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Michael L Klein

Publications and source records attributed to Michael L Klein.

84 records · Page 5Linked to original sources
PubMed2002

Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamics.

The dissociation of a weak acid - a histidine residue - in water was investigated by means of constrained Car-Parrinello ab initio molecular dynamics. Both linear and coordination constraints were employed, and the structural, electronic, and dynamical transformations along the respective reaction coordinates were analyzed. The calculated potentials of mean force for the dissociation of a hydrogen atom from the Nepsilon and Ndelta positions of the imidazole ring reveal that protonated forms are approximately 9.0-9.5 kcal/mol more stable than the deprotonated. This result seems to agree well with the experimental estimate based on pKa. A possible transition state for the deprotonation has also been identified. Analysis of the electron localization function indicates that the proton transfer along the selected reaction path is not a fully concerted process.

Histidine↗
PubMed2002

Vapor-liquid interfacial properties of mutually saturated water/1-butanol solutions.

Adsorption and ordering at the vapor-liquid interfaces of mutually saturated water/1-butanol solutions at a temperature of 298.15 K were investigated using configurational-bias Monte Carlo simulations in the Gibbs ensemble and compared to the surface properties of neat water and 1-butanol liquids. A dense 1-butanol monolayer is observed at the surface of the water-rich phase, which results in a substantial decrease of its surface tension. In contrast, there is no enrichment of water molecules at the surface of the butanol-rich phase, and its surface tension is not significantly changed. Analysis of the interfacial structures reveals that these systems exhibit orientational ordering and composition heterogeneity. Analysis of the hydrogen-bonding distributions suggests that the formation of the 1-butanol monolayer is driven by an excellent match between water and the primary alcohol; that is, additional hydrogen bonds are formed between the excess free hydrogens of surface water and the excess hydrogen-bond acceptor sites of 1-butanol.

1-Butanol↗
PubMed2002

First-principles study of aqueous hydroxide solutions.

Car-Parrinello molecular dynamics simulations have been carried out for aqueous NaOH and KOH solutions under ambient conditions over a wide range of concentrations. From these simulations, we have observed a continuous change of the water structure with added hydroxide, characterized by a significant shift of the second peak of the OO radial distribution functions to shorter distances. At the highest concentration investigated, the normal tetrahedral coordination of pure water is completely missing, a result that is consistent with a recent neutron diffraction experiment. The added hydroxide also gives rise to some unique spectroscopic features, including a "free" O-H stretch, a broadening of the normal water OH stretching band, and a large blue shift of both the librational band and the low-frequency translation. These results are in good agreement with the experimental data. Finally, it was demonstrated that the structural and dynamical behavior is inextricably linked to the formation of compact hydroxide-water complexes.

Journal Article↗
PubMed2002

De novo design of biomimetic antimicrobial polymers.

The design of polymers and oligomers that mimic the complex structures and remarkable biological properties of proteins is an important endeavor with both fundamental and practical implications. Recently, a number of nonnatural peptides with designed sequences have been elaborated to provide biologically active structures; in particular, facially amphiphilic peptides built from beta-amino acids have been shown to mimic both the structures as well as the biological function of natural antimicrobial peptides such as magainins and cecropins. However, these natural peptides as well as their beta-peptide analogues are expensive to prepare and difficult to produce on a large scale, limiting their potential use to certain pharmaceutical applications. We therefore have designed a series of facially amphiphilic arylamide polymers that capture the physical and biological properties of this class of antimicrobial peptides, but are easy to prepare from inexpensive monomers. The design process was aided by molecular calculations with density functional theory-computed torsional potentials. This new class of amphiphilic polymers may be applied in situations where inexpensive antimicrobial agents are required.

Anti-Bacterial Agents↗
PubMed2002

Molecular dynamics investigation of membrane-bound bundles of the channel-forming transmembrane domain of viral protein U from the human immunodeficiency virus HIV-1.

Molecular dynamics (MD) simulations have been carried out on bundles of the channel-forming transmembrane (TM) domain of the viral protein U (VPU(1-27) and VPU(6-27)) from the human immunodeficiency virus (HIV-1). Simulations of hexameric and pentameric bundles of VPU(6-27) in an octane/water membrane mimetic system suggested that the pentamer is the preferred oligomer. Accordingly, an unconstrained pentameric helix bundle of VPU(1-27) was then placed in a hydrated palmitoyl-oleyl-3-n-glycero-phosphatidylethanolamine (POPE) lipid bilayer and its structural properties calculated from a 3-ns MD run. Some water molecules, initially inside the channel lumen, were expelled halfway through the simulation and the bundle adopted a conical structure reminiscent of previous MD results obtained for VPU(6-27) in an octane/water system. The pore constriction generated may correspond to a closed state of the channel and underlies the relocation of the W residue toward the pore lumen. The relative positions of the helices with respect to the bilayer and their interactions with the lipids are discussed. The observed structure is stabilized via specific interactions between the VPU helices and the carbonyl oxygen atoms of the lipid molecules, particularly at the Q and S residues.

Carbon↗
PubMed2002

Computer simulation studies of model biological membranes.

This Account is focused on computer simulation studies of model biological membrane systems with potential applications in biomedical research. In the past decade, classical molecular dynamics has provided novel insights into the properties of model biomembrane systems, including the nature of the DNA-lipid interactions, the effect of pore-forming transmembrane peptides on the lipid environment, and the partitioning of volatile anesthetic molecules. Such simulations, employing full atomic detail, are typically restricted to systems of dimensions less than approximately 10 nm. Simplified models of the coarse-grain type have been intended to bridge the gap between full atomistic detail and the mesoscopic (micron) regime. The use of such models is illustrated with the example of anesthetics in a phospholipid bilayer.

Anesthetics↗
PubMed2002

Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations.

Computer simulation has emerged as a powerful tool for studying the structural and functional properties of complex biological membranes. In the last few years, the use of recently developed simulation methodologies and current generation force fields has permitted novel applications of molecular dynamics simulations, which have enhanced our understanding of the different physical processes governing biomembrane structure and dynamics. This review focuses on frontier areas of research with important biomedical applications. We have paid special attention to polyunsaturated lipids, membrane proteins and ion channels, surfactant additives in membranes, and lipid-DNA gene transfer complexes.

Animals↗
PubMed2002

Effects of the nonimmobilizer hexafluroethane on the model membrane dimyristoylphosphatidylcholine.

BACKGROUND: Nonimmobilizers are agents that lack anesthetic properties, although their chemical structure is very similar to known anesthetics. The primary action site of both agents, whether at the membrane or target protein level, is still a matter of debate. However, increasing evidence points to the distinct modifications of the membrane physical properties that such agents induce. Such modification may play a role in the mechanism of anesthesia, and may therefore be related to the differences in their clinical behavior. METHODS: Molecular dynamics (MD) computer simulations have been used to investigate the distribution of a nonimmobilizer, hexafluroethane (HFE, C(2)F(6)), in a lipid membrane. The biologically relevant liquid-crystal phase of a hydrated dimyristoyl phosphatidyl choline (DMPC) bilayer was used as a membrane model. Two MD simulations corresponding to HFE mole fractions of 6% and 25% have been performed at room temperature and constant ambient pressure, for a duration of 2 nanoseconds each. RESULTS: The equilibrium configurations of HFE in the bilayer show that the nonimmobilizer molecules are evenly distributed along the lipid hydrocarbon chains with a slight preference for the bilayer center. This partitioning induces an expansion of the bilayer thickness and a lateral contraction of the membrane (decrease of the area per lipid). The presence of HFE has essentially no effect on the lipid acyl chain conformations in agreement with nuclear magnetic resonance (NMR) measurements of the chain order parameters. The partitioning of the nonimmobilizer does not influence the orientation of the lipid head-group dipole moment. CONCLUSIONS: The modifications induced by the presence of the nonimmobilizer HFE on a model membrane are distinct from those previously found for halothane (CF(3)CHBrCl), its anesthetic analogue, and appear to result from different distributions in the lipid bilayer. The results of the MD simulations show that (1) the changes in the average area per lipid and in the membrane thickness are opposite for the two agents and (2) HFE induces no change in the lipid head-group orientation, in contrast to halothane. These different effects (1) on the physical properties of the lipid bilayer and (2) on the electrostatic properties of the membrane-water interface may be linked to different clinical effects, and thus might contribute to the mechanism of general anesthesia.

Algorithms↗
PubMedDate not supplied

Shrinkage of a rapidly growing tumor by drug-loaded polymersomes: pH-triggered release through copolymer degradation.

Carrier-mediated delivery of drugs into the cytosol is often limited by either release from the carrier or release from an internalizing endolysosome. Here, loading, delivery, and cytosolic uptake of drug mixtures from degradable polymersomes are shown to exploit both the thick membrane of these block copolymer vesicles and their aqueous lumen as well as pH-triggered release within endolysosomes. Our initial in vivo studies demonstrate growth arrest and shrinkage of rapidly growing tumors after a single intravenous injection of polymersomes composed of poly(ethylene glycol)-polyester. Vesicles are shown to break down into membrane-lytic micelles within hours at 37 degrees C and low pH, although storage at 4 degrees C allows retention of drug for over a month. It is then shown that cell entry of the polymersomes into endolysosomes is followed by copolymer-induced endolysosomal rupture with release of cytotoxic drugs. Above a critical poration concentration (CCPC) that is easily achieved within endolysosomes and that scales with copolymer proportions and molecular weight, the copolymer micelles are seen to disrupt lipid membranes and thereby enhance drug activity. Neutral polymersomes and related macrosurfactant assemblies can thus create novel pathways within cells for controlled release and delivery.

Animals↗