scholarly journals A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane

2007 ◽  
Vol 405 (2) ◽  
pp. 261-268 ◽  
Author(s):  
Veronica T. Dufe ◽  
Daniel Ingner ◽  
Olle Heby ◽  
Alex R. Khomutov ◽  
Lo Persson ◽  
...  
Keyword(s):  
Leishmania Donovani ◽  
Homology Modelling ◽  
Critical Role ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Irreversible Inhibitor ◽  
Polyamine Biosynthesis ◽  
Oxime Formation ◽  
Large Conformational Change ◽  
Similar Mode

The critical role of polyamines in key processes such as cell growth, differentiation and macromolecular synthesis makes the enzymes involved in their synthesis potential targets in the treatment of certain types of cancer and parasitic diseases. Here we present a study on the inhibition of human and Leishmania donovani ODC (ornithine decarboxylase), the first committed enzyme in the polyamine biosynthesis pathway, by APA (1-amino-oxy-3-aminopropane). The present study shows APA to be a potent inhibitor of both human and L. donovani ODC with a Ki value of around 1.0 nM. We also show that L. donovani ODC binds the substrate, the co-enzyme pyridoxal 5′-phosphate and the irreversible inhibitor α-difluoromethylornithine (a curative agent of West African sleeping sickness) with less affinity than human ODC. We have also determined the three-dimensional structure of human ODC in complex with APA, which revealed the mode of the inhibitor binding to the enzyme. In contrast with earlier reports, the structure showed no indication of oxime formation between APA and PLP (pyridoxal 5′-phosphate). Homology modelling suggests a similar mode of binding of APA to L. donovani ODC. A comparison of the ODC–APA–PLP structure with earlier ODC structures also shows that the protease-sensitive loop (residues 158–168) undergoes a large conformational change and covers the active site of the protein. The understanding of the structural mode of APA binding may constitute the basis for the development of more specific inhibitors of L. donovani ODC.

scholarly journals Crystal structure of a tankyrase 1–telomere repeat factor 1 complex

2016 ◽  
Vol 72 (4) ◽  
pp. 320-327 ◽  
Author(s):  
Bo Li ◽  
Ruihong Qiao ◽  
Zhizhi Wang ◽  
Weihong Zhou ◽  
Xin Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Large Scale ◽  
Sparse Matrix ◽  
Critical Role ◽  
Three Dimensional ◽  
Mitotic Cell ◽  
Ankyrin Repeat ◽  
Dimensional Structure ◽  
Telomere Repeat ◽  
Tankyrase 1

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.

Three-Dimensional Structure of Ribosome-Sec61p Translocation Complexes From Mammals

2000 ◽  
Vol 6 (S2) ◽  
pp. 264-265
Author(s):  
J-F. Ménétret ◽  
D. G. Morgan ◽  
M. Radermacher ◽  
A. Neuhof ◽  
T. A. Rapoport ◽  
...  
Keyword(s):  
Critical Role ◽  
Three Dimensional ◽  
Channel Morphology ◽  
Dimensional Structure ◽  
Central Channel ◽  
Mass Analysis ◽  
Biologically Relevant ◽  
Ribosome Binding ◽  
Physical Mechanisms ◽  
3D Architecture

Co-translational translocation at the endoplasmic reticulum (ER) plays a critical role in the targeting of both soluble and membrane proteins to their correct intra- and intercellular compartments. We are studying the 3D architecture of the ribosome-Sec61p complex (translocon), with the aim of understanding the physical mechanisms of gating and transport. To this end, we are using single particle electron cryo-microscopy and 3D reconstruction of frozen hydrated channel complexes, to obtain interpretable and biologically relevant maps.Previously, we have shown that both co- and post-translational translocation utilize a common central channel comprised of a ring-like Sec61p oligomer. Moreover, this channel morphology is shared with the related Sec YE complex from B. subtilus. Mass analysis, volume calculations and ribosome binding experiments suggest a stoichiometry of 3-4 Sec61p heterotrimers per ring. We currently favor 4 copies of the Sec61p complex per channel, as projection maps demonstrate 4 nearly equi-spaced peaks around the central pore.

scholarly journals Disruptive coloration and binocular disparity: breaking camouflage

2019 ◽  
Vol 286 (1896) ◽  
pp. 20182045 ◽  
Author(s):  
Wendy J. Adams ◽  
Erich W. Graf ◽  
Matt Anderson
Keyword(s):  
Critical Role ◽  
Three Dimensional ◽  
Stereoscopic Vision ◽  
Dimensional Structure ◽  
Depth Information ◽  
Edge Enhancement ◽  
Depth Cues ◽  
Disruptive Coloration ◽  
True Shape ◽  
Binocular Depth

Many species employ camouflage to disguise their true shape and avoid detection or recognition. Disruptive coloration is a form of camouflage in which high-contrast patterns obscure internal features or break up an animal's outline. In particular, edge enhancement creates illusory, or ‘fake’ depth edges within the animal's body. Disruptive coloration often co-occurs with background matching, and together, these strategies make it difficult for an observer to visually segment an animal from its background. However, stereoscopic vision could provide a critical advantage in the arms race between perception and camouflage: the depth information provided by binocular disparities reveals the true three-dimensional layout of a scene, and might, therefore, help an observer to overcome the effects of disruptive coloration. Human observers located snake targets embedded in leafy backgrounds. We analysed performance (response time) as a function of edge enhancement, illumination conditions and the availability of binocular depth cues. We confirm that edge enhancement contributes to effective camouflage: observers were slower to find snakes whose patterning contains ‘fake’ depth edges. Importantly, however, this effect disappeared when binocular depth cues were available. Illumination also affected detection: under directional illumination, where both the leaves and snake produced strong cast shadows, snake targets were localized more quickly than in scenes rendered under ambient illumination. In summary, we show that illusory depth edges, created via disruptive coloration, help to conceal targets from human observers. However, cast shadows and binocular depth information improve detection by providing information about the true three-dimensional structure of a scene. Importantly, the strong interaction between disparity and edge enhancement suggests that stereoscopic vision has a critical role in breaking camouflage, enabling the observer to overcome the disruptive effects of edge enhancement.

scholarly journals Determination of the membrane topology of PORCN, an O-acyl transferase that modifies Wnt signalling proteins

Open Biology ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 200400
Author(s):  
Lisa M. Galli ◽  
Marc O. Anderson ◽  
J. Gabriel Fraley ◽  
Luis Sanchez ◽  
Raymund Bueno ◽  
...  
Keyword(s):  
Homology Modelling ◽  
Three Dimensional ◽  
Cancer Therapeutics ◽  
Membrane Topology ◽  
Dimensional Structure ◽  
Dependent Manner ◽  
Acyl Transferase ◽  
Wnt Proteins ◽  
C Terminus ◽  
Membrane Spanning

Wnt gradients elicit distinct cellular responses, such as proliferation, specification, differentiation and survival in a dose-dependent manner. Porcupine (PORCN), a membrane-bound O-acyl transferase (MBOAT) that resides in the endoplasmic reticulum, catalyses the addition of monounsaturated palmitate to Wnt proteins and is required for Wnt gradient formation and signalling. In humans, PORCN mutations are causal for focal dermal hypoplasia (FDH), an X-linked dominant syndrome characterized by defects in mesodermal and endodermal tissues. PORCN is also an emerging target for cancer therapeutics. Despite the importance of this enzyme, its structure remains poorly understood. Recently, the crystal structure of DltB, an MBOAT family member from bacteria, was solved. In this report, we use experimental data along with homology modelling to DltB to determine the membrane topology of PORCN. Our studies reveal that PORCN has 11 membrane domains, comprising nine transmembrane spanning domains and two reentrant domains. The N-terminus is oriented towards the lumen while the C-terminus is oriented towards the cytosol. Like DltB, PORCN has a funnel-like structure that is encapsulated by multiple membrane-spanning helices. This new model for PORCN topology allows us to map residues that are important for biological activity (and implicated in FDH) onto its three-dimensional structure.

scholarly journals IN SILICO CHARACTERISATION AND HOMOLOGY MODELLING OF TOLL/TOLL LIKE RECEPTORS (TLRS) FROM PENAEID SHRIMPS

2020 ◽  
Vol 67 (1) ◽  
Author(s):  
A. Angela Mercy ◽  
N. Hemamalini ◽  
K. Aruljothi ◽  
B. Chrisolite ◽  
K. Karalmarx
Keyword(s):  
Protein Quality ◽  
Transmembrane Protein ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Receptor Protein ◽  
Dimensional Structure ◽  
Toll Like Receptors ◽  
Physico Chemical ◽  
Penaeid Shrimps

Toll or Toll-like receptors are conserved receptors, which act as the first line of defense against infection by pathogens. To use Toll/Toll like receptors as drug targets, it is essential to understand their physico-chemical properties and three dimensional structures. In the present study, physico-chemical properties and secondary structure of Toll/Toll like receptors from selected species of penaeid shrimps viz., Penaeus chinensis, P. vannamei, P. monodon and P. japonicus were computed using online servers. Three dimensional structure was predicted by homology modelling using different softwares, SWISS-MODEL, Phyre2 and Geno3D softwares were validated using online tools to find the best model for the protein under study. From the physicochemical properties, nature of the Toll/Toll like receptor protein was revealed as acidic, thermostable, hydrophobic and transmembrane protein. Structural analysis indicated the presence of alpha helices and random coils as predominant elements followed by extended stands and beta turns. Three dimensional structures predicted using SWISS-MODEL was validated as extremely good model using Protein Quality Predictor online server.

scholarly journals Deep Homology-Based Protein Contact-Map Prediction

2020 ◽  
Author(s):  
Omer Ronen ◽  
Or Zuk
Keyword(s):  
Fundamental Problem ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Physical Contact ◽  
Dimensional Structure ◽  
Evolutionary Information ◽  
Contact Map ◽  
Sequence Alignments ◽  
Three Dimensional Structure

AbstractPrediction of Proteins’ three dimensional structure and their contact maps from their amino-acid sequences is a fundamental problem in structural computational biology. The structure and contacts shed light on protein function, enhance our basic understanding of their molecular biology and may potentially aid in drug design. In recent years we have seen significant progress in protein contact map prediction from Multiple Sequence Alignments (MSA) of the target protein and its homologous, using signals of co-evolution and applying deep learning methods.Homology modelling is a popular and successful approach, where the structure of a protein is determined using information from known template structures of similar proteins, and has been shown to improve prediction even in cases of low sequence identity. Motivated by these observations, we developed Periscope, a method for homology-assisted contact map prediction using a deep convolutional network. Our method automatically integrates the co-evolutionary information from the MSA, and the physical contact information from the template structures.We apply our method to families of CAMEO and membrane proteins, and show improved prediction accuracy compared to the MSA-only based method RaptorX. Finally, we use our method to improve the subsequent task of predicting the proteins’ three dimensional structure based on the (improved) predicted contact map, and show initial promising results in this task too - our overall accuracy is comparable to the template-based Modeller software, yet the two methods are complementary and succeed on different targets.

scholarly journals Functional and molecular modelling studies of two hereditary fructose intolerance-causing mutations at arginine 303 in human liver aldolase

2000 ◽  
Vol 350 (3) ◽  
pp. 823-828 ◽  
Author(s):  
Rita SANTAMARIA ◽  
Gabriella ESPOSITO ◽  
Luigi VITAGLIANO ◽  
Vincenza RACE ◽  
Immacolata PAGLIONICO ◽  
...  
Keyword(s):  
Homology Modelling ◽  
Three Dimensional ◽  
Catalytic Efficiency ◽  
Dimensional Structure ◽  
Kinetic Properties ◽  
Wild Type ◽  
Hereditary Fructose Intolerance ◽  
Fructose Intolerance ◽  
Aldolase B ◽  
Fructose 1,6 Bisphosphate

We have identified a novel hereditary fructose intolerance mutation in the aldolase B gene (i.e. liver aldolase) that causes an arginine-to-glutamine substitution at residue 303 (Arg303 → Gln). We previously described another mutation (Arg303 → Trp) at the same residue. We have expressed the wild-type protein and the two mutated proteins and characterized their kinetic properties. The catalytic efficiency of protein Gln303 is approx. 1/100 that of the wild-type for substrates fructose 1,6-bisphosphate and fructose 1-phosphate. The Trp303 enzyme has a catalytic efficiency approx. 1/4800 that of the wild-type for fructose 1,6-bisphosphate; no activity was detected with fructose 1-phosphate. The mutation Arg303 → Trp thus substitution impairs enzyme activity more than Arg303 → Gln. Three-dimensional models of wild-type, Trp303 and Gln303 aldolase B generated by homology-modelling techniques suggest that, because of its larger size, tryptophan exerts a greater deranging effect than glutamine on the enzyme's three-dimensional structure. Our results show that the Arg303 → Gln substitution is a novel mutation causing hereditary fructose intolerance and provide a functional demonstration that Arg303, a conserved residue in all vertebrate aldolases, has a dominant role in substrate binding during enzyme catalysis.

Structure–specificity relationships in Abp, a GH27 β-L-arabinopyranosidase fromGeobacillus stearothermophilusT6

2014 ◽  
Vol 70 (11) ◽  
pp. 2994-3012 ◽  
Author(s):  
Shifra Lansky ◽  
Rachel Salama ◽  
Hodaya V. Solomon ◽  
Hadar Feinberg ◽  
Hassan Belrhali ◽  
...  
Keyword(s):  
Active Sites ◽  
Critical Role ◽  
Three Dimensional ◽  
Structural Data ◽  
Size Exclusion ◽  
Dimensional Structure ◽  
Structural Basis ◽  
X Ray ◽  
Three Dimensional Structure ◽  
Tim Barrel

L-Arabinose sugar residues are relatively abundant in plants and are found mainly in arabinan polysaccharides and in other arabinose-containing polysaccharides such as arabinoxylans and pectic arabinogalactans. The majority of the arabinose units in plants are present in the furanose form and only a small fraction of them are present in the pyranose form. The L-arabinan-utilization system inGeobacillus stearothermophilusT6, a Gram-positive thermophilic soil bacterium, has recently been characterized, and one of the key enzymes was found to be an intracellular β-L-arabinopyranosidase (Abp). Abp, a GH27 enzyme, was shown to remove β-L-arabinopyranose residues from synthetic substrates and from the native substrates sugar beet arabinan and larch arabinogalactan. The Abp monomer is made up of 448 amino acids, and based on sequence homology it was suggested that Asp197 is the catalytic nucleophile and Asp255 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) a bound L-arabinose product are reported as determined by X-ray crystallography. These structures demonstrate that the three-dimensional structure of the Abp monomer correlates with the general fold observed for GH27 proteins, consisting of two main domains: an N-terminal TIM-barrel domain and a C-terminal all-β domain. The two catalytic residues are located in the TIM-barrel domain, such that their carboxylic functional groups are about 5.9 Å from each other, consistent with a retaining mechanism. An isoleucine residue (Ile67) located at a key position in the active site is shown to play a critical role in the substrate specificity of Abp, providing a structural basis for the high preference of the enzyme towards arabinopyranoside over galactopyranoside substrates. The crystal structure demonstrates that Abp is a tetramer made up of two `open-pincers' dimers, which clamp around each other to form a central cavity. The four active sites of the Abp tetramer are situated on the inner surface of this cavity, all opening into the central space of the cavity. The biological relevance of this tetrameric structure is supported by independent results obtained from size-exclusion chromatography (SEC), dynamic light-scattering (DLS) and small-angle X-ray scattering (SAXS) experiments. These data and their comparison to the structural data of related GH27 enzymes are used for a more general discussion concerning structure–selectivity aspects in this glycoside hydrolase (GH) family.

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