Applications of molecular dynamics simulations coupled with Harris functional approximation to argon

We have demonstrated molecular dynamics simulations using a combination of the classical molecular dynamics with density functional theory for argon clusters. Three different molecular dynamics schemes, which differ in their treatment of the potential energy and forces, have been carried out. The first uses a Lennard-Jones potential. In the second, the potential is computed using the Harris functional, and in the third, a combination of Lennard-Jones and Harris functional potentials is used. In addition to direct examination of the trajectories, the velocity autocorrelation function and its power spectrum have been computed to demonstrate the agreement between these three methods. The present studies show that a scheme that used a combination of model potentials and density functional theory provides a very useful tool for the dynamics simulation of systems that contain some fragments in which the analytical model potentials are not available. © 1994 John Wiley & Sons, Inc.     

A new H/D exchange- and mass spectrometry-based method for thermodynamic analysis of protein-DNA interactions

The application of SUPREX (stability of unpurified proteins from rates of H/D exchange) to the thermodynamic analysis of protein-DNA complexes is described. A series of five model protein-DNA complexes involving two known DNA binding proteins, Arc repressor and CopG, were analyzed in order to determine the accuracy, precision, and generality of the SUPREX technique for quantifying the strength of protein-DNA interactions. For protein-DNA complexes that reversibly unfold in a two-state manner, we demonstrate that reasonably precise Kd values in agreement with those determined by conventional techniques can be determined by SUPREX. In the case of protein-DNA complexes that are not well modeled by a two-state unfolding mechanism, we find that relative binding affinities can be determined in the SUPREX experiment.     

Selection and rapid purification of murine antibody fragments that bind a transition-state analog by phage display

Functional antibody fragments may be displayed on the surface of filamentous bacteriophage by introducing variable region genes into the viral genome at a gene encoding a viral coat protein. “Phage display” enables the isolation of antibody genes from large libraries according to the binding specificities they encode. We have constructed a new phage-display vector encoding a polyhistidine tag that has been used for rapid purification of soluble antibody fragments. An antibody library derived from immunized mice was cloned into this vector. This library was panned against the transition state analog RT3, and a high proportion of binders isolated after two rounds of panning. PCR analysis revealed that there were 24 different pattern groups. Sequencing of 15 clones within the major pattern group revealed 10 related clones with a range of point mutations. Thus, phage display can provide a large diverse repertoire of candidate catalytic antibodies based on TSA selection and screening.     

Photochemical redox titrations with tungsten(V)

A titration method has been developed for the determination of micromolar quantities of dichromate, vanadate and hexacyanoferrate(III) with in situ photochemical generation of tungsten(V) as the titrant. Precision of 1–3% was obtained. Spectrophotometric end-points were utilized because of the intense blue color of the titrant (λ_max 770nm; _max7.10³). Because the titrant reacts with oxygen, a closed, argon-flushed, circulating photolysis apparatus was constructed. Optimal solution condi- tions were investigated ; tungsten reagent must be added as the solid just before titra-tion. An induced reaction between dichromate and glucose was found, but satisfactory linear calibration curves were obtained. With reduced photolytic intensity, 0.2 μeq of dichromate can be determined.     

On the evaluation of multivariate polynomials and their derivatives

LetH be a polynomial inn>1 variables over the fields of real or complex numbers. An algorithm is presented here for the simultaneous evaluation ofH and its first and second (F-) derivativesH andH, or of any combination ofH,H,H. The evaluations ofH alone or ofH andH together are of the same order inn andd whered is the degree ofH, while the computation ofH,H, andH isd times this order. The process takes account of the sparsity pattern ofH by using a tree structure induced by the nonzero coefficients. It also allows for simultaneous operation with several polynomials with the same sparsity pattern. The data structure for the method is rather simple in nature and can be adapted easily to specific types of polynomials. Several possible implementations and their complexity are discussed.     

Facile assembly of fused benzo[4,5]furo heterocycles

A concise synthesis of fused benzo[4,5]furo heterocycles 18 has been developed. Chemo/regioselective Suzuki coupling between 1,2-dihaloarene 17 and alpha-hydroxyphenylboronic acid or ester 20 gives biaryl phenol 19, which then undergoes copper(I) thiophene-2-carboxylate (CuTC)-mediated intramolecular cyclization to afford 18 in good overall yield. This method has broad substrate scope and allows facile assembly of a wide variety of benzo[4,5]furo heterocycles.     

Neutron activation analysis of Nigerian crude oils

Since the advent of the Nuclear Age mankind has been both fascinated by the potential of nuclear processes, and fearful of its destructive power. Nuclear technologies have undergone rapid development, while most of society is left with a poor understanding about the benefits and risks involved. Our Nuclear Society: from Chemobyl to PET Scans, and Energy, Technology and Risk are two courses developed at the University of Maryland in an effort to introduce students from all backgrounds to issues and applications of nuclear science. Course material and presentation strategies are geared toward keeping the course interesting and informative for all students.     

Mapping tertiary interactions in protein folding reactions: a novel mass spectrometry- and chemical synthesis-based approach

A novel mass spectrometry- and chemical synthesis-based approach for studying protein folding reactions is described, and its initial application to study the folding/unfolding reaction of a homo-hexameric enzyme 4-oxalocrotonate (4OT) is reported. This new approach involves the application of total chemical synthesis to prepare protein analogues that contain a photoreactive amino acid site-specifically incorporated into their primary amino acid sequence. To this end, a photoreactive amino acid-containing analogue of 4OT in which Pro-1 was replaced with p-benzoyl-l-phenylalanine (Bpa) was prepared. This analogue can be used to map structurally specific protein-protein interactions in 4OT’s native folded state. These photocrosslinking studies and peptide mapping results with (P1Bpa)4OT indicate that this construct is potentially useful for probing the structural properties of equilibrium and kinetic intermediates in 4OT’s folding reaction.