scholarly journals Unravelling the structure of the pneumococcal autolytic lysozyme

2005 ◽  
Vol 391 (1) ◽  
pp. 41-49 ◽  
Author(s):  
Begoña Monterroso ◽  
Consuelo López-Zumel ◽  
José L. García ◽  
José L. Sáiz ◽  
Pedro García ◽  
...  
Keyword(s):  
Homology Modelling ◽  
Tight Binding ◽  
Three Dimensional ◽  
Divergent Evolution ◽  
Glycosyl Hydrolases ◽  
Three Dimensional Model ◽  
Lytic Enzymes ◽  
C Terminus ◽  
Global Fold ◽  
Positively Charged

The LytC lysozyme of Streptococcus pneumoniae forms part of the autolytic system of this important pathogen. This enzyme is composed of a C-terminal CM (catalytic module), belonging to the GH25 family of glycosyl hydrolases, and an N-terminal CBM (choline-binding module), made of eleven homologous repeats, that specifically recognizes the choline residues that are present in pneumococcal teichoic and lipoteichoic acids. This arrangement inverts the general assembly pattern of the major pneumococcal autolysin, LytA, and the lytic enzymes encoded by pneumococcal bacteriophages that place the CBM (made of six repeats) at the C-terminus. In the present paper, a three-dimensional model of LytC built by homology modelling of each module and consistent with spectroscopic and hydrodynamic studies is shown. In addition, the putative catalytic-pair residues are identified. Despite the inversion in the modular arrangement, LytC and the bacteriophage-encoded Cpl-1 lysozyme most probably adopt a similar global fold. However, the distinct choline-binding ability and their substrate-binding surfaces may reflect a divergent evolution directed by the different roles played by them in the host (LytC) or in the bacteriophage (Cpl-1). The tight binding of LytC to the pneumococcal envelope, mediated by the acquisition of additional choline-binding repeats, could facilitate the regulation of the potentially suicidal activity of this autolysin. In contrast, a looser attachment of Cpl-1 to the cell wall and the establishment of more favourable interactions between its highly negatively charged catalytic surface and the positively charged chains of pneumococcal murein could enhance the lytic activity of the parasite-encoded enzyme and therefore liberation of the phage progeny.

scholarly journals Substrate (aglycone) specificity of human cytosolic beta-glucosidase

2003 ◽  
Vol 373 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Jean-Guy BERRIN ◽  
Mirjam CZJZEK ◽  
Paul A. KROON ◽  
W. Russell MCLAUCHLAN ◽  
Antoine PUIGSERVER ◽  
...  
Keyword(s):  
Structural Model ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Amino Acid Residues ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Mutant Proteins ◽  
Metabolizing Enzyme ◽  
Beta Glucosidase

Human cytosolic β-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays β-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (β/α)8-barrel fold characteristic of family 1 β-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val168→Tyr, Phe225→Ser, Tyr308→Ala and Tyr308→Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val168→Tyr mutation did not affect Km on p-nitrophenyl (pNP)-glycosides, but increased Km 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe225→Ser and Tyr308→Ala mutations, and, to a lesser degree, the Tyr308→Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.

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 Comparisons among the larger genome segments of six nodaviruses and their encoded RNA replicases

2001 ◽  
Vol 82 (8) ◽  
pp. 1855-1866 ◽  
Author(s):  
Karyn N. Johnson ◽  
Kyle L. Johnson ◽  
Ranjit Dasgupta ◽  
Theresa Gratsch ◽  
L. Andrew Ball
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Rna Polymerase ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Three Dimensional Model ◽  
Protein Precursor ◽  
Structural Homologues ◽  
Nodamura Virus

The Nodaviridae are a family of isometric RNA viruses that infect insects and fish. Their genomes, which are among the smallest known for animal viruses, consist of two co-encapsidated positive-sense RNA segments: RNA1 encodes the viral contribution to the RNA-dependent RNA polymerase (RdRp) which replicates the viral genome, whereas RNA2 encodes the capsid protein precursor. In this study, the RNA1 sequences of two insect nodaviruses – Nodamura virus (the prototype of the genus) and Boolarra virus – are reported as well as detailed comparisons of their encoded RdRps with those of three other nodaviruses of insects and one of fish. Although the 5′ and 3′ untranslated regions did not reveal common features of RNA sequence or secondary structure, these divergent viruses showed similar genome organizations and encoded RdRps that had from 26 to 99% amino acid sequence identity. All six RdRp amino acid sequences contained canonical RNA polymerase motifs in their C-terminal halves and conserved elements of predicted secondary structure throughout. A search for structural homologues in the protein structure database identified the poliovirus RdRp, 3Dpol, as the best template for homology modelling of the RNA polymerase domain of Pariacoto virus and allowed the construction of a congruent three-dimensional model. These results extend our understanding of the relationships among the RNA1 segments of nodaviruses and the predicted structures of their encoded RdRps.

Involvement of cysteine 306 and alanine 63 in the thermostability and oligomeric organization of glucose isomerase from Streptomyces sp. SK

Biologia ◽  
2009 ◽  
Vol 64 (5) ◽  
Author(s):  
Mohamed Borgi ◽  
Moez Rhimi ◽  
Nushin Aghajari ◽  
Mamdouh Ben Ali ◽  
Michel Juy ◽  
...  
Keyword(s):  
Half Life ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Electrophoretic Analysis ◽  
Glucose Isomerase ◽  
Site Directed Mutagenesis ◽  
Three Dimensional Model ◽  
Streptomyces Sp ◽  
Enzyme Active Site ◽  
Enzyme Thermostability

AbstractThe implication of the original alanine 63 (Ala63) and the unique cysteine 306 (Cys306) residues in the thermostability of the Streptomyces sp. SK glucose isomerase (SKGI) were investigated by site-directed mutagenesis and homology modelling. The Cys306 to Ala mutation within SKGI dramatically affected its thermal stability by decreasing the half-life from 80 to 15 min at 90°C while the Ala63 to Ser replacement shifted this half-life to 65 min. The electrophoretic analysis proves that the residue Cys306 participates in oligomerization of the SKGI. Its stabilizing role is materialized by hydrogen bonds established with arginines at positions 284 and 259, as deduced from the constructed three-dimensional model. We have also shown that the presence of an Ala63 instead of Ser63 seems to be more suitable for enzyme thermostability by maintaining hydrophobic pocket that contributes to the protection of the enzyme active site.

An electrodiffusion model for effects of surface glycocalyx layer on microvessel permeability

2003 ◽  
Vol 284 (4) ◽  
pp. H1240-H1250 ◽  
Author(s):  
Bingmei M. Fu ◽  
Bin Chen ◽  
Wenhao Chen
Keyword(s):  
Charge Density ◽  
Three Dimensional ◽  
Total Charge ◽  
Three Dimensional Model ◽  
Density Profiles ◽  
Solute Permeability ◽  
Endothelial Surface ◽  
Microvessel Permeability ◽  
Microvessel Wall ◽  
Positively Charged

To investigate the charge effect of the endothelial surface glycocalyx on microvessel permeability, we extended the three-dimensional model developed by Fu et al. ( J Biomech Eng 116: 502–513, 1994) for the interendothelial cleft to include a negatively charged glycocalyx layer at the entrance of the cleft. Both electrostatic and steric exclusions on charged solutes were considered within the glycocalyx layer and at the interfaces. Four charge-density profiles were assumed for the glycocalyx layer. Our model indicates that the overall solute permeability across the microvessel wall including the surface glycocalyx layer and the cleft region is independent of the charge-density profiles as long as they have the same maximum value and the same total charge. On the basis of experimental data, this model predicts that the charge density would be 25–35 meq/l in the glycolcalyx of frog mesenteric capillaries. An intriguing prediction of this model is that when the concentrations of cations and anions are unequal in the lumen due to the presence of negatively charged proteins, the negatively charged glycocalyx would provide more resistance to positively charged solutes than to negatively charged ones.

Three-Dimensional Model for Virtual Surgical Simulation, during Complex Skull Base Surgery and Aneurysm Surgery

Skull Base ◽  
2008 ◽  
Vol 18 (S 01) ◽  
Author(s):  
Akio Morita ◽  
Toshikazu Kimura ◽  
Shigeo Sora ◽  
Kengo Nishimura ◽  
Hisayuki Sugiyama ◽  
...  
Keyword(s):  
Skull Base ◽  
Surgical Simulation ◽  
Skull Base Surgery ◽  
Three Dimensional ◽  
Aneurysm Surgery ◽  
Dimensional Model ◽  
Three Dimensional Model

Digitalization system of ancient architecture decoration art based on neural network and image features

2020 ◽  
pp. 1-12
Author(s):  
Wu Xin ◽  
Qiu Daping
Keyword(s):  
Neural Network ◽  
Construction Industry ◽  
Three Dimensional ◽  
Performance Testing ◽  
Image Features ◽  
Three Dimensional Model ◽  
Performance Effect ◽  
Data Process ◽  
And Performance ◽  
Construction Mode

The inheritance and innovation of ancient architecture decoration art is an important way for the development of the construction industry. The data process of traditional ancient architecture decoration art is relatively backward, which leads to the obvious distortion of the digitalization of ancient architecture decoration art. In order to improve the digital effect of ancient architecture decoration art, based on neural network, this paper combines the image features to construct a neural network-based ancient architecture decoration art data system model, and graphically expresses the static construction mode and dynamic construction process of the architecture group. Based on this, three-dimensional model reconstruction and scene simulation experiments of architecture groups are realized. In order to verify the performance effect of the system proposed in this paper, it is verified through simulation and performance testing, and data visualization is performed through statistical methods. The result of the study shows that the digitalization effect of the ancient architecture decoration art proposed in this paper is good.

Sign in / Sign up

Export Citation Format

Share Document