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

Evolutionary and structural analyses of heterodimeric proteins composed of subunits with same fold

Heterodimeric proteins with homologous subunits of same fold are involved in various biological processes. The objective of this study is to understand the evolution of structural and functional features of such heterodimers. Using a non-redundant dataset of 70 such heterodimers of known 3D structure and an independent dataset of 173 heterodimers from yeast, we note that the mean sequence identity between interacting homologous subunits is only 23-24% suggesting that, generally, highly diverged paralogues assemble to form such a heterodimer. We also note that the functional roles of interacting subunits/domains are generally quite different. This suggests that, though the interacting subunits/domains are homologous, the high evolutionary divergence characterize their high functional divergence which contributes to a gross function for the heterodimer considered as a whole. The inverse relationship between sequence identity and RMSD of interacting homologues in heterodimers is not followed. We also addressed the question of formation of homodimers of the subunits of heterodimers by generating models of fictitious homodimers on the basis of the 3D structures of the heterodimers. Interaction energies associated with these homodimers suggests that, in overwhelming majority of the cases, such homodimers are unlikely to be stable. Majority of the homologues of heterodimers of known structures form heterodimers (51.8%) and a small proportion (14.6%) form homodimers. Comparison of 3D structures of heterodimers with homologous homodimers suggests that interfacial nature of residues is not well conserved. In over 90% of the cases we note that the interacting subunits of heterodimers are co-localized in the cell. Proteins 2015; 83:1766-1786. (c) 2015 Wiley Periodicals, Inc.

Universality of the Stochastic Airy Operator

We introduce a new method for studying universality of random matrices. Let T-n be the Jacobi matrix associated to the Dyson beta ensemble with uniformly convex polynomial potential. We show that after scaling, Tn converges to the stochastic Airy operator. In particular, the top edge of the Dyson beta ensemble and the corresponding eigenvectors are universal. As a byproduct, these ideas lead to conjectured operator limits for the entire family of soft edge distributions. (C) 2015 Wiley Periodicals, Inc.

Continuum in the X-Z-Y Weak Bonds: Z= Main Group Elements

The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero-shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X-and Y-group for a particular Z-can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general. (C) 2015 Wiley Periodicals, Inc.

Effect of methylene group insertions on the structural rigidity of Aib containing helices

Nonprotein amino acids are being extensively used in the design of synthetic peptides to create new structure mimics. In this study we report the effect of methylene group insertions in a heptapeptide Boc-Ala(1)-Leu(2)-Aib(3)-Xxx(4)-Ala(5)-Leu(6)-Aib(7)-OMe which nicely folds into a mixed 3(10)-/-helical structure when Xxx= Ala. Analogs of this peptide have been made and studied by replacing central Xxx(4) residue with Glycine (-residue), -Alanine (-la), -aminobutyric acid (Gaba), and epsilon-aminocaproic acid (epsilon-Aca). NMR and circular dichroism were used to study the solution structure of these peptides. Crystals of the peptides containing alanine, -la, and Gaba reveal that increasing the number of central methylene (-CH2-) groups introduces local perturbations even as the helical structure is retained. (c) 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 720-732, 2015.

A C-0 Interior Penalty Method for a Fourth-order Variational Inequality of the Second Kind

In this article, we propose a C-0 interior penalty ((CIP)-I-0) method for the frictional plate contact problem and derive both a priori and a posteriori error estimates. We derive an abstract error estimate in the energy norm without additional regularity assumption on the exact solution. The a priori error estimate is of optimal order whenever the solution is regular. Further, we derive a reliable and efficient a posteriori error estimator. Numerical experiments are presented to illustrate the theoretical results. (c) 2015Wiley Periodicals, Inc.

Archeal lectins: An identification through a genomic search

Forty-six lectin domains which have homologues among well established eukaryotic and bacterial lectins of known three-dimensional structure, have been identified through a search of 165 archeal genomes using a multipronged approach involving domain recognition, sequence search and analysis of binding sites. Twenty-one of them have the 7-bladed -propeller lectin fold while 16 have the -trefoil fold and 7 the legume lectin fold. The remainder assumes the C-type lectin, the -prism I and the tachylectin folds. Acceptable models of almost all of them could be generated using the appropriate lectins of known three-dimensional structure as templates, with binding sites at one or more expected locations. The work represents the first comprehensive bioinformatic study of archeal lectins. The presence of lectins with the same fold in all domains of life indicates their ancient origin well before the divergence of the three branches. Further work is necessary to identify archeal lectins which have no homologues among eukaryotic and bacterial species. Proteins 2016; 84:21-30. (c) 2015 Wiley Periodicals, Inc.

Accelerating method of moments based package-board 3D parasitic extraction using FPGA

In this article, a Field Programmable Gate Array (FPGA)-based hardware accelerator for 3D electromagnetic extraction, using Method of Moments (MoM) is presented. As the number of nets or ports in a system increases, leading to a corresponding increase in the number of right-hand-side (RHS) vectors, the computational cost for multiple matrix-vector products presents a time bottleneck in a linear-complexity fast solver framework. In this work, an FPGA-based hardware implementation is proposed toward a two-level parallelization scheme: (i) matrix level parallelization for single RHS and (ii) pipelining for multiple-RHS. The method is applied to accelerate electrostatic parasitic capacitance extraction of multiple nets in a Ball Grid Array (BGA) package. The acceleration is shown to be linearly scalable with FPGA resources and speed-ups over 10x against equivalent software implementation on a 2.4GHz Intel Core i5 processor is achieved using a Virtex-6 XC6VLX240T FPGA on Xilinx's ML605 board with the implemented design operating at 200MHz clock frequency. (c) 2016 Wiley Periodicals, Inc. Microwave Opt Technol Lett 58:776-783, 2016

3D scaffold alters cellular response to graphene in a polymer composite for orthopedic applications

Graphene-based polymer nanocomposites are being studied for biomedical applications. Polymer nanocomposites can be processed differently to generate planar two-dimensional (2D) substrates and porous three-dimensional (3D) scaffolds. The objective of this work was to investigate potential differences in biological response to graphene in polymer composites in the form of 2D substrates and 3D scaffolds. Polycaprolactone (PCL) nanocomposites were prepared by incorporating 1% of graphene oxide (GO) and reduced graphene oxide (RGO). GO increased modulus and strength of PCL by 44 and 22% respectively, whereas RGO increased modulus and strength by 22 and 16%, respectively. RGO increased the water contact angle of PCL from 81 degrees to 87 degrees whereas GO decreased it to 77 degrees. In 2D, osteoblast proliferated 15% more on GO composites than on PCL whereas RGO composite showed 17% decrease in cell proliferation, which may be attributed to differences in water wettability. In 3D, initial cell proliferation was markedly retarded in both GO (36% lower) and RGO (55% lower) composites owing to increased roughness due to the presence of the protruding nanoparticles. Cells organized into aggregates in 3D in contrast to spread and randomly distributed cells on 2D discs due to the macro-porous architecture of the scaffolds. Increased cell-cell contact and altered cellular morphology led to significantly higher mineralization in 3D. This study demonstrates that the cellular response to nanoparticles in composites can change markedly by varying the processing route and has implications for designing orthopedic implants such as resorbable fracture fixation devices and tissue scaffolds using such nanocomposites. (c) 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 732-749, 2016.