scholarly journals Structural modeling of GSK3β implicates the inactive (DFG-out) conformation as the target bound by TDZD analogs

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Meenakshisundaram Balasubramaniam ◽  
Nirjal Mainali ◽  
Suresh Kuarm Bowroju ◽  
Paavan Atluri ◽  
Narsimha Reddy Penthala ◽  
...  
Keyword(s):  
Glycogen Synthase ◽  
Three Dimensional ◽  
Binding Mode ◽  
Competitive Inhibitor ◽  
Dimensional Structure ◽  
High Potency ◽  
Subsequent Formation ◽  
Inactive Conformation ◽  
Competitive Inhibitors ◽  
Physiological Pathways

Abstract Glycogen synthase kinase-3β (GSK3β) controls many physiological pathways, and is implicated in many diseases including Alzheimer’s and several cancers. GSK3β-mediated phosphorylation of target residues in microtubule-associated protein tau (MAPTAU) contributes to MAPTAU hyperphosphorylation and subsequent formation of neurofibrillary tangles. Inhibitors of GSK3β protect against Alzheimer’s disease and are therapeutic for several cancers. A thiadiazolidinone drug, TDZD-8, is a non-ATP-competitive inhibitor targeting GSK3β with demonstrated efficacy against multiple diseases. However, no experimental data or models define the binding mode of TDZD-8 with GSK3β, which chiefly reflects our lack of an established inactive conformation for this protein. Here, we used metadynamic simulation to predict the three-dimensional structure of the inactive conformation of GSK3β. Our model predicts that phosphorylation of GSK3β Serine9 would hasten the DFG-flip to an inactive state. Molecular docking and simulation predict the TDZD-8 binding conformation of GSK3β to be inactive, and are consistent with biochemical evidence for the TDZD-8–interacting residues of GSK3β. We also identified the pharmacophore and assessed binding efficacy of second-generation TDZD analogs (TDZD-10 and Tideglusib) that bind GSK3β as non-ATP-competitive inhibitors. Based on these results, the predicted inactive conformation of GSK3β can facilitate the identification of novel GSK3β inhibitors of high potency and specificity.

scholarly journals A computer-based approach for developing linamarase inhibitory agents

2020 ◽  
Vol 5 (7) ◽  
Author(s):  
Lucas Paul ◽  
Celestin N. Mudogo ◽  
Kelvin M. Mtei ◽  
Revocatus L. Machunda ◽  
Fidele Ntie-Kang
Keyword(s):  
Structure Elucidation ◽  
Three Dimensional ◽  
Data Bank ◽  
Competitive Inhibitor ◽  
Industrial Applications ◽  
Dimensional Structure ◽  
Full Understanding ◽  
The Poor ◽  
Computer Based ◽  
Inhibitory Agents

AbstractCassava is a strategic crop, especially for developing countries. However, the presence of cyanogenic compounds in cassava products limits the proper nutrients utilization. Due to the poor availability of structure discovery and elucidation in the Protein Data Bank is limiting the full understanding of the enzyme, how to inhibit it and applications in different fields. There is a need to solve the three-dimensional structure (3-D) of linamarase from cassava. The structural elucidation will allow the development of a competitive inhibitor and various industrial applications of the enzyme. The goal of this review is to summarize and present the available 3-D modeling structure of linamarase enzyme using different computational strategies. This approach could help in determining the structure of linamarase and later guide the structure elucidation in silico and experimentally.

scholarly journals Optimization of the crystallizability of a single-chain antibody fragment

2014 ◽  
Vol 70 (12) ◽  
pp. 1701-1706 ◽  
Author(s):  
Jana Škerlová ◽  
Vlastimil Král ◽  
Milan Fábry ◽  
Juraj Sedláček ◽  
Václav Veverka ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Antibody Fragment ◽  
Binding Mode ◽  
Antibody Fragments ◽  
Dimensional Structure ◽  
Single Chain ◽  
Single Chain Antibody ◽  
Diagnostic Potential ◽  
Storage Buffer ◽  
Single Chain Antibody Fragment

Single-chain variable antibody fragments (scFvs) are molecules with immense therapeutic and diagnostic potential. Knowledge of their three-dimensional structure is important for understanding their antigen-binding mode as well as for protein-engineering approaches such as antibody humanization. A major obstacle to the crystallization of single-chain variable antibody fragments is their relatively poor homogeneity caused by spontaneous oligomerization. A new approach to optimization of the crystallizability of single-chain variable antibody fragments is demonstrated using a representative single-chain variable fragment derived from the anti-CD3 antibody MEM-57. A Thermofluor-based assay was utilized to screen for optimal conditions for antibody-fragment stability and homogeneity. Such an optimization of the protein storage buffer led to a significantly improved ability of the scFv MEM-57 to yield crystals.

scholarly journals GMP and IMP Are Competitive Inhibitors of CMY-10, an Extended-Spectrum Class C β-Lactamase

2017 ◽  
Vol 61 (5) ◽  
Author(s):  
Jung-Hyun Na ◽  
Young Jun An ◽  
Sun-Shin Cha
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Binding Mode ◽  
Competitive Inhibitor ◽  
Phosphate Group ◽  
The Other ◽  
Extended Spectrum ◽  
Competitive Inhibitors ◽  
Class C

ABSTRACT Nucleotides were effective in inhibiting the class C β-lactamase CMY-10. IMP was the most potent competitive inhibitor, with a Ki value of 16.2 μM. The crystal structure of CMY-10 complexed with GMP or IMP revealed that nucleotides fit into the R2 subsite of the active site with a unique vertical binding mode where the phosphate group at one terminus is deeply bound in the subsite and the base at the other terminus faces the solvent.

scholarly journals Three-dimensional structure of the Gly121Tyr dimeric form of ornithine decarboxylase from Lactobacillus 30a

1999 ◽  
Vol 55 (12) ◽  
pp. 1978-1985 ◽  
Author(s):  
Jacqueline Vitali ◽  
Donald Carroll ◽  
Rochika G. Chaudhry ◽  
Marvin L. Hackert
Keyword(s):  
Ornithine Decarboxylase ◽  
Single Point ◽  
Three Dimensional ◽  
Binding Mode ◽  
Dimensional Structure ◽  
Single Point Mutation ◽  
Salt Bridges ◽  
Cell Parameters ◽  
Guanine Base ◽  
Dimeric Form

Ornithine decarboxylases catalyze the conversion of ornithine to putrescine at the beginning of the polyamine pathway. Ornithine decarboxylase (ODC) from Lactobacillus 30a is a 990612 Da dodecamer composed of six homodimers. A single point mutation (Gly121Tyr) was found to prevent association of dimers into dodecamers. The dimeric protein has been crystallized at pH 7.0 in the presence of guanosine triphosphate (GTP). Crystals belong to space group P3221, with unit-cell parameters a = 111.8, c = 135.9 Å and one monomer in the asymmetric unit. The structure was determined by molecular replacement and refined using simulated annealing to R = 0.211 at 2.7 Å resolution. The GTP-binding site was analyzed in detail. The protein exhibits a novel binding mode for GTP which is different from that seen in most G-proteins or GTPases. Central to this binding scheme appear to be three lysines, Lys190, Lys374 and Lys382, which form salt bridges with the three phosphates, and Thr191, which hydrogen bonds with the guanine base. Furthermore, the structure suggests that there is some flexibility in the wing domain, which can change its orientation as the protein adapts to its environment. The active site is similar to that of the native enzyme, consistent with the observation that the enzyme activity does not depend on its dodecameric state.

scholarly journals Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes

2020 ◽  
Vol 6 (36) ◽  
pp. eabc0023
Author(s):  
Jānis Rūmnieks ◽  
Ilva Liekniņa ◽  
Gints Kalniņš ◽  
Mihails Šišovs ◽  
Ināra Akopjana ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Binding Mode ◽  
Structural Proteins ◽  
Mutation Rates ◽  
Dimensional Structure ◽  
Coat Proteins ◽  
Protein Fold ◽  
Three Dimensional Structure ◽  
Dsrna Binding ◽  
Particle Shapes

The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage–based vaccine design.

scholarly journals The ClgR Protein Regulates Transcription of the clpP Operon in Bifidobacterium breve UCC 2003

2005 ◽  
Vol 187 (24) ◽  
pp. 8411-8426 ◽  
Author(s):  
Marco Ventura ◽  
Ziding Zhang ◽  
Michelle Cronin ◽  
Carlos Canchaya ◽  
John G. Kenny ◽  
...  
Keyword(s):  
Promoter Region ◽  
Specific Binding ◽  
Three Dimensional ◽  
Binding Mode ◽  
Dna Interaction ◽  
Dimensional Structure ◽  
Mobility Shift ◽  
Significant Similarity ◽  
Bifidobacterium Breve

ABSTRACT Five clp genes (clpC, clpB, clpP1, clpP2, and clpX), representing chaperone- and protease-encoding genes, were previously identified in Bifidobacterium breve UCC 2003. In the present study, we characterize the B. breve UCC 2003 clpP locus, which consists of two paralogous genes, designated clpP1 and clpP2, whose deduced protein products display significant similarity to characterized ClpP peptidases. Transcriptional analyses showed that the clpP1 and clpP2 genes are transcribed in response to moderate heat shock as a bicistronic unit with a single promoter. The role of a clgR homologue, known to control the regulation of clpP gene expression in Streptomyces lividans and Corynebacterium glutamicum, was investigated by gel mobility shift assays and DNase I footprint experiments. We show that ClgR, which in its purified form appears to exist as a dimer, requires a proteinaceous cofactor to assist in specific binding to a 30-bp region of the clpP promoter region. In pull-down experiments, a 56-kDa protein copurified with ClgR, providing evidence that the two proteins also interact in vivo and that the copurified protein represents the cofactor required for ClgR activity. The prediction of the ClgR three-dimensional structure provides further insights into the binding mode of this protein to the clpP1 promoter region and highlights the key amino acid residues believed to be involved in the protein-DNA interaction.

scholarly journals The active site and substrate-binding mode of 1-aminocyclopropane-1-carboxylate oxidase determined by site-directed mutagenesis and comparative modelling studies

2004 ◽  
Vol 380 (2) ◽  
pp. 339-346 ◽  
Author(s):  
Young Sam SEO ◽  
Ahrim YOO ◽  
Jinwon JUNG ◽  
Soon-Kee SUNG ◽  
Dae Ryook YANG ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Binding Mode ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Directed Mutagenesis ◽  
Comparative Modelling

The active site and substrate-binding mode of MD-ACO1 (Malus domestica Borkh. 1-aminocyclopropane-1-carboxylate oxidase) have been determined using site-directed mutagenesis and comparative modelling methods. The MD-ACO1 protein folds into a compact jelly-roll motif comprised of eight α-helices, 12 β-strands and several long loops. The active site is well defined as a wide cleft near the C-terminus. The co-substrate ascorbate is located in cofactor Fe2+-binding pocket, the so-called ‘2-His-1-carboxylate facial triad’. In addition, our results reveal that Arg244 and Ser246 are involved in generating the reaction product during enzyme catalysis. The structure agrees well with the biochemical and site-directed mutagenesis results. The three-dimensional structure together with the steady-state kinetics of both the wild-type and mutant MD-ACO1 proteins reveal how the substrate specificity of MD-ACO1 is involved in the catalytic mechanism, providing insights into understanding the fruit ripening process at atomic resolution.

Homology Modeling of Aeromonas hydrophila Laccase and its Molecular Docking with the 2,5-Xylidine

2013 ◽  
Vol 798-799 ◽  
pp. 83-86
Author(s):  
Dong Xia Du ◽  
Shi Ping Shan ◽  
De Yuan Zhang ◽  
Yue Lin He
Keyword(s):  
Molecular Docking ◽  
Homology Modeling ◽  
Aeromonas Hydrophila ◽  
Three Dimensional ◽  
Industrial Effluents ◽  
Binding Pocket ◽  
Binding Mode ◽  
Major Effect ◽  
Dimensional Structure ◽  
Three Dimensional Structure

Laccases belonging to multicopper oxidase family oxidize a broad range of reducing substrates, especially industrial effluents-derived polyphenols, which causing major effect on human health as well as environment. In order to investigate the molecular mechanism of interaction between laccase and its substrate, it is a good idea to analyze three-dimensional structure of laccase. Based on crystal structure ofEscherichia colilaccase CueO, the three-dimensional structure ofAeromonas hydrophilaLaccase (Ah-lac) was constructed by homology modeling and further evaluated using PROSA energy and ERRAT. The substrate binding site in Ah-lac was predicted and the binding mode of 2,5-Xylidine as a putative ligand to Ah-lac was presented using molecular docking. The residues of Met378 and His382 in the binding pocket are responsible for the interactions with 2,5-Xylidine via two hydrogen bonds. The two residues could be important for substrate recognition.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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