Mesoscale computer modeling of lipid-DNA complexes for gene therapy

We report on a molecular simulation method, which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a coarse-grained representation of the intramolecular details and via intermolecular potentials, which effectively mimic the hydrophobic effect without an explicit solvent. The broad utility of the model is illustrated by demonstrating excellent agreement with x-ray diffraction experimental data for the dependence of the spacing between DNA chains on the concentration of CLs. At high concentrations, the large electrostatic pressure induces the formation of pores in the membranes through which the DNA molecules may escape the complex. We relate this observation to the origin of recently observed enhanced transfection efficiency of lamellar CL-DNA complexes at high charge densities.     

Analytical model for ion acceleration by high-intensity laser pulses

We present a general expression for the maximum ion energy observed in experiments with thin foils irradiated by high-intensity laser pulses. The analytical model is based on a radially confined surface charge set up by laser accelerated electrons on the target rear side. The only input parameters are the properties of the laser pulse and the target thickness. The predicted maximum ion energy and the optimal laser pulse duration are supported by dedicated experiments for a broad range of different ions.     

Insight into catalytically relevant correlated motions in human purine nucleoside phosphorylase

The catalytic site of the homotrimeric enzyme human purine nucleoside phosphorylase enzyme (hPNP) features residue F200 and the 241-265 loop directly skirting the purine base and a residue belonging to the adjacent monomer, F159, immediately conterminous to the ribosyl moiety. Crystallographic B-factors of apo human purine nucleoside phosphorylase, and hPNP complexed with substrate/transition state (TS) analogues, show that residue E250 is the centroid of a highly mobile loop region. Furthermore, superimposition of apo hPNP and hPNP complexed with TS analogue Immucillin-H shows a tightening of the active site, caused by the ligand-dependent 241-265 loop rearrangement taking place upon substrate/inhibitor binding, suggesting a putative dynamic role of the loop in binding/catalysis. However, crystallographic structures reveal only average atomic positions, and more detailed information is needed to discern the dynamic behavior of hPNP. The Essential Dynamics (ED) method is used here to investigate the existence of correlated motions in hPNP and consequently proposes mutagenesis assays to estimate the relative importance of these motions in the phosphorolytic efficiency of the reaction catalyzed by hPNP. We compare the concerted motions obtained from multiple molecular dynamics simulations of apo and Michaelis complex of hPNP both in vacuo and in solution. The results of the principal component analysis for the apo hPNP indicate the existence of strong correlations predominantly in the vicinity of residue F159. However, for the Michaelis complex, concerted motions are seen mostly around both active site residue F200 and loop residue E250. Additionally, for a simulation depicting the relaxation of tight complexed hPNP with a TS analogue, toward its relaxed apo form (after removal of the TS analog), a combination of the apo hPNP and Michaelis complex motions is found, with prominent concerted modes centered around neighboring residues F159, F200, and E250. Finally, we probed the extent to which these concerted motions bear an intrinsic catalytic role by performing experimental site-directed mutagenesis on some residues, followed by kinetic analysis. The F159G and F200G mutants displayed a strong increase in K(M) and modest decrease in k(cat), suggesting that these concerted motions may provide dynamical roles in substrate binding and/or catalysis. However, further structural data for the hPNP mutants are needed to confirm our hypothesis.     

Transition states for glucopyranose interconversion

Glucose is a central molecule in biology and chemistry, and the anomerization reaction has been studied for more than 150 years. Transition-state structure is the last impediment to an in-depth understanding of its solution chemistry. We have measured kinetic isotope effects on the rate constants for approach of alpha-glucopyranose to its equilibrium with beta-glucopyranose, and these were converted into unidirectional kinetic isotope effects using equilibrium isotope effects. Saturation transfer 13C NMR spectroscopy has yielded the relative free energies of the transition states for the ring-opening and ring-closing reactions, and both transition states contribute to the experimental kinetic isotope effects. Both transition states of the anomerization process have been modeled with high-level computational theory with constraints from the primary, secondary, and solvent kinetic isotope effects. We have found the transition states for anomerization, and we have also concluded that it is forbidden for the water molecule to form a hydrogen bond bridge to both OH1 and O5 of glucose simultaneously in either transition state.     

Transition-state structure of human 5'-methylthioadenosine phosphorylase

Kinetic isotope effects (KIEs) and computer modeling using density functional theory were used to approximate the transition state of human 5'-methylthioadenosine phosphorylase (MTAP). KIEs were measured on the arsenolysis of 5'-methylthioadenosine (MTA) catalyzed by MTAP and were corrected for the forward commitment to catalysis. Intrinsic KIEs were obtained for [1'-(3)H], [1'-(14)C], [2'-(3)H], [4'-(3)H], [5'-(3)H(2)], [9-(15)N], and [Me-(3)H(3)] MTAs. The primary intrinsic KIEs (1'-(14)C and 9-(15)N) suggest that MTAP has a dissociative S(N)1 transition state with its cationic center at the anomeric carbon and insignificant bond order to the leaving group. The 9-(15)N intrinsic KIE of 1.039 also establishes an anionic character for the adenine leaving group, whereas the alpha-primary 1'-(14)C KIE of 1.031 indicates significant nucleophilic participation at the transition state. Computational matching of the calculated EIEs to the intrinsic isotope effects places the oxygen nucleophile 2.0 Angstrom from the anomeric carbon. The 4'-(3)H KIE is sensitive to the polarization of the 3'-OH group. Calculations suggest that a 4'-(3)H KIE of 1.047 is consistent with ionization of the 3'-OH group, indicating formation of a zwitterion at the transition state. The transition state has cationic character at the anomeric carbon and is anionic at the 3'-OH oxygen, with an anionic leaving group. The isotope effects predicted a 3'-endo conformation for the ribosyl zwitterion, corresponding to a H1'-C1'-C2'-H2' torsional angle of 33 degrees. The [Me-(3)H(3)] and [5'-(3)H(2)] KIEs arise predominantly from the negative hyperconjugation of the lone pairs of sulfur with the sigma (C-H) antibonding orbitals. Human MTAP is characterized by a late S(N)1 transition state with significant participation of the phosphate nucleophile.     

The Ordered Gradual Covering Location Problem on a Network

In this paper we develop a network location model that combines the characteristics of ordered median and gradual cover models resulting in the Ordered Gradual Covering Location Problem (OGCLP). The Gradual Cover Location Problem (GCLP) was specifically designed to extend the basic cover objective to capture sensitivity with respect to absolute travel distance. The Ordered Median Location problem is a generalization of most of the classical locations problems like p-median or p-center problems. The OGCLP model provides a unifying structure for the standard location models and allows us to develop objectives sensitive to both relative and absolute customer-to-facility distances. We derive Finite Dominating Sets (FDS) for the one facility case of the OGCLP. Moreover, we present efficient algorithms for determining the FDS and also discuss the conditional case where a certain number of facilities is already assumed to exist and one new facility is to be added. For the multi-facility case we are able to identify a finite set of potential facility locations a priori, which essentially converts the network location model into its discrete counterpart. For the multi-facility discrete OGCLP we discuss several Integer Programming formulations and give computational results.     

The peninsula of neutron nuclear stability in the vicinity of N = 258

The properties of extremely neutron-excessive nuclei with Z ?? 70, including the region of transuranium elements, are calculated beyond the previously theoretically known neutron drip line (NDL). The calculations are based on the Hartree-Fock approach using Skyrme forces (SkM*, SkI2, SLy4, Ska) with allowance for axial deformation and pairings in the BCS approximation. It is shown that the series of isotones with neutron number N = 258 outside of 2n NDL forms a peninsula of stable nuclei (PSN) with respect to the emission of one neutron. For SkM* forces, a PSN is formed by ³⁴⁴Rn, ³⁴⁶Ra, ³⁴⁸Th, and ³⁵⁰U nuclides.     

Synthesis and Biological Activity of Oxidation Products of the Antiprogestine Mifepristone

 Selenium dioxide oxidation allows the selective introduction of a hydroxyl group at position 6 of the steroid skeleton of the antihormone (11β, 17β)-11-(4-dimethylamino-phenyl)-17-hydroxyl-17-(1-propynyl)-estra-4,9-dien-3-one (mifepristone, RU 486) and leads in a one-step procedure to two diastereomeric oxidation products. Their structure (6α- and 6β-hydroxy-mifepristone) was determined by NMR spectroscopy. The antiprogestinic activity of the oxidation products is comparable to that of mifepristone.     

Noise sensitivity of Boolean functions and applications to percolation

It is shown that a large class of events in a product probability space are highly sensitive to noise, in the sense that with high probability, the configuration with an arbitrary small percent of random errors gives almost no prediction whether the event occurs. On the other hand, weighted majority functions are shown to be noise-stable. Several necessary and sufficient conditions for noise sensitivity and stability are given. Consider, for example, bond percolation on ann+1 byn grid. A configuration is a function that assigns to every edge the value 0 or 1. Let ω be a random configuration, selected according to the uniform measure. A crossing is a path that joins the left and right sides of the rectangle, and consists entirely of edges ℓ with ω(ℓ)=1. By duality, the probability for having a crossing is 1/2. Fix an ɛ ∈ (0, 1). For each edge ℓ, let ω′(ℓ)=ω(ℓ) with probability 1 − ɛ, and ω′(ℓ)=1 − ω(ℓ) with probability ɛ, independently of the other edges. Letp(τ) be the probability for having a crossing in ω, conditioned on ω′ = τ. Then for alln sufficiently large,P{τ : |p(τ) − 1/2| > ɛ}<ɛ.