Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as Protein Blocks (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative disallowed conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (phi, =180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (c) 2014 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 21-36, 2015.

Halogen Bonding Controls the Regioselectivity of the Deiodination of Thyroid Hormones and their Sulfate Analogues

The type1 iodothyronine deiodinase (1D-1) in liver and kidney converts the L-thyroxine (T4), a prohormone, by outer-ring (5) deiodination to biologically active 3,3,5-triiodothyronine (T3) or by inner-ring (5) deiodination to inactive 3,3,5-triiodothronine (rT3). Sulfate conjugation is an important step in the irreversible inactivation of thyroid hormones. While sulfate conjugation of the phenolic hydroxyl group stimulates the 5-deiodination of T4 and T3, it blocks the 5-deiodination of T4. We show that thyroxine sulfate (T4S) undergoes faster deiodination as compared to the parent thyroid hormone T4 by synthetic selenium compounds. It is also shown that ID-3 mimics, which are remarkably selective to the inner-ring deiodination of T4 and T3, changes the selectivity completely when T4S is used as a substrate. From the theoretical investigations, it is observed that the strength of halogen bonding increases upon sulfate conjugation, which leads to a change in the regioselectivity of ID-3 mimics towards the deiodination of T4S. It has been shown that these mimics perform both the 5- and 5-ring deiodinations by an identical mechanism.

REDUCED ORDER MODELLING OF COMBUSTION INSTABILITY IN A BACKWARD FACING STEP COMBUSTOR

This paper develops a fully coupled time domain Reduced Order Modelling (ROM) approach to model unsteady combustion dynamics in a backward facing step combustor The acoustic field equations are projected onto the canonical acoustic eigenmodes of the systems to obtain a coupled system of modal evolution equations. The heat release response of the flame is modelled using the G-equation approach. Vortical velocity fluctuations that arise due to shear layer rollup downstream of the step are modelled using a simplified 1D-advection equation whose phase speed is determined from a linear, local, temporal stability analysis of the shear layer just downstream of the step. The hydrodynamic stability analysis reveals a abrupt change in the value of disturbance phase speed from unity for Re < Re-crit to 0.5 for Re > Re-crit, where Remit for the present geometry was found to be approximate to 10425. The results for self-excited flame response show highly wrinkled flame shapes that are qualitatively similar to those seen in prior experiments of acoustically forced flames. The effect of constructive and destructive interference between the two contributions to flame surface wrinkling results in high amplitude wrinkles for the case when K-c -> 1.

Synthesis, luminescence properties and EPR investigation of hydrothermally derived uniform ZnO hexagonal rods

One-dimensional (1D) zinc oxide (ZnO) hexagonal rods have been successfully synthesized by surfactant free hydrothermal process at different temperatures. It can be found that the reaction temperature play a crucial role in the formation of ZnO uniform hexagonal rods. The possible formation processes of 1-D ZnO hexagonal rods were investigated. The zinc hydroxide acts as the morphology-formative intermediate for the formation of ZnO nanorods. Upon excitation at 325 nm, the sample prepared at 180 degrees C show several emission bands at 400 nm (similar to 3.10 eV), 420 nm (similar to 2.95 eV), 482 nm (similar to 2.57 eV) and 524 nm (similar to 2.36 eV) corresponding to different kind of defects. TL studies were carried out by pre-irradiating samples with gamma-rays ranging from 1 to 7 kGy at room temperature. A well resolved glow peak at similar to 354 degrees C was recorded which can be ascribed to deep traps. Furthermore, the defects associated with surface states in ZnO nano-structures are characterized by electron paramagnetic resonance. (C) 2014 Elsevier B.V. All rights reserved.

Compressive flow behavior of Al-Si based alloy: Role of heat treatment

The flow characteristics of a near eutectic Al-Si based cast alloy have been examined in compression at strain rates varying from 3 x 10(-4) to 10(2) s(-1) and at three different temperatures, i.e., room temperature (RT), 100 degrees C and 200 degrees C. The dependence of the flow behavior on heat treatment is studied by testing the alloy in non-heat treated (NHT) and heat treated (HT) conditions. The heat treatment has strong influence on strain rate sensitivity (SRS), strength and work hardening behavior of the alloy. It is observed that the strength of the alloy increases with increase in strain rate and it increases more rapidly above the strain rate of 10(-1) s(-1) in HT condition at all the temperatures, and at 100 degrees C and 200 degrees C in NHT condition. The thermally dependent process taking place in the HT matrix is responsible for the observed greater SRS in HT condition. The alloy in HT condition exhibits a larger work hardening rate than in NHT condition during initial stages of straining. However, the hardening rate decreases more sharply at higher strains in HT condition due to precipitate shearing and higher rate of Si particle fracture. Thermal hardening is observed at 200 degrees C in NHT condition due to precipitate formation, which results in increased SRS at higher temperatures. Thermal softening is observed in HT condition at 200 C due to precipitate coarsening, which leads to a decrease in SRS at higher temperatures. Stress simulations by a finite element method support the experimentally observed particle and matrix fracture behavior. A negative SRS and serrated flow are observed in the lower strain rate regime (3 x 10(-4)-10(-2) s(-1)) at RT and 100 degrees C, in both NHT and HT conditions. The observations show that both dynamic strain aging (DSA) and precipitate shearing play a role in serrated flow. (C) 2015 Elsevier B.V. All rights reserved.

J-Edited Pure Shift NMR for the Facile Measurement of (n)J(HH) for Specific Protons

We report a novel 1D J-edited pure shift NMR experiment (J-PSHIFT) that was constructed from a pseudo 2D experiment for the direct measurement of proton-proton scalar couplings. The experiment gives homonuclear broad-band H-1-decoupled H-1 NMR spectra, which provide a single peak for chemically distinct protons, and only retain the homonuclear-scalar-coupled doublet pattern at the chemical-shift positions of the protons in the coupled network of a specific proton. This permits the direct and unambiguous measurement of the magnitudes of the couplings. The incorporation of a 1D selective correlation spectroscopy (COSY)/ total correlation spectroscopy (TOCSY) block in lieu of the initial selective pulse, results in the exclusive detection of the correlated spectrum of a specific proton.

A spectral element for wave propagation in honeycomb sandwich construction considering core flexibility

Spectral elements are found to be extremely resourceful to study the wave propagation characteristics of structures at high frequencies. Most of the aerospace structures use honeycomb sandwich constructions. The existing spectral elements use single layer theories for a sandwich construction wherein the two face sheets vibrate together and this model is sufficient for low frequency excitations. At high frequencies, the two face sheets vibrate independently. The Extended Higher order SAndwich Plate theory (EHSaPT) is suitable for representing the independent motion of the face sheets. A 1D spectral element based on EHSaPT is developed in this work. The wave number and the wave speed characteristics are obtained using the developed spectral element. It is shown that the developed spectral element is capable of representing independent wave motions of the face sheets. The propagation speeds of a high frequency modulated pulse in the face sheets and the core of a honeycomb sandwich are demonstrated. Responses of a typical honeycomb sandwich beam to high frequency shock loads are obtained using the developed spectral element and the response match very well with the finite element results. It is shown that the developed spectral element is able to represent the flexibility of the core resulting into independent wave motions in the face sheets, for which a finite element method needs huge degrees of freedom. (C) 2015 Elsevier Ltd. All rights reserved.

Modeling of Piezocomposites using Variational Asymptotic Method

This work presents the development of piezocomposites made up of Macro Fiber Composites (MFCs) for aerospace applications and specifically involves, their computational analysis, material characterization and certain parametric studies. MFC was developed by NASA Langley Research Center in 1996 and currently is being distributed by Smart Material Co. 1] worldwide and finds applications both as an actuator as well as for sensor in various engineering applications. In this work, MFC is being modeled as an actuator and a theoretical formulation based on Variational Asymptotic Method (VAM) 2] is presented to analyse the laminates made up of MFCs. VAM minimizes the total electro-mechanical energy for the MFC laminate and approaches the exact solution asymptotically by making use of certain small parameters inherent to the problem through dimensional reduction. VAM provides closed form solutions for 1D constitutive law, recovery relations of warpings, 3D stress/strain fields and displacements and hence an ideal tool for carrying out parametric and design studies in such applications. VAM is geometrically exact and offers rigorous material characterization through cross-sectional analysis and dimensional reduction.

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.

Screening and assignment of phenylboronic acid and its anhydride formation by NMR spectroscopy

The study discusses an approach that allows simultaneous determination of boronic acid and its anhydride without the need for tedious physical separation of the mixture. The assignment of the proton spectra of monomer, dimer and trimer was achieved by combining utility of 1D and 2D experimental techniques including 2D DOSY. The differential intensities of NMR peaks and supplementary resonances were detected in low polar solvents, such as, chloroform, toluene and in a non-polar solvent benzene. A fascinating phenomenon is observed at lower temperature where there is a formation of aryl boronic acid with the disappearance of boraxine formation. (C) 2015 Elsevier B.V. All rights reserved.

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Exploring the Consequences of a Representative ``Disallowed'' Conformation of Aib on a 3(10)-Helical Fold

The structural effects of a representative ``disallowed'' conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D (H-1, C-13) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)- helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib(star)-Oxa) of 2, in a conformation (phi, psi = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)- helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations. (C) 2014 Wiley Periodicals, Inc. Biopolymers

Vacancy mediated clipping of multi-layered graphene: A precursor for 1, 2 and 3D carbon structures

Using first principles calculations, we show that the overlapping defects in bi-layer graphene (both AA-and AB-stacked) interact forming inter-layer covalent bonds, giving rise to two-dimensional (2D) clipped structures, without explicit use of functional groups. These clipped structures can be transformed into one-dimensional (1D) double wall nanotubes (DWCNT) or multi-layered three dimensional (3D) bulk structures. These clipped structures show good mechanical strength due to covalent bonding between multi-layers. Clipping also provides a unique way to simultaneously harness the conductivity of both walls of a double wall nanotube through covalently bonded scattering junctions. With additional conducting channels and improved mechanical stability, these clipped structures can lead to a myriad of applications in novel devices. (C) 2015 Elsevier Ltd. All rights reserved.

High aspect ratio, processable coordination polymer gel nanotubes based on an AIE-active LMWG with tunable emission

A new TPE based low molecular weight gelator (LMWG) which displays both AIE and MCIE phenomena in gel state has been synthesized. LMWG self-assembles to form 1D nanofibers which undergo morphology transformation to coordination polymer gel (CPG) nanotubes upon metal ion coordination. CPG shows enhanced mechanical stability along with tunable emission properties.