Turbulence-induced melting of a nonequilibrium vortex crystal in a forced thin fluid film

To gain a better understanding of recent experiments on the turbulence-induced melting of a periodic array of vortices in a thin fluid film, we perform a direct numerical simulation of the two-dimensional Navier-Stokes equations forced such that, at low Reynolds numbers, the steady state of the film is a square lattice of vortices. We find that as we increase the Reynolds number, this lattice undergoes a series of nonequilibrium phase transitions, first to a crystal with a different reciprocal lattice and then to a sequence of crystals that oscillate in time. Initially, the temporal oscillations are periodic; this periodic behaviour becoming more and more complicated with increasing Reynolds number until the film enters a spatially disordered nonequilibrium statistical steady state that is turbulent. We study this sequence of transitions using fluid-dynamics measures, such as the Okubo-Weiss parameter that distinguishes between vortical and extensional regions in the flow, ideas from nonlinear dynamics, e.g. Poincare maps, and theoretical methods that have been developed to study the melting of an equilibrium crystal or the freezing of a liquid and that lead to a natural set of order parameters for the crystalline phases and spatial autocorrelation functions that characterize short- and long-range order in the turbulent and crystalline phases, respectively.

Nanoscale Heterostructures with Molecular-Scale Single-Crystal Metal Wires

Creating nanoscale heterostructures with molecular-scale (<2 nm) metal wires is critical for many applications and remains a challenge. Here, we report the first time synthesis of nanoscale heterostructures with single-crystal molecular-scale Au nanowires attached to different nanostructure substrates. Our method involves the formation of Au nanoparticle seeds by the reduction of rocksalt AuCl nanocubes heterogeneously nucleated on the Substrates and subsequent nanowire growth by oriented attachment of Au nanoparticles from the Solution phase. Nanoscale heterostructures fabricated by such site-specific nucleation and growth are attractive for many applications including nanoelectronic device wiring, catalysis, and sensing.

Inhibition of a Protein Tyrosine Phosphatase Using Mesoporous Oxides

The feasibility of utilizing mesoporous matrices of alumina and silica for the inhibition of enzymatic activity is presented here. These studies were performed on a protein tyrosine phosphatase by the name chick retinal tyrosine phosphotase-2 (CRYP-2), a protein that is identical in sequence to the human glomerular epithelial protein-1 and involved in hepatic carcinoma. The inhibition of CRYP-2 is of tremendous therapeutic importance. Inhibition of catalytic activity was examined using the Sustained delivery of p-nitrocatechol sulfate (pNCS) from bare and amine functionalized mesoporous silica (MCM-48) and mesoporous alumina (Al2O3). Among the various mesoporous matrices employed, amine functionalized MCM-48 exhibited the best release of pNCS and also inhibition of CRYP-2. The maximum speed of reaction nu(max) (= 160 +/- 10 mu mol/mnt/mg) and inhibition constant K-i (=85.0 +/- 5.0 mu mol) estimated using a competitive inhibition model were Found to be very similar to inhibition activities of protein tyrosine phosphatases using other methods.

How Effective Is The Data On Co-Occurrence Of Domains In Multi-Domain Proteins In Prediction Of Protein-Protein Interactions?

We explore the fuse of information on co-occurrence of domains in multi-domain proteins in predicting protein-protein interactions. The basic premise of our work is the assumption that domains co-occurring in a polypeptide chain undergo either structural or functional interactions among themselves. In this study we use a template dataset of domains in multidomain proteins and predict protein-protein interactions in a target organism. We note that maximum number of correct predictions of interacting protein domain families (158) is made in S. cerevisiae when the dataset of closely related organisms is used as the template followed by the more diverse dataset of bacterial proteins (48) and a dataset of randomly chosen proteins (23). We conclude that use of multi-domain information from organisms closely-related to the target can aid prediction of interacting protein families.

Stabilizing High-Energy Crystal Structure in Silver Nanowires with Underpotential Electrochemistry

We demonstrate that commonly face-centered cubic (fcc) metallic nanowires can be stabilized in hexagonal structures even when their surface energy contribution is relatively small. With a modified electrochemical growth process, we have grown purely single-crystalline 4H silver nanowires (AgNWs) of diameters as large as 100 nm within nanoporous anodic alumina and polycarbonate templates. The growth process is not limited by the/Ag Nernst equilibrium potential, and time-resolved imaging with high-resolution transmission electron microscopy (TEM) indicates a kinematically new mechanism of nanowire growth. Most importantly, our experiments aim to separate the effects of confinement and growth conditions on the crystal structure of nanoscale systems.

Structural Studies on the Second Mycobacterium smegmatis Dps: Invariant and Variable Features of Structure, Assembly and Function

A second DNA binding protein from stationary-phase cells of Mycobacterium smegmatis (MsDps2) has been identified from the bacterial genome. It was cloned, expressed and characterised and its crystal structure was determined. The core dodecameric structure of MsDps2 is the same as that of the Dps from the organism described earlier (MsDps1). However, MsDps2 possesses a long N-terminal tail instead of the C-terminal tail in MsDps1. This tail appears to be involved in DNA binding. It is also intimately involved in stabilizing the dodecamer. Partly on account of this factor, MsDps2 assembles straightway into the dodecamer, while MsDps1 does so on incubation after going through an intermediate trimeric stage. The ferroxidation centre is similar in the two proteins, while the pores leading to it exhibit some difference. The mode of sequestration of DNA in the crystalline array of molecules, as evidenced by the crystal structures, appears to be different in MsDps1 and MsDps2, highlighting the variability in the mode of Dps–DNA complexation. A sequence search led to the identification of 300 Dps molecules in bacteria with known genome sequences. Fifty bacteria contain two or more types of Dps molecules each, while 195 contain only one type. Some bacteria, notably some pathogenic ones, do not contain Dps. A sequence signature for Dps could also be derived from the analysis.

Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein

Acyl carrier protein (ACIP) plays a central role in many metabolic processes inside the cell, and almost 4% of the total enzymes inside the cell require it as a cofactor. Here, we report self-acylation properties in ACPs from Plasmodium falciparum and Brassica napus that are essential components of type II fatty acid biosynthesis (FAS II), disproving the existing notion that this phenomenon is restricted only to ACPs involved in polyketide biosynthesis. We also provide strong evidence to suggest that catalytic self-acylation is intrinsic to the individual ACP. Mutational analysis of these ACPs revealed the key residue(s) involved in this phenomenon. We also demonstrate that these FAS 11 ACPs exhibit a high degree of selectivity for self-acylation employing only dicarboxylic acids as substrates. A plausible mechanism for the self-acylation reaction is also proposed.

Synergistic crystal facet engineering and structural control of WO3 films exhibiting unprecedented photoelectrochemical performance

WO3 nanoplate arrays with (002) oriented facets grown on fluorine doped SnO2 (FTO) glass substrates are tailored by tuning the precursor solution via a facile hydrothermal method. A 2-step hydrothermal method leads to the preferential growth of WO3 film with enriched (002) facets, which exhibits extraordinary photoelectrochemical (PEC) performance with a remarkable photocurrent density of 3.7 mA cm–2 at 1.23 V vs. revisable hydrogen electrode (RHE) under AM 1.5 G illumination without the use of any cocatalyst, corresponding to ~93% of the theoretical photocurrent of WO3. Density functional theory (DFT) calculations together with experimental studies reveal that the enhanced photocatalytic activity and better photo-stability of the WO3 films are attributed to the synergistic effect of highly reactive (002) facet and nanoplate structure which facilitates the photo–induced charge carrier separation and suppresses the formation of peroxo-species. Without the use of oxygen evolution cocatalysts, the excellent PEC performance, demonstrated in this work, by simply tuning crystal facets and nanostructure of pristine WO3 films may open up new opportunities in designing high performance photoanodes for PEC water splitting.

Three-dimensional structure of heat shock protein 90 from Plasmodium falciparum: molecular modelling approach to rational drug design against malaria

We have recently implicated heat shock protein 90 from Plasmodium falciparum (PfHsp90) as a potential drug target against malaria. Using inhibitors specific to the nucleotide binding domain of Hsp90, we have shown potent growth inhibitory effects on development of malarial parasite in human erythrocytes. To gain better understanding of the vital role played by PfHsp90 in parasite growth, we have modeled its three dimensional structure using recently described full length structure of yeast Hsp90. Sequence similarity found between PfHsp90 and yeast Hsp90 allowed us to model the core structure with high confidence. The superimposition of the predicted structure with that of the template yeast Hsp90 structure reveals an RMSD of 3.31 angstrom. The N-terminal and middle domains showed the least RMSD (1.76 angstrom) while the more divergent C-terminus showed a greater RMSD (2.84 angstrom) with respect to the template. The structure shows overall conservation of domains involved in nucleotide binding, ATPase activity, co-chaperone binding as well as inter-subunit interactions. Important co-chaperones known to modulate Hsp90 function in other eukaryotes are conserved in malarial parasite as well. An acidic stretch of amino acids found in the linker region, which is uniquely extended in PfHsp90 could not be modeled in this structure suggesting a flexible conformation. Our results provide a basis to compare the overall structure and functional pathways dependent on PfHsp90 in malarial parasite. Further analysis of differences found between human and parasite Hsp90 may make it possible to design inhibitors targeted specifically against malaria.

The generalized anomeric effect in the 1,3-thiazolidines: Evidence forboth sulphur and nitrogen as electron donors. Crystal structures of various N-acylthiazolidines including mercury(II) complexes. Possible relevance to penicillin action

Evidence for the generalized anomeric effect (GAE) in the N-acyl-1,3-thiazolidines, an important structural motif in the penicillins, was sought in the crystal structures of N-(4-nitrobenzoyl)-1,3-thiazolidine and its (2:1) complex with mercuric chloride, N-acetyl-2-phenyl-1,3-thiazolidine, and the (2:1) complex of N-benzoyl-1,3-thiazolidine with mercuric bromide. An inverse relationship was generally observed between the. C-2-N and C-2-S bond lengths of the thiazolidine ring, supporting the existence of the GAE. (Maximal bond length changes were similar to 0.04 angstrom for C-2-N-3, S-1-C-2, and similar to 0.08 angstrom for N-3-C-6.) Comparison with N-acylpyrrolidines and tetrahydrothiophenes indicates that both the nitrogen-to-sulphur and sulphur-to-nitrogen GAE's operate simultaneously in the 1,3-thiazolidines, the former being dominant. (This is analogous to the normal and exo-anomeric effects in pyranoses, and also leads to an interesting application of Baldwin's rules.) The nitrogen-to-sulphur GAE is generally enhanced in the mercury(II) complexes (presumably via coordination at the sulphur); a 'competition' between the GAE and the amide resonance of the N-acyl moiety is apparent. There is evidence for a 'push-pull' charge transfer between the thiazolidine moieties in the mercury(II) complexes, and for a 'back-donation' of charge from the bromine atoms to the thiazolidine moieties in the HgBr2 complex. (The sulphur atom appears to be sp(2) hybridised in the mercury(II) complexes, possibly for stereoelectronic reasons.) These results are apparently relevant to the mode of action of the penicillins. (c) 2006 Elsevier B.V. All rights reserved.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Role of Magmas in protein transport and human mitochondria biogenesis

Magmas, a conserved mammalian protein essential for eukaryotic development, is overexpressed in prostate carcinomas and cells exposed to granulocyte-macrophage colony-stimulating factor (GM-CSF). Reduced Magmas expression resulted in decreased proliferative rates in cultured cells. However, the cellular function of Magmas is still elusive. In this report, we have showed that human Magmas is an ortholog of Saccharomyces cerevisiae Pam16 having similar functions and is critical for protein translocation across mitochondrial inner membrane. Human Magmas shows a complete growth complementation of delta pam16 yeast cells at all temperatures. On the basis of our analysis, we report that Magmas localizes into mitochondria and is peripherally associated with inner mitochondrial membrane in yeast and humans. Magmas forms a stable subcomplex with J-protein Pam18 or DnaJC19 through its C-terminal region and is tethered to TIM23 complex of yeast and humans. Importantly, amino acid alterations in Magmas leads to reduced stability of the subcomplex with Pam18 that results in temperature sensitivity and in vivo protein translocation defects in yeast cells. These observations highlight the central role of Magmas in protein import and mitochondria biogenesis. In humans, absence of a functional DnaJC19 leads to dilated cardiac myophathic syndrome (DCM), a genetic disorder with characteristic features of cardiac myophathy and neurodegeneration. We propose that the mutations resulting in decreased stability of functional Magmas:DnaJC19 subcomplex at human TIM23 channel leads to impaired protein import and cellular respiration in DCM patients. Together, we propose a model showing how Magmas:DnaJC19 subcomplex is associated with TIM23 complex and thus regulates mitochondrial import process.

New measures for estimating surface complementarity and packing at protein-protein interfaces

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein-protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein-protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein-protein contacts, especially from large protein complexes and large-scale structural studies(http://pallab.serc. iisc.ernet.in/nip_nsc). (C) 201 Federation of European Biochemical Societies. Published by Elsevier B. V. All rights reserved.

Role of an RNA polymerase interacting protein, MsRbpA, from Mycobacterium smegmatis in phenotypic tolerance to rifampicin

Rifampicin and its derivatives are at the forefront of the current standard chemotherapeutic regimen for active tuberculosis; they act by inhibiting the transcription activity of prokaryotic RNA polymerase. Rifampicin is believed to interact with the beta subunit of RNA polymerase. However, it has been observed that protein-protein interactions with RNA polymerase core enzyme lead to its reduced susceptibility to rifampicin. This mechanism became more diversified with the discovery of RbpA, a novel RNA polymerase-binding protein, in Streptomyces coelicolor that could mitigate the effect of rifampicin on RNA polymerase activity. MsRbpA is a homologue of RbpA in Mycobacterium smegmatis. On deciphering the role of MsRbpA in M. smegmatis we found that it interacts with RNA polymerase and increases the rifampicin tolerance levels, both in vitro and in vivo. It interacts with the beta subunit of RNA polymerase. However, it was found to be incapable of rescuing rifampicin-resistant RNA polymerases in the presence of rifampicin at the respective IC50.