Descripción: The electronic structures and conformational studies of the cyclopeptides, O-methyl-α-amanitin, phalloidin and antamanide, were obtained from molecular parameters on the basis of semiempiric and ab initio methods.

Descripción: By combining the photoswitching and localization of individual fluorophores with spectroscopy on the single molecule level, we demonstrate simultaneous multicolor imaging with low crosstalk and down to 15 nm spatial resolution using only two detection color channels. The applicability of the method to biological specimens is demonstrated on mammalian cells. The combination of far-field fluorescence nanoscopy with the recording of a single switchable molecular species at a time opens up a new class of functional imaging techniques. © 2008 American Chemical Society.

Descripción: The crystal structure of the title compound, C12H8-N2O6S, has been determined by single-crystal X-ray diffraction. The compound crystallizes in the noncentrosymmetric P21 space group. The substituted aromatic ring has a slightly deformed boat conformation. The ο-NO2 and p-NO2 groups are twisted out of the plane of the phenyl ring. The unsubstituted aromatic ring is planar and the dihedral angle between the mean plane of the rings is 71.1 (2)○. Short C - H⋯O intermolecular contacts stabilize the three-dimensional structure.

Descripción: The title complex, aqua(2,2′-bipyridy-N,N′(3-thiapentanedioate-O,S,O′)zinc(II) tetrahydrate, [Zn(C4H4-O4S)(C10H8N 2)(H2O)].4H2O, is mononuclear with a coordination sphere consisting of one S, two N and three O atoms. The Zn atom is linked to a tridentate thiodiacetate ligand, a bidentate 2,2′-bipyridine ligand and an aqua ligand resulting in a slightly distorted octahedral coordination geometry. The molecular units are linked together in the crystal by an extensive hydrogen-bonding network and by intermolecular S⋯S interactions.

Descripción: The phytochemical study of two species of Jaborosa caulescens (var. caulescens and var. bipinnatifida) yielded the four new withanolides 1-4. The structures of the new compounds were determined using a combination of spectroscopic techniques (including 1D and 2D NMR) and Molecular Modeling.

Descripción: This paper describes a matrix formulation for the correlated hole theory within the framework of the domain-averaged model in many electron systems (atoms, molecules, condensed matter, etc.). General relationships between this quantity and one-particle reduced density matrices for any independent particle or correlated state functions are presented. This formulation turns out to be suitable for computational purposes due to the straightforward introduction of cumulants of two-particle reduced density matrices within the quantum field structure. Numerical calculations in selected simple molecular systems have been performed in order to determine preliminary correlated values for such a quantity.

Descripción: The three transition-metal complexes, (meso-5,7,7,12,14,14-hexa methyl-1,4,8,11-tetra azacyclo tetra decane-κ4 N)bis (perchlorato-κO)copper(II), [Cu(ClO4)2(C18H40N4)], (I), (meso-5,7,7,12,14,14-hexa methyl-1,4,8,11-tetra azacyclo tetra decane-κ4 N)bis (nitrato-κO)zinc(II), [Zn(NO3)2(C18H40N4)], (II), and aqua chlorido (meso-5,7,7,12,14,14-hexa methyl-1,4,8,11-tetraazacyclo tetra decane-κ4 N)copper(II) chloride, [CuCl(C18H40N4)(H2O)]Cl, (III), are described. The mol ecules display a very similarly distorted 4+2 octa hedral environment for the cation [located at an inversion centre in (I) and (II)], defined by the macrocycle N4 group in the equatorial sites and two further ligands in trans-axial positions [two O-ClO3 ligands in (I), two O-NO2 ligands in (II) and one chloride and one aqua ligand in (III)]. The most significant difference in mol ecular shape resides in these axial ligands, the effect of which on the intra- and inter molecular hydrogen bonding is discussed. In the case of (I), all strong hydrogen-bond donors are saturated in intra molecular inter actions, while weak inter molecular C - H⋯O contacts result in a three-dimensional network. In (II) and (III), instead, there are N - H and O - H donors left over for inter molecular inter actions, giving rise to the formation of strongly linked but weakly inter acting chains. © 2013 International Union of Crystallography.

Descripción: A new polymeric phase of zinc(II) oxydiacetate, catena-poly[[[diaquazinc(II)]-μ-oxydiacetato] hydrate], {[Zn(C4H4-O5)(H2O)2] ·H2O}n, isomorphous with the Co homologue [Hatfield, Helms, Rohrs, Singh, Wasson & Weller (1987). Proc. Indian Acad. Sci. Chem. Sci. 98, 23-31], is reported. It presents a chain-like structure, generated by ZnO6 cores which are bridged by carboxylate groups in an anti-anti conformation along the unique crystallographic b axis. The chains are held together through hydrogen-bonding interactions with the three water molecules.

Descripción: This paper reviews basic concepts of modern molecular biology with the premise that its influence in today's medicine is so important that its knowledge cannot remain limited to a few experts. I first analyze the overall structure and organization of human genes, their split nature and the flow of genetic information from DNA to protein. The role of transcriptional control in the regulation of gene expression and cell differentiation is described by introducing experimental examples that define the importance of "master" genes. Basic concepts of genetic engineering, the generation of transgenic and knock out animals and the uses of molecular biology in clinical diagnosis, paternity tests and forensic medicine are presented. Finally, I discuss the possibilities of gene therapy and the fantasies and realities of transgenesis and cloning by nuclear transplant in humans.

Descripción: Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis, J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO2 -water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. © 2009 American Institute of Physics.

Descripción: 2-Cys peroxiredoxins (2-Cys Prxs) are ubiquitous peroxidases with important roles in cellular antioxidant defense and hydrogen peroxide-mediated signaling. Post-translational modifications of conserved cysteines cause the transition from low to high molecular weight oligomers, triggering the functional change from peroxidase to molecular chaperone. However, it remains unclear how non-covalent interactions of 2-Cys Prx with metabolites modulate the quaternary structure. Here, we disclose that ATP and Mg2+ (ATP/Mg) promote the self-polymerization of chloroplast 2-Cys Prx (polypeptide 23.5 kDa) into soluble higher order assemblies (>2 MDa) that proceed to insoluble aggregates beyond 5mMATP. Remarkably, the withdrawal of ATP or Mg2+ brings soluble oligomers and insoluble aggregates back to the native conformation without compromising the associated functions. As confirmed by transmission electron microscopy, ATP/Mg drive the toroid-like decamers (diameter 13 nm) to the formation of large sphere-like particles (diameter ∼30 nm). Circular dichroism studies on ATP-labeled 2-Cys Prx reveal that ATP/Mg enhance the proportion of β-sheets with the concurrent decrease in the content of α-helices. In line with this observation, the formation of insoluble aggregates is strongly prevented by 2,2,2-trifluoroethanol, a cosolvent employed to induce α-helical conformations. We further find that the response of self-polymerization to ATP/Mg departs abruptly from that of the associated peroxidase and chaperone activities when two highly conserved residues, Arg129 and Arg152, are mutated. Collectively, our data uncover that non-covalent interactions of ATP/Mg with 2-Cys Prx modulate dynamically the quaternary structure, thereby coupling the non-redox chemistry of cell energy with redox transformations at cysteine residues. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Descripción: The major cAMP receptors in eukaryotes are the regulatory (R) subunits of PKA, an allosteric enzyme conserved in fungi through mammals. While mammals have four R-subunit genes, Saccharomyces cerevisiae has only one, Bcy1. To achieve a molecular understanding of PKA activation in yeast and to explore the evolution of cyclic-nucleotide binding (CNB) domains, we solved the structure of cAMP-bound Bcy1(168-416). Surprisingly, the relative orientation of the two CNB domains in Bcy1 is very different from mammalian R-subunits. This quaternary structure is defined primarily by a fungi-specific sequence in the hinge between the αB/αC helices of the CNB-A domain. The unique interface between the two CNB domains in Bcy1 defines the allosteric mechanism for cooperative activation of PKA by cAMP. Some interface motifs are isoform-specific while others, although conserved, play surprisingly different roles in each R-subunit. Phylogenetic analysis shows that structural differences in Bcy1 are shared by fungi of the subphylum Saccharomycotina. © 2010 Elsevier Ltd.

Descripción: Riboflavin, an essential cofactor for all organisms, is biosynthesized in plants, fungi and microorganisms. The penultimate step in the pathway is catalyzed by the enzyme lumazine synthase. One of the most distinctive characteristics of this enzyme is that it is found in different species in two different quaternary structures, pentameric and icosahedral, built from practically the same structural monomeric unit. In fact, the icosahedral structure is best described as a capsid of twelve pentamers. Despite this noticeable difference, the active sites are virtually identical in all structurally studied members. Furthermore, the main regions involved in the catalysis are located at the interface between adjacent subunits in the pentamer. Thus, the two quaternary forms of the enzyme must meet similar structural requirements to achieve their function, but, at the same time, they should differ in the sequence traits responsible for the different quaternary structures observed. Here, we present a combined analysis that includes sequence-structure and evolutionary studies to find the sequence determinants of the different quaternary assemblies of this enzyme. A data set containing 86 sequences of the lumazine synthase family was recovered by sequence similarity searches. Seven of them had resolved three-dimensional structures. A subsequent phylogenetic reconstruction by maximum parsimony (MP) allowed division of the total set into two clusters in accord with their quaternary structure. The comparison between the patterns of three-dimensional contacts derived from the known three-dimensional structures and variation in sequence conservation revealed a significant shift in structural constraints of certain positions. Also, to explore the changes in functional constraints between the two groups, site-specific evolutionary rate shifts were analyzed. We found that the positions involved in icosahedral contacts suffer a larger increase in constraints than the rest. We found eight sequence sites that would be the most important icosahedral sequence determinants. We discuss our results and compare them with previous work. These findings should contribute to refinement of the current structural data, to the design of assays that explore the role of these positions, to the structural characterization of new sequences, and to initiation of a study of the underlying evolutionary mechanisms.

Descripción: Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function. © 2012 Roman et al.

Descripción: Two copper complex solvatomorphs, namely (3,10-C-meso-3,5,7,7,10,12,14,14- octamethyl-1,4,8,11-tetraazacyclotetradecane)bis(perchlorato-κO)copper(II) 1.2-hydrate, [Cu(ClO4)2(C18H 40N4)]·1.2H2O, (I), and (3,10-C-meso-3,5,7,7,10,12,14,14-octamethyl-1,4,8,11-tetraazacyclotetradecane) bis(perchlorato-κO)copper(II), [Cu(ClO4)2(C 18H40N4)], (II), are described and compared with each other and with a third, already reported, anhydrous diastereomer, denoted (III). Both compounds present very similar centrosymmetic coordination environments, with the CuII cation lying on an inversion centre in a distorted 4+2 octahedral environment, defined by the macrocyclic N4 group in the equatorial sites and two perchlorate groups in trans-axial positions [one of the perchlorate ligands in (I) is partially disordered]. The most significant difference in molecular shape is seen in the orientation of the perchlorate anions, and the influence of this on the intramolecular hydrogen bonding is discussed. The (partially) hydrated state of (I) favours the formation of chains along [011], while the anhydrous character of (II) and (III) promotes loosely bound structures with low packing indices. © 2013 International Union of Crystallography.

Descripción: New insights into equilibrium and dynamical aspects of electron photodetachment reactions in small water clusters were given. It focuses on assessing the effects of thermal and polarization fluctuations provided by three cluster environments with different extents of spatial confinement, on the microscopic mechanisms that drive the reaction. These fluctuations, in turn, determine the characteristics of the electron localization and the subsequent detachment following photoexcitation of the probe.

Descripción: The kinetics of the reaction of 2,4-dinitrochlorobenzene (DNClB) with aniline and substituted anilines such as p-anisidine, p-toluidine and N-methylaniline have been studied in toluene. Except for N-methylaniline the reactions have shown a third order in amine rate dependence which is consistent with aggregates of the amine acting as the nucleophile. On the other hand, the reaction of DNClB with N-methylaniline under the same conditions shows a linear dependence of the second order rate coefficient, kA, vs [amine], which is consistent with the previous mechanism.

Descripción: In the present work, we have used the papillomavirus E7 oncoprotein to pursue structure-function and evolutionary studies that take into account intrinsic disorder and the conformational diversity of globular domains. The intrinsically disordered (E7N) and globular (E7C) domains of E7 show similar degrees of conservation and co-evolution. We found that E7N can be described in terms of conserved and coevolving linear motifs separated by variable linkers, while sequence evolution of E7C is compatible with the known homodimeric structure yet suggests other activities for the domain. Within E7N, inter-residue relationships such as residue co-evolution and restricted intermotif distances map functional coupling and co-occurrence of linear motifs that evolve in a coordinate manner. Within E7C, additional cysteine residues proximal to the zinc-binding site may allow redox regulation of E7 function. Moreover, we describe a conserved binding site for disordered domains on the surface of E7C and suggest a putative target linear motif. Both homodimerization and peptide binding activities of E7C are also present in the distantly related host PHD domains, showing that these two proteins share not only structural homology but also functional similarities, and strengthening the view that they evolved from a common ancestor. Finally, we integrate the multiple activities and conformations of E7 into a hierarchy of structure-function relationships. © 2012 Chemes et al.

Descripción: We have studied the hydration and diffusion of the hydroxyl radical O H0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the O H0 has one water molecule bound to the O H0 oxygen (57% of the time), and one water molecule bound to the O H0 hydrogen (88% of the time). In the hydrogen bonds between the O H0 and the water that surrounds it the O H0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the O H0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the O H0 obtained from the simulation was 7.1× 10-9 m2 s-1, which is higher than those of the water and the O H-. © 2005 American Institute of Physics.