Role of Water in the Enzymatic Catalysis: Study of ATP plus AMP -> 2ADP Conversion by Adenylate Kinase

The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP. molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a. phosphate transfer and then the release of two ADP molecules. We have computed a novel two-dimensional configurational free energy surface (2DCFES), with one reaction coordinate each for the LID and the NMP domain motions, while considering explicit water interactions. Our computed 2DCFES clearly reveals the existence of a stable half-open half-closed (HOHC) intermediate stale of the enzyme. Cycling of the enzyme through the HOHC state reduces the conformational free energy barrier for. the reaction by about 20 kJ/mol. We find that the stability of the HOHC state (missed in all earlier studies with implicit solvent model) is largely because of the increase of specific interactions of the polar amino acid side chains with water, particularly with the arginine and the histidine residues. Free energy surface of the LID domain is rather rugged, which can conveniently slow down LID's conformational motion, thus facilitating a new substrate capture after the product release in the catalytic cycle.

Stability of Filaments in Star-Forming Clouds and the Formation of Prestellar Cores in Them

The exact process(es) that generate(s) dense filaments which then form prestellar cores within them is unclear. Here we study the formation of a dense filament using a relatively simple set-up of a pressure-confined, uniform-density cylinder. We examine if its propensity to form a dense filament and further, to the formation of prestellar cores along this filament, bears on the gravitational state of the initial volume of gas. We report a radial collapse leading to the formation of a dense filamentary cloud is likely when the initial volume of gas is at least critically stable (characterised by the approximate equality between the mass line-density for this volume and its maximum value). Though self-gravitating, this volume of gas, however, is not seen to be in free-fall. This post-collapse filament then fragments along its length due to the growth of a Jeans-like instability to form prestellar cores. We suggest dense filaments in typical star-forming clouds classified as gravitationally super-critical under the assumption of: (i) isothermality when in fact, they are not, and (ii) extended radial profiles as against pressure-truncated, that significantly over-estimates their mass line-density, are unlikely to experience gravitational free-fall. The radial density and temperature profile derived for this post-collapse filament is consistent with that deduced for typical filamentary clouds mapped in recent surveys of nearby star-forming regions.

``Conformational Simulation'' of Sulfamethizole by Molecular Complexation and Insights from Charge Density Analysis: Role of Intramolecular S center dot center dot center dot O Chalcogen Bonding

Intramolecular S center dot center dot center dot O chalcogen bonding and its potential to lock molecular conformation have been examined in the crystal forms of sulfamethizole, a sulfonamide antibiotic. Molecular complexes of sulfamethizole, including salts and cocrystal, have been synthesized, and their crystal structures were analyzed in order to examine the possible conformational preferences of the molecule in various ionic states and supramolecular environments (neutral/cocrystal, anionic salt, and cationic salt forms). The electrostatic potential mapped on Hirshfeld surfaces generated for these crystal forms provides insights into the possible binding modes of the drug in different environments. Further, the observed conformation locking feature has been rationalized in terms of the experimental charge density features of the intramolecular S center dot center dot O chalcogen bonding in sulfamethizole. The study quantitatively illustrates and rationalizes an intriguing case of a local minimum of molecular conformation being exclusively preferred over the global minimum, as it facilitates more efficient intermolecular interactions in a supramolecular environment.

Numerical study of bluff body flow structures

Our recent progress in numerical studies of bluff body flow structures and a new method for the numerical analysis of near wake flow field for high Reynolds number flow are introduced. The paper consists of three parts. In part one, the evolution of wake vortex structure and variation of forces on a flat plate in harmonic oscillatory flows and in in-line steady-harmonic combined flows are presented by an improved discrete vortex method, as the Keulegan-Carpenter number (KC) varies from 2 to 40 and ratios of U-m to U-0 are of O(10(-1)), O(10) and O(10), respectively. In part 2, a domain decomposition hybrid method, combining the finite-difference and vortex methods for numerical simulation of unsteady viscous separated flow around a bluff body, is introduced. By the new method, some high resolution numerical visualization on near wake evolution behind a circular cylinder at Re = 10(2), 10(3) and 3 x 10(3) are shown. In part 3, the mechanism and the dynamic process for the three-dimensional evolution of the Karman vortex and vortex filaments in braid regions as well as the early features of turbulent structure in the wake behind a circular cylinder are presented numerically by the vortex dynamics method.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.

In situ study of nanostructure and morphological development during the crystal-mesophase transition of poly(di-n-hexylsilane) and poly(di-n-butylsilane) by X-ray and hot-stage AFM

Nanostructure and morphology and their development of poly(di-n-hexylsilane) (PDHS) and poly(di-n-butylsilane) (PDBS) during the crystal-mesophase transition are investigated using small angle X-ray scattering (SAXS), wide angle X-ray diffraction and hot-stage atomic force microscopy. At room temperature, PDHS consists of stacks of lamellae separated by mesophase layers, which can be well accounted using an ideal two-phase model. During the crystal-mesophase transition, obvious morphological changes are observed due to the marked changes in main chain conformation and intermolecular distances between crystalline phase and mesophase. In contrast to PDHS, the lamellae in PDBS barely show anisotropy in dimensions at room temperature. The nonperiodic structure and rather small electronic density fluctuation in PDBS lead to the much weak SAXS. The nonperiodic structure is preserved during the crystal-mesophase transition because of the similarity of main chain conformation and intermolecular distances between crystalline phase and mesophase.

Surface-enhanced resonance Raman spectroscopic study of yeast iso-1-cytochrome c and its mutant

The structural stability and redox properties of yeast iso-1-cytochrome c and its mutant, F82H, were studied by surface-enhanced resonance Raman scattering (SERRS) spectroscopy. Phenylalanine, which exists at the position-82 in yeast iso-1-cytochrome c, is replaced by histidine in the mutant. The SERRS spectra of the proteins on the bare silver electrodes indicate that the mutant possesses a more stable global structure with regard to the adsorption-induced conformational alteration. The redox potential of the mutant negatively shifts by about 400 mV, relative to that of yeast iso-1-cytochrome c. This is ascribed to axial ligand switching and higher solvent accessibility of the heme iron in the mutant during the redox reactions.

Resonance Raman spectroscopic study of cytochrome c mutants

The spectroscopic characteristics of cytochrome c(WT) and its mutants(Y67F and N521) in the low frequency region were studied by Resonance Raman technique. The results show that the replacement of phenylalanine for Tyr 67 in WT had a very slight effect on the hydrogen-bonding and conformation of the amino acid residues around propionic acid side chains of heme group. However, large effects on the hydrogen-bonding of internal water with its surrounding amino acid residues and hydrophobility of the home cavity were observed as Asn 52 was substituted with isoleucine, which resulted in conformational regulations of home group and surrounding amino acid residues.

AN INFRARED SPECTROSCOPIC STUDY OF THE STRUCTURAL PHASE-TRANSITION IN THE PEROVSKITE-TYPE LAYER COMPOUND [N-C16H33NH3]2COCL4

The solid-solid phase transitions in the perovskite-type layer compound [n- C16H33NH3]2CoCl4 have been studied by infrared spectroscopy. A new phase transition at 340 K was found by comparison with differential scanning calorimetry results. A temperature dependence study of the infrared spectra provides evidence of the occurrence of structural phase transitions related to the dynamics of the alkylammonium ions and hydrogen bonds. The main transition at 374 K corresponds to the conformational order-disorder change in the chain, which probably couples with reorientational motions of the NH3 polar heads. GTG or GTG' defects appear in the high temperature disordered phase.

Anti-AIDS agents 81. Design, synthesis, and structure-activity relationship study of betulinic acid and moronic acid derivatives as potent HIV maturation inhibitors.

In our continuing study of triterpene derivatives as potent anti-HIV agents, different C-3 conformationally restricted betulinic acid (BA, 1) derivatives were designed and synthesized in order to explore the conformational space of the C-3 pharmacophore. 3-O-Monomethylsuccinyl-betulinic acid (MSB) analogues were also designed to better understand the contribution of the C-3' dimethyl group of bevirimat (2), the first-in-class HIV maturation inhibitor, which is currently in phase IIb clinical trials. In addition, another triterpene skeleton, moronic acid (MA, 3), was also employed to study the influence of the backbone and the C-3 modification toward the anti-HIV activity of this compound class. This study enabled us to better understand the structure-activity relationships (SAR) of triterpene-derived anti-HIV agents and led to the design and synthesis of compound 12 (EC(50): 0.0006 microM), which displayed slightly better activity than 2 as a HIV-1 maturation inhibitor.

Study of electron-beam propagation through preionized dense foam plasmas

The transport of an intense electron-beam produced by the Vulcan petawatt laser through dense plasmas has been studied by imaging with high resolution the optical emission due to electron transit through the rear side of coated foam targets. It is observed that the MeV-electron beam undergoes strong filamentation and the filaments organize themselves in a ringlike structure. This behavior has been modeled using particle-in-cell simulations of the laser-plasma interaction as well as of the transport of the electron beam through the preionized plasma. In the simulations the filamentary structures are reproduced and attributed to the Weibel instability.

Role of conformational constraints of position 7 of the disulphide bridge of h-alpha-CGRP derivatives in their agonist versus antagonist properties

Previous structure-activity studies have shown that the disulphide bridge of calcitonin gene-related peptide (CGRP) is important for the highly potent, CGRP receptor-mediated effects of this peptide. In this study penicillamine (Pen) was substituted for one or both of the cysteinyl residues to determine conformational and topographical properties of the disulphide bridge favourable for binding to CGRP receptors and/or receptor activation. Pen constrains the conformational flexibility of disulphide bridges in other peptides. Binding affinities were measured using a radioligand binding assay with membranes prepared from pig coronary arteries and I-125-h-alpha-CGRP. Functional effects were characterized using a previously reported pig coronary artery relaxation bioassay. The binding affinity of [Pen(2)]h-alpha-CGRP was not significantly different from that of h-alpha-CGRP. All other analogues showed reduced affinity for CGRP receptors. [Pen(2)]h-alpha-CGRP also caused relaxation of coronary arteries. The remaining analogues either caused relaxation with significantly reduced potency or failed to relax the arteries at concentrations up to 1 x 10(-5) M. All analogues that did not relax coronary arteries contained a D-Pen in position 7 and inhibited CGRP-induced relaxation. [D-Pen(2,7)]h-alpha- CGRP was the most potent antagonist with a K-B value of 630 nM. This affinity is similar to that of the classical CGRP receptor antagonist, h-alpha-CGRP(8-37), on these arteries (K-B, 212 nM). These studies show that modifying the topography of the disulphide bridge can cause large and variable effects on ligand binding and activation of CGRP receptors. The contribution of position 7 to the conformation and topography of the disulphide bridge of h-alpha-CGRP is crucial to the future design of agonists of CGRP receptors. Furthermore, position 7 is important for the development of new CGRP receptor antagonists with structures based on the whole sequence of h-alpha-CGRP.

The Effect of Tacticity on the Conformational Properties of Poly(1-olefin sulfone)s

The effect of tacticity on the conformational properties of poly(olefin sulfone)s was studied. Tactic polymers, prepared from racemic thiirane monomers using chiral inititators were compared with atactic polymers prepared by free radical co-polymerisation of the 1-olefin with sulfur dioxide. Analysis of the XRD patterns showed that the tactic polymers formed more ordered structures in the bulk with longer layer spacings, consistent with a model in which their side chains meet at the tips in contrast with the atactic polymers whose side chains interdigitate. 13C MAS nmr experiments suggest that as tacticity increases so too does the proportion of C-S bonds in the gauche conformation, however the proportion of S-C bonds in the trans conformation falls, in contrast to a reported molecular mechanics study. Finally, DSC measurements on the polymers with longer side chains showed the presence of two endotherms on heating, illustrating definite liquid crystalline behaviour.

Study of the transamidative ring expansion of N--halogenoalkyl--lactams of alkyl chain lengths 2–12 in liquid ammonia and other liquid amines: syntheses of 7-, 8- and 9-membered 1,5-diaza cyclic ketones, including routes to (±)-dihydroperiphylline and (±)-celabenzine

N-(3-Halogenopropyl)-4-phenylazetidin-2-ones undergo amination in liquid ammonia followed by transamidative ring expansion to give the eight-membered 4-phenyl -1,5-diazacyclooctan-2-one in excellent yield. Ring expansion of the amines in liquid ammonia is found to be much more effective than in hydrocarbon solvents. Formation of 7-, 8-, and 9-membered azalactams from the requisite -halogenoalkyl--lactams is an excellent synthetic process, though it is not applicable to 10membered rings. In the cases of rings of 13-, 15- and 17-members, although amination and apparent expansion takes place, the large rings appear not to be stable to ammonia and the final products are acyclic amides. N-[4-Halogenobut-2(Z)-enyl]-4-phenylazetidin-2-one satisfactorily forms a 9-membered (Z)-olefinic azalactam, but the (E)-isomer gives an acyclic amino amide. By using alkyl-substituted -lactam side-chains, C-substituted medium rings can be obtained; the relative instability of N-acyl -lactams to ammonia, however, leads to acylamino amides rather than expanded rings.Employing ethylamine in place of ammonia, it is shown that N-ethylated azalactams are formed satisfactorily, and using allylamine, N-allyl medium rings capable of further elaboration are obtained. The chemistry of these systems is discussed. Using transamidation in liquid ammonia, a short synthesis of the 9-membered spermidine alkaloid (±)-dihydroperiphylline is reported. Synthesis of key intermediates, whose transformation into the 13-membered alkaloids of the celabenzine group has already been effected, has been carried out.X-Ray single-crystal structure determinations for 4-phenyl-1,5-diazacyclononan-2-one, trans-4-phenyl-8-methyl-1,5-diazacyclooctan-2-one and (Z)-4-phenyl-1,5-diazacyclonon-7-en-2-one are reported, and comment is made on certain conformational features.