The Coil-to-Helix Transition in IlvN Regulates the Allosteric Control of Escherichia coli Acetohydroxyacid Synthase I

The solution structure of IlvN, the regulatory subunit of Escherichia coil acetohydroxyacid synthase I, in the valine-bound form has been determined using high-resolution multidimensional, multinuclear nuclear magnetic resonance (NMR) methods. IlvN in the presence or absence of the effector molecule is present as a 22.5 kDa dimeric molecule. The ensemble of 20 low-energy structures shows a backbone root-mean-square deviation of 0.73 +/- 0.13 angstrom and a root-mean-square deviation of 1.16 +/- 0.13 angstrom for all heavy atoms. Furthermore, more than 98% of the backbone phi and psi dihedral angles occupy the allowed and additionally allowed regions of the Ramachandran map, which is indicative of the fact that the structures are of high stereochemical quality. Each protomer exhibits a beta alpha beta beta alpha beta alpha topology that is a characteristic feature of the ACT domain seen in metabolic enzymes. In the valine-bound form, IlvN exists apparently as a single conformer. In the free form, IlvN exists as a mixture of conformational states that are in intermediate exchange on the NMR time scale. Thus, a large shift in the conformational equilibrium is observed upon going from the free form to the bound form. The structure of the valine-bound form of IlvN was found to be similar to that of the ACT domain of the unliganded form of IlvH. Comparisons of the structures of the unliganded forms of these proteins suggest significant differences. The structural and conformational properties of IlvN determined here have allowed a better understanding of the mechanism of regulation of branched chain amino acid biosynthesis.

Experimental study of phase equilibria in the system Cu-Al-Sn

Phase equilibria in the Cu-rich corner of the ternary system Cu-Al-Sn have been re-investigated. Final equilibrium microstructures of 20 ternary alloy compositions near Cu3Al were used to refine the ternary phase diagram. The microstructures were characterized using optical microscopy (OM), x-ray diffraction (XRD), electron probe microanalysis and transmission electron microscopy. Isothermal sections at 853, 845, 833, 818, 808, 803 and 773 K have been composed. Vertical sections have been drawn at 2 and 3 at% Sn, showing beta(1) as a stable phase. Three-phase fields (alpha + beta + beta(1)) and (beta + beta(1) + gamma(1)) result from beta -> alpha + beta(1) eutectoid and beta + gamma(1) -> beta(1) peritectoid reactions forming metastable beta(1) in the binary Cu-Al. With the lowering of temperature from 853 to 818 K, these three-phase fields are shifted to lower Sn concentrations, with simultaneous shrinkage and shifting of (beta + beta(1)) two-phase field. The three-phase field (alpha + beta + gamma(1)) resulting from the binary reaction beta -> alpha + gamma(1) shifts to higher Sn contents, with associated shrinkage of the beta field, with decreasing temperature. With further reduction of temperature, a new ternary invariant reaction beta + beta(1) -> alpha + gamma(1) is observed at similar to 813 K. The beta disappears completely at 803 K, giving rise to the three-phase field (alpha + beta(1) + gamma(1)). Some general guidelines on the role of ternary additions (M) on the stability of the ordered beta(1) phase are obtained by comparing the results of this study with data in the literature on other systems in the systems group Cu-Al-M.

Cooperativity and Structural Relaxations in PVDF/PMMA Blends in the Presence of MWNTs: An Assessment through SAXS and Dielectric Spectroscopy

Intermolecular cooperativity and structural relaxations in PVDF/PMMA blends were studied in this work with respect to different surface modified (amine, similar to NH2; carboxyl acid, similar to COOH and pristine) multiwalled nanotubes (MWNTs) at 1 wt % near blend's T-g and in the vicinity of demixing using dielectric spectroscopy, SAXS, DSC, and WAXD. Intermolecular cooperativity at T-g and configurational entropy was addressed in the framework of cooperative rearranging region (CRR) at T-g. Because of specific interactions between PVDF and NH2-MWNTs, the local composition fluctuates at its average value resulting in a broad T-g. The scale of cooperativity (xi(CRR)) and the number of segments in the cooperative volume (N-CRR) is comparatively smaller in the blends with NH2-MWNTs. This clearly suggests that the number of segments cooperatively relaxing is reduced in the blends due to specific interactions leading to more heterogeneity. The configurational entropy at T-g, as derived from Vogel-Fulcher and Adam-Gibbs analysis, was reduced in the blends in presence of MWNTs manifesting in entropic penalty of the chains. The crystallite size and the amorphous miscibility was evaluated using SAXS and was observed to be strongly contingent on the surface functional groups on MWNTs. Three distinct relaxations-alpha(c) due to relaxations in the crystalline phase of PVDF, alpha(m) indicating the amorphous miscibility in PVDF/PMMA blends, and alpha beta concerning the segmental dynamics of PMMA-were observed in the blends in the temperature range T-g < T < T-c. The dynamics as well as the nature of relaxations were observed to be dependent the surface functionality on the MWNTs. The dielectric permittivity was also enhanced in presence of MWNTs, especially with NH2-MWNTs, with minimal losses. The influence of the MWNTs on the spherulite size and crystalline morphology of the blends was also confirmed by POM and SEM.

UNIQUENESS OF SOLUTIONS TO SCHRODINGER EQUATIONS ON H-TYPE GROUPS

This paper deals with the Schrodinger equation i partial derivative(s)u(z, t; s) - Lu(z, t; s) = 0; where L is the sub-Laplacian on the Heisenberg group. Assume that the initial data f satisfies vertical bar f(z, t)vertical bar less than or similar to q(alpha)(z, t), where q(s) is the heat kernel associated to L. If in addition vertical bar u(z, t; s(0))vertical bar less than or similar to q(beta)(z, t), for some s(0) is an element of R \textbackslash {0}, then we prove that u(z, t; s) = 0 for all s is an element of R whenever alpha beta < s(0)(2). This result holds true in the more general context of H-type groups. We also prove an analogous result for the Grushin operator on Rn+1.

Comparative Study of Protein Unfolding in Aqueous Urea and Dimethyl Sulfoxide Solutions: Surface Polarity, Solvent Specificity, and Sequence of Secondary Structure Melting

Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here, we alter the solvent environment in a controlled manner by choosing two different cosolvents of water, urea, and dimethyl sulfoxide (DMSO) and study unfolding of four different proteins to understand the respective sequence of melting by computer simulation methods. We indeed find interesting differences in the sequence of melting of alpha helices and beta sheets in these two solvents. For example, in 8 M urea solution, beta-sheet parts of a protein are found to unfold preferentially, followed by the unfolding of alpha helices. In contrast, 8 M DMSO solution unfolds alpha helices first, followed by the separation of beta sheets for the majority of proteins. Sequence of unfolding events in four different alpha/beta proteins and also in chicken villin head piece (HP-36) both in urea and DMSO solutions demonstrate that the unfolding pathways are determined jointly by relative exposure of polar and nonpolar residues of a protein and the mode of molecular action of a solvent on that protein.

A Genetic Analysis of the Functional Interactions within Mycobacterium tuberculosis Single-Stranded DNA Binding Protein

Single-stranded DNA binding proteins (SSBs) are vital in all organisms. SSBs of Escherichia coli (EcoSSB) and Mycobacterium tuberculosis (MtuSSB) are homotetrameric. The N-terminal domains (NTD) of these SSBs (responsible for their tetramerization and DNA binding) are structurally well defined. However, their C-terminal domains (CTD) possess undefined structures. EcoSSB NTD consists of beta 1-beta 1'-beta 2-beta 3-alpha-beta 4-beta 45(1)-beta 45(2)-beta 5 secondary structure elements. MtuSSB NTD includes an additional beta-strand (beta 6) forming a novel hook-like structure. Recently, we observed that MtuSSB complemented an E. coli Delta ssb strain. However, a chimeric SSB (m beta 4-beta 5), wherein only the terminal part of NTD (beta 4-beta 5 region possessing L-45 loop) of EcoSSB was substituted with that from MtuSSB, failed to function in E. coli in spite of its normal DNA binding and oligomerization properties. Here, we designed new chimeras by transplanting selected regions of MtuSSB into EcoSSB to understand the functional significance of the various secondary structure elements within SSB. All chimeric SSBs formed homotetramers and showed normal DNA binding. The m beta 4-beta 6 construct obtained by substitution of the region downstream of beta 5 in m beta 4-beta 5 SSB with the corresponding region (beta 6) of MtuSSB complemented the E. coli strain indicating a functional interaction between the L-45 loop and the beta 6 strand of MtuSSB.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Isolated singularities of polyharmonic operator in even dimension

We consider the equation Delta(2)u = g(x, u) >= 0 in the sense of distribution in Omega' = Omega\textbackslash {0} where u and -Delta u >= 0. Then it is known that u solves Delta(2)u = g(x, u) + alpha delta(0) - beta Delta delta(0), for some nonnegative constants alpha and beta. In this paper, we study the existence of singular solutions to Delta(2)u = a(x) f (u) + alpha delta(0) - beta Delta delta(0) in a domain Omega subset of R-4, a is a nonnegative measurable function in some Lebesgue space. If Delta(2)u = a(x) f (u) in Omega', then we find the growth of the nonlinearity f that determines alpha and beta to be 0. In case when alpha = beta = 0, we will establish regularity results when f (t) <= Ce-gamma t, for some C, gamma > 0. This paper extends the work of Soranzo (1997) where the author finds the barrier function in higher dimensions (N >= 5) with a specific weight function a(x) = |x|(sigma). Later, we discuss its analogous generalization for the polyharmonic operator.

Deformation, Phase Transformation and Recrystallization in the Shear Bands Induced by High-Strain Rate Loading in Titanium and its Alloys

alpha-titanium and its alloys with a dual-phase structure (alpha+beta) were deformed dynamically under strain rate of about 10(4) s(-1). The formation and microstructural evolution of the localized shear bands were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The results reveal that both the strain and strain rate should be considered simultaneously as the mechanical conditions for shear band formation, and twinning is an important mode of deformation. Both experimental and calculation show that the materials within the bands underwent a superhigh strain rate (9 x 10(5) s(-1)) deformation, which is two magnitudes of that of average strain rate required for shear band formation; the dislocations in the bands can be constricted and developed into cell structures; the phase transformation from alpha to alpha(2) within the bands was observed, and the transformation products (alpha(2)) had a certain crystallographic orientation relationship with their parent; the equiaxed grains with an average size of 10 mu m in diameter observed within the bands are proposed to be the results of recrystallization.

The Displacement and Strain Field of Three-Dimensional Rheologic Model of Earthquake Preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.

The Displacement and Strain Field of Three-Dimensional Rheologic Model of Earthquake Preparation

Based on the three-dimensional elastic inclusion model proposed by Dobrovolskii, we developed a rheological inclusion model to study earthquake preparation processes. By using the Corresponding Principle in the theory of rheologic mechanics, we derived the analytic expressions of viscoelastic displacement U(r, t) , V(r, t) and W(r, t), normal strains epsilon(xx) (r, t), epsilon(yy) (r, t) and epsilon(zz) (r, t) and the bulk strain theta (r, t) at an arbitrary point (x, y, z) in three directions of X axis, Y axis and Z axis produced by a three-dimensional inclusion in the semi-infinite rheologic medium defined by the standard linear rheologic model. Subsequent to the spatial-temporal variation of bulk strain being computed on the ground produced by such a spherical rheologic inclusion, interesting results are obtained, suggesting that the bulk strain produced by a hard inclusion change with time according to three stages (alpha, beta, gamma) with different characteristics, similar to that of geodetic deformation observations, but different with the results of a soft inclusion. These theoretical results can be used to explain the characteristics of spatial-temporal evolution, patterns, quadrant-distribution of earthquake precursors, the changeability, spontaneity and complexity of short-term and imminent-term precursors. It offers a theoretical base to build physical models for earthquake precursors and to predict the earthquakes.

Hydrazides and hydrazones as versatile Michael-Donors for iminium-catalyzed conjugate addition reactions

396 : il., graf.

Activación de aldehídos a,b-insaturados mediante aminocatálisis en procesos enantioselectivos. Cicloadiciones (3+2) y reacciones en cascada Michael/Henry

During the research that it is summarized in the present memory, the activation of enals via iminium ion catalysis in different transformations has been studied. Firstly, a 1,3-dipolar cycloaddition between stable azomethine ylides and a,b-unsaturated aldehydes catalyzed by a chiral imidazolidinone derivative has been optimized. Employing this methodology we have synthesized a large range of densely substituted pyrroloisoquinolines and pyrrolophthalazines with good yields and high values of diastereo- and enantioselectivity. Moreover, a mechanistic study has been carried out based on DFT calculations and experimental data which have allowed us to propose that the (3+2) cycloaddition reaction follows a sequential Michael addition/Mannich cyclization pathway. The formation of the iminium ion as a result of the condensation between the a,b-unsaturated aldehyde and the catalyst plays an essential role, regarding both reactivity and stereoselectivity. On the other hand we have developed a methodology to carry out a cascade Michael/Henry reaction followed by a sequential dehydration. Starting from simple substrates (2-nitromethylacrilates and a,b-unsaturated aldehydes) and employing a prolinol-derivative catalyst a series of quiral nitrocyclohexadienes have been synthesized.

Asymmetric organocatalytic cascade reactions

302 p. : gráf.