computer Simulation↗
PubMed2004

Understanding nature's design for a nanosyringe.

Synthetic and natural peptide assemblies can possess transport or conductance activity across biomembranes through the formation of nanopores. The fundamental mechanisms of membrane insertion necessary for antimicrobial or synthetic pore formation are poorly understood. We observe a lipid-assisted mechanism for passive insertion into a model membrane from molecular dynamics simulations. The assembly used in the study, a generic nanotube functionalized with hydrophilic termini, is assisted in crossing the membrane core by transleaflet lipid flips. Lipid tails occlude a purely hydrophobic nanotube. The observed insertion mechanism requirements for hydrophobic-hydrophilic matching have implications for the design of synthetic channels and antibiotics.

Biosensing Techniques↗
PubMed2004

Dissociation of hydrogen fluoride in HF(H(2)O)(7).

We have previously demonstrated that H-bond arrangement has a significant influence on the energetics, structure and chemistry of water clusters. In this work, the effect of H-bond orientation on the dissociation of hydrogen fluoride with seven water molecules is studied by means of graph theory and high level ab initio methods. It is found that cubic structures of HF(H(2)O)(7) are more stable than structures of other topologies reported in the literature. Electronic calculations on all possible H-bond orientations of cubie-HF(H(2)O)(7) show that ionized structures are energetically more favorable than nonionized ones. This is an indication that seven water molecules might be capable of ionizing hydrogen fluoride.

Journal Article↗
PubMed2004

Association between C-reactive protein and age-related macular degeneration.

CONTEXT: C-reactive protein (CRP) is a systemic inflammatory marker associated with risk for cardiovascular disease (CVD). Some risk factors for CVD are associated with age-related macular degeneration (AMD), but the association between CRP and AMD is unknown. OBJECTIVE: To test the hypothesis that elevated CRP levels are associated with an increased risk for AMD. DESIGN, SETTING, AND PARTICIPANTS: A total of 930 (91%) of 1026 participants at 2 centers in the Age-Related Eye Disease Study (AREDS), a multicenter randomized trial of antioxidant vitamins and minerals, were enrolled in this case-control study. There were 183 individuals without any maculopathy, 200 with mild maculopathy, 325 with intermediate disease, and 222 with advanced AMD (geographic atrophy or neovascular AMD). The AMD status was assessed by standardized grading of fundus photographs, and stored fasting blood specimens drawn between January 1996 and April 1997 were analyzed for high-sensitivity CRP levels. MAIN OUTCOME MEASURE: Association between CRP and AMD. RESULTS: The CRP levels were significantly higher among participants with advanced AMD (case patients) than among those with no AMD (controls; median values, 3.4 vs 2.7 mg/L; P =.02). After adjustment for age, sex, and other variables, including smoking and body mass index, CRP levels were significantly associated with the presence of intermediate and advanced stages of AMD. The odds ratio (OR) for the highest vs the lowest quartile of CRP was 1.65 (95% confidence interval [CI], 1.07-2.55; P for trend =.02). The OR for CRP values at or above the 90th percentile (10.6 mg/L) was 1.92 (95% CI, 1.20-3.06), and the OR for CRP values at or above the mean plus 2 SDs (16.8 mg/L) was 2.03 (95% CI, 1.03-4.00). A trend for an increased risk for intermediate and advanced AMD with higher levels of CRP was seen for smokers (OR, 2.16; 95% CI, 1.33-3.49) and those who never smoked (OR, 2.03; 95% CI, 1.19-3.46) with the highest level of CRP. CONCLUSION: Our results suggest that elevated CRP level is an independent risk factor for AMD and may implicate the role of inflammation in the pathogenesis of AMD.

Aged↗
PubMed2004

First principles computational study of the active site of arginase.

Ab initio density functional theory (DFT) methods were used to investigate the structural features of the active site of the binuclear enzyme rat liver arginase. Special emphasis was placed on the crucial role of the second shell ligand interactions. These interactions were systematically studied by performing calculations on models of varying size. It was determined that a water molecule, and not hydroxide, is the bridging exogenous ligand. The carboxylate ligands facilitate the close approach of the Mn (II) ions by attenuating the metal-metal electrostatic repulsion. Of the two metals, Mn(A) was shown to carry a larger positive charge. Analysis of the electronic properties of the active site revealed that orbitals involving the terminal Asp234 residue, as well as the flexible micro-1,1 bridging Asp232, lie at high energies, suggesting weaker coordination. This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated.

Animals↗
PubMed2004

Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamics.

Molecular dynamics results are presented for a coarse-grain model of 1,2-di-n-alkanoyl-sn-glycero-3-phosphocholine, water, and a capped cylindrical model of a transmembrane peptide. We first demonstrate that different alkanoyl-length lipids are miscible in the liquid-disordered lamellar (Lalpha) phase. The transmembrane peptide is constructed of hydrophobic sites with hydrophilic caps. The hydrophobic length of the peptide is smaller than the hydrophobic thickness of a bilayer consisting of an equal mixture of long and short alkanoyl tail lipids. When incorporated into the membrane, a meniscus forms in the vicinity of the peptide and the surrounding area is enriched in the short lipid. The meniscus region draws water into it. In the regions that are depleted of water, the bilayers can fuse. The lipid headgroups then rearrange to solvate the newly formed water pores, resulting in an inverted phase. This mechanism appears to be a viable pathway for the experimentally observed Lalpha-to-inverse hexagonal (HII) peptide-induced phase transition.

Computer Simulation↗
PubMed2003

Hydrogen bonding in water.

Computer simulations using density functional theory based ab initio path integral molecular dynamics have been carried out to investigate hydrogen bonding in water under ambient conditions. Structural predictions for both H2O and D2O, which include the effects of zero-point energy, thermal motion, and many body polarization effects, are contrasted with classical simulations that ignore nuclear quantum effects. The calculated effect of H/D isotope substitution on the water structure is much smaller than the difference between the classical and quantum path integral results, and is in excellent agreement with the measured H/D difference data from both neutron and x-ray scattering.

Journal Article↗
PubMed2003

Analysis of the ARMD1 locus: evidence that a mutation in HEMICENTIN-1 is associated with age-related macular degeneration in a large family.

Age-related macular degeneration (AMD) is a common cause of severe vision loss. Identification of the genes involved in AMD will lead to a better understanding of this disease at the molecular level, which will eventually lead to early detection, prevention and treatment. Previously, we mapped the ARMD1 gene to 1q25-31 in a large family with AMD. Here, we narrow the ARMD1 locus to 14.9 Mb between LAMB2 and D1S3469, a region containing 50 known genes. Twenty candidate genes within this region were screened for mutations. Only one DNA variation, an A16,263G transition in exon 104 of HEMICENTIN-1, was found to segregate exclusively with the disease haplotype in members of this large family with AMD. This variation produces a non-conservative substitution of arginine for glutamine at amino acid position 5345 (Gln5345Arg). It was also identified in 11 other individuals, all of whom share a haplotype, which envelops HEMICENTIN-1, with the large AMD family. The affected status of all but one of those individuals conforms to the age-dependent penetrance observed in AMD. The amino acid at position 5345 of HEMICENTIN-1 was conserved as glutamine in eight species analyzed. RT-PCR analysis demonstrated that exon 104 of HEMICENTIN-1 is alternatively spliced in various cell types. Exclusive segregation of Gln5345Arg with the disease haplotype in this large family, amino acid conservation of glutamine at this position among mammals, the non-conservative nature of the substitution and similarities to EFEMP1 support the conclusion that HEMICENTIN-1 is the ARMD1 gene.

Amino Acid Sequence↗
PubMed2003

Nuclear quantum effects and hydrogen bonding in liquids.

We have employed ab initio path integral molecular dynamics simulations to investigate the role of nuclear quantum effects on the strength of hydrogen bonds in liquid hydrogen fluoride. Nuclear quantum effects are shown to be responsible for a stronger hydrogen bond and an enhanced dipole-dipole interaction, which lead, in turn, to a shortening of the H...F intrachain distance. The simulation results are analyzed in terms of the electronic density shifts with respect to a purely classical treatment of the nuclei. The observed enhanced hydrogen-bond interaction, which arises from a coupling of intra- and intermolecular effects, should be a general phenomenon occurring in all hydrogen-bonded systems.

Hydrofluoric Acid↗
PubMed2003

Age-related macular degeneration--a genome scan in extended families.

We performed a genomewide scan and genetic linkage analysis, to identify loci associated with age-related macular degeneration (AMD). We collected 70 families, ranging from small nuclear families to extended multigenerational pedigrees and consisting of a total of 344 affected and 217 unaffected members available for genotyping. We performed linkage analyses using parametric and allele-sharing models. We performed the analyses on the complete pedigrees but also subdivided the families into nuclear pedigrees. Finally, to dissect potential genetic factors responsible for differences in disease manifestation, we stratified the sample by two major AMD phenotypes (neovascular AMD and geographic atrophy) and by age of affected family members at the time of our evaluation. We have previously demonstrated linkage between AMD and 1q25-31 in a single large family. In the combined sample, we have detected the following loci with scores exceeding a LOD=2 cutoff under at least one of the models considered: 1q31 (HLOD=2.07 at D1S518), 3p13 (HLOD=2.19 at D3S1304/D3S4545), 4q32 (HLOD=2.66 at D4S2368, for the subset of families with predominantly dry AMD), 9q33 (LODZlr=2.01 at D9S930/D9S934), and 10q26 (HLOD=3.06 at D10S1230). Using correlation analysis, we have found a statistically significant correlation between LOD scores at 3p13 and 10q26, providing evidence for epistatic interactions between the loci and, hence, a complex basis of AMD. Our study has identified new loci that should be considered in future mapping and mutational analyses of AMD and has strengthened the evidence in support of loci suggested by other studies.

Aging↗
PubMed2003

Simulating the nucleation of water/ethanol and water/n-nonane mixtures: mutual enhancement and two-pathway mechanism.

A combination of the aggregation-volume-bias and configurational-bias Monte Carlo algorithms and the umbrella sampling technique was applied to investigate two different binary vapor-liquid nucleation systems: water/ethanol and water/n-nonane. The simulations are able to reproduce the different nonideal nucleation behavior observed experimentally for these two systems, i.e., the mutual enhancement of nucleation rates for water/ethanol mixtures and the two-pathway nucleation for water/n-nonane mixtures. Structural analysis provides microscopic explanations for the observed nucleation behavior. In particular, the simulations show a large and size-dependent surface enrichment of ethanol in the water/ethanol droplets, which confirms the previous experimental interpretation for this system. The immiscibility observed even for small water/n-nonane clusters causes the two-pathway nucleation mechanism.

Journal Article↗
PubMed2003

Probing the configurational space of a metalloprotein core: an ab initio molecular dynamics study of Duo Ferro 1 binuclear Zn cofactor.

We present three theoretical models of various degree of completeness to explore the chemical phase space available to the Glu4His2Zn2 cofactor found in the four-helix bundle of de novo designed metalloprotein Duo Ferro 1. We have found that the planewave DFT geometry optimization of 94-atom Model I, which contains both the protein scaffold constraints as well as the second shell hydrogen bonding network, reproduces the crystal structure bonding with remarkable accuracy (0.34 A). Surprisingly, the geometry optimization of 66-atom Model II (lacking the second shell hydrogen bonding) and 48-atom Model III (being also free of the protein scaffold constraints) still result in the fidelity with the crystallographic structure (RMSDs 0.29 and 0.34 A, respectively). To examine whether these structures are close to the global minimum as well as to investigate various conformational transitions to which the di-Zn cofactor may be susceptible to, we have carried out a 10 ps Car-Parrinello Molecular Dynamics (CPMD) simulation of Model III. We suggest that weak hydrogen bonds between imidazole hydrogens and carboxylate oxygens modulate the dynamical behavior of the system. One part of the molecule was found to be rigid due to the particular H(imidazole)-O(carboxylate) interaction restricting both the motion of the imidazole ring as well as the terminal carboxylate conformational mobility. The second half of the system was very flexible demonstrating a coupling of a transient formation of H(imidazole)-O(carboxylate) bonds with the spinning of the imidazole ring and syn-anti isomerization of the terminal carboxylate group. In addition, two low-energy snapshots from the 10 ps CPMD run were quenched, and their geometries were optimized, leading to two new isomers 48 kJ/mol lower in energy than the one associated with the crystal structure. We suggest that periodic quenching of the CPMD simulation snapshots of a minimalist model may be used as an efficient method to generate a large number of competitive local minima, which may be consequently pruned by imposing the protein scaffold constraints as well as further tuned by the second shell hydrogen bonding network.

Kinetics↗
PubMed2003

Lack of an association of apolipoprotein E gene polymorphisms with familial age-related macular degeneration.

BACKGROUND: Previously, the epsilon 4 allele of apolipoprotein E (APOE) was reported to have a significant association with a decreased risk of age-related macular degeneration (AMD). In addition, the epsilon 2 allele of APOE was reported to be possibly associated with an increased risk of AMD. OBJECTIVE: To determine if APOE polymorphisms, previously reported to be associated with AMD, affect its expression in medium to large families, as well as in unrelated patients with AMD. METHODS: The APOE genotype was determined by HhaI restriction digests of polymerase chain reaction-amplified products in a collection of 259 affected and 207 unaffected individuals from 56 AMD families. Genotypes were determined similarly in a set of 104 unrelated AMD patients and in 113 unaffected control subjects. Diagnosis of AMD was based on clinical examination and evaluation of fundus photographs. Evidence of an association between alleles of APOE and AMD in families was tested by the following 4 statistical methods: chi2 analysis of simple allele counting, logistic regression analysis adjusting for age, construction of likelihood ratios of haplotype frequencies, and the pedigree disequilibrium test. RESULTS: None of the statistical methods used showed a significant association between the common alleles of APOE and AMD in our collection of families or in the set of unrelated AMD patients. CONCLUSIONS: No evidence was found to support an association between AMD in medium to large families and the epsilon 4 or epsilon 2 alleles of APOE. Neither was any evidence found for an association of APOE polymorphisms with the set of unrelated patients with AMD. However, a trend for a decreased risk of AMD associated with APOE epsilon 4 was observed in the set of unrelated patients with a family history of AMD.

Aged↗
PubMed2003

Genetics of age-related macular degeneration.

Gene discoveries will lead to more effective them pies for AMD by identifying specific underlying disease mechanisms that might be corrected by drugs or gene therapy. For example, investigations are currently being carried out using pigment epithelium-derived factor (FEDF). The gene for this potent inhibitor of angiogenesis has been incorporated into an adenoviral vector and delivered into the eye by intravitreal injection to inhibit growth of new blood vessels in eyes with neovascular AMD. In the future, as the genetics of this complex disease are unraveled, more effective treatments and preventative measures that target specific molecular defects underlying the development of AMD can be expected.

Humans↗