scholarly journals Crystal Structure of the Dog Allergen Can f 6

2019 ◽  
Author(s):  
Gina M Clayton ◽  
Janice White ◽  
John W Kappler ◽  
Sanny K Chan
Keyword(s):  
Ligand Binding ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Cross Reactivity ◽  
Binding Partner ◽  
Sequence Identity ◽  
Natural Ligand ◽  
Binding Cavity ◽  
Can F 1 ◽  
High Degree

AbstractLipocalins represent the most important protein family of the mammalian respiratory allergens. Four of the seven named dog allergens are lipocalins: Can f 1, Can f 2, Can f 4, and Can f 6. We present the structure of Can f 6 along with data on the biophysical and biological activity of this protein in comparison with other animal lipocalins. The Can f 6 structure displays the classic lipocalin calyx-shaped ligand binding cavity within a central β-barrel similar to other lipocalins. Despite low sequence identity between the different dog lipocalin proteins, there is a high degree of structural similarity. On the other hand, Can f 6 has a similar primary sequence to cat, horse, mouse lipocalins as well as a structure that may underlie their cross reactivity. Interestingly, the entrance to the ligand binding pocket is capped by a His instead of the usually seen Tyr that may help select its natural ligand binding partner. Our highly pure recombinant Can f 6 is able to bind to human IgE (hIgE) demonstrating biological antigenicity.

Data Integration Through Protein Ontology

2011 ◽  
pp. 106-122
Author(s):  
Amandeep S. Sidhu ◽  
Tharam S. Dillon ◽  
Elizabeth Chang
Keyword(s):  
Hierarchical Classification ◽  
Structural Similarity ◽  
Protein Annotation ◽  
Functional Identification ◽  
Sequence Identity ◽  
Alternative Protein ◽  
Traditional Approaches ◽  
High Degree ◽  
Keyword Searches

Traditional approaches to integrate protein data generally involved keyword searches, which immediately excludes unannotated or poorly annotated data. An alternative protein annotation approach is to rely on sequence identity, or structural similarity, or functional identification. Some proteins have high degree of sequence identity, or structural similarity, or similarity in functions that are unique to members of that family alone. Consequently, this approach can’t be generalized to integrate the protein data. Clearly, these traditional approaches have limitations in capturing and integrating data for Protein Annotation. For these reasons, we have adopted an alternative method that does not rely on keywords or similarity metrics, but instead uses ontology. In this chapter we discuss conceptual framework of Protein Ontology that has a hierarchical classification of concepts represented as classes, from general to specific; a list of attributes related to each concept, for each class; a set of relations between classes to link concepts in ontology in more complicated ways then implied by the hierarchy, to promote reuse of concepts in the ontology; and a set of algebraic operators for querying protein ontology instances.

Structural insights into the molecular mechanism ofEscherichia coliSdiA, a quorum-sensing receptor

2014 ◽  
Vol 70 (3) ◽  
pp. 694-707 ◽  
Author(s):  
Truc Kim ◽  
Thao Duong ◽  
Chun-ai Wu ◽  
Jongkeun Choi ◽  
Nguyen Lan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Quorum Sensing ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Bacterial Species ◽  
Control Cell ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Binding Domain ◽  
Titration Calorimetry

Escherichia coliSdiA is a quorum-sensing (QS) receptor that responds to autoinducers produced by other bacterial species to control cell division and virulence. Crystal structures reveal thatE. coliSdiA, which is composed of an N-terminal ligand-binding domain and a C-terminal DNA-binding domain (DBD), forms a symmetrical dimer. Although each domain shows structural similarity to other QS receptors, SdiA differs from them in the relative orientation of the two domains, suggesting that its ligand-binding and DNA-binding functions are independent. Consistently, in DNA gel-shift assays the binding affinity of SdiA for theftsQP2 promoter appeared to be insensitive to the presence of autoinducers. These results suggest that autoinducers increase the functionality of SdiA by enhancing the protein stability rather than by directly affecting the DNA-binding affinity. Structural analyses of the ligand-binding pocket showed that SdiA cannot accommodate ligands with long acyl chains, which was corroborated by isothermal titration calorimetry and thermal stability analyses. The formation of an intersubunit disulfide bond that might be relevant to modulation of the DNA-binding activity was predicted from the proximal position of two Cys residues in the DBDs of dimeric SdiA. It was confirmed that the binding affinity of SdiA for theuvrYpromoter was reduced under oxidizing conditions, which suggested the possibility of regulation of SdiA by multiple independent signals such as quorum-sensing inducers and the oxidation state of the cell.

scholarly journals Investigating the role of N-terminal domain in phosphodiesterase 4B-inhibition by molecular dynamics simulation

2020 ◽  
Author(s):  
Vidushi Sharma ◽  
Sharad Wakode
Keyword(s):  
Ligand Binding ◽  
Root Mean Square ◽  
Active Site ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Mean Square ◽  
Sequence Identity ◽  
Terminal Domain ◽  
Phosphodiesterase 4B

AbstractPhosphodiesterase 4B (PDE4B) is a potential therapeutic target for the inflammatory respiratory diseases such as congestive obstructive pulmonary disease (COPD) and asthma. The sequence identity of ∼88% with its isoform PDE4D is the key barrier in developing selective PDE4B inhibitors which may help to overcome associated side effects. Despite high sequence identity, both isoforms differ in few residues present in N-terminal (UCR2) and C-terminal (CR3) involved in catalytic site formation. Previously, we designed and tested specific PDE4B inhibitors considering N-terminal residues as a part of the catalytic cavity. In continuation, current work thoroughly presents an MD simulation-based analysis of N-terminal residues and their role in ligand binding. The various parameters viz. root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuation (RMSF), principal component analysis (PCA), dynamical cross-correlation matrix (DCCM) analysis, secondary structure analysis, and residue interaction mapping were investigated to establish rational. Results showed that UCR2 reduced RMSF values for the metal binding pocket (31.5±11 to 13.12±6 Å2) and the substrate-binding pocket (38.8±32 to 17.3±11 Å2). UCR2 enhanced anti-correlated motion at the active site region that led to the improved ligand-binding affinity of PDE4B from −24.57±3 to −35.54±2 kcal/mol. Further, the atomic-level analysis indicated that T-pi and π-π interactions between inhibitors and residues are vital forces that regulate inhibitor association to PDE4B with high affinity. In conclusion, UCR2, the N-terminal domain, embraces the dynamics of PDE4B active site and stabilizes PDE4B inhibitor interactions. Therefore the N-terminal domain needs to be included by designing next-generation, selective PDE4B-inhibitors as potential anti-inflammatory drugs.

scholarly journals Ribose-Binding Protein Mutants With Improved Interaction Towards the Non-natural Ligand 1,3-Cyclohexanediol

2021 ◽  
Vol 9 ◽  
Author(s):  
Diogo Tavares ◽  
Jan Roelof van der Meer
Keyword(s):  
Ligand Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Binding Pocket ◽  
Ligand Binding Pocket ◽  
Natural Ligand ◽  
Protein Mutants ◽  
Periplasmic Binding Proteins ◽  
Natural Ligands ◽  
Ribose Binding Protein

Bioreporters consist of genetically modified living organisms that respond to the presence of target chemical compounds by production of an easily measurable signal. The central element in a bioreporter is a sensory protein or aptamer, which, upon ligand binding, modifies expression of the reporter signal protein. A variety of naturally occurring or modified versions of sensory elements has been exploited, but it has proven to be challenging to generate elements that recognize non-natural ligands. Bacterial periplasmic binding proteins have been proposed as a general scaffold to design receptor proteins for non-natural ligands, but despite various efforts, with only limited success. Here, we show how combinations of randomized mutagenesis and reporter screening improved the performance of a set of mutants in the ribose binding protein (RbsB) of Escherichia coli, which had been designed based on computational simulations to bind the non-natural ligand 1,3-cyclohexanediol (13CHD). Randomized mutant libraries were constructed that used the initially designed mutants as scaffolds, which were cloned in an appropriate E. coli bioreporter system and screened for improved induction of the GFPmut2 reporter fluorescence in presence of 1,3-cyclohexanediol. Multiple rounds of library screening, sorting, renewed mutagenesis and screening resulted in 4.5-fold improvement of the response to 1,3-cyclohexanediol and a lower detection limit of 0.25 mM. All observed mutations except one were located outside the direct ligand-binding pocket, suggesting they were compensatory and helping protein folding or functional behavior other than interaction with the ligand. Our results thus demonstrate that combinations of ligand-binding-pocket redesign and randomized mutagenesis can indeed lead to the selection and recovery of periplasmic-binding protein mutants with non-natural compound recognition. However, current lack of understanding of the intermolecular movement and ligand-binding in periplasmic binding proteins such as RbsB are limiting the rational production of further and better sensory mutants.

scholarly journals Gene Regulatory Potential of Nonsteroidal Vitamin D Receptor Ligands

2005 ◽  
Vol 19 (8) ◽  
pp. 2060-2073 ◽  
Author(s):  
Mikael Peräkylä ◽  
Marjo Malinen ◽  
Karl-Heinz Herzig ◽  
Carsten Carlberg
Keyword(s):  
Ligand Binding ◽  
Cellular Proliferation ◽  
Bone Mineralization ◽  
Binding Pocket ◽  
Drug Candidate ◽  
Hydroxyl Groups ◽  
Ligand Binding Pocket ◽  
Natural Ligand

Abstract The seco-steroid 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3] is a promising drug candidate due to its pleiotropic function including the regulation of calcium homeostasis, bone mineralization and cellular proliferation, differentiation, and apoptosis. We report here a novel class of nonsteroidal compounds, represented by the bis-aromatic molecules CD4409, CD4420, and CD4528, as ligands of the 1α,25(OH)2D3 receptor (VDR). Taking the known diphenylmethane derivative LG190178 as a reference, this study provides molecular evaluation of the interaction of nonsteroidal ligands with the VDR. All four nonsteroidal compounds were shown to induce VDR-retinoid X receptor heterodimer complex formation on a 1α,25(OH)2D3 response element, stabilize the agonistic conformation of the VDR ligand-binding domain, enable the interaction of VDR with coactivator proteins and contact with their three hydroxyl groups the same residues within the ligand-binding pocket of the VDR as 1α,25(OH)2D3. Molecular dynamics simulations demonstrated that all four nonsteroidal ligands take a shape within the ligand-binding pocket of the VDR that is very similar to that of the natural ligand. CD4528 is mimicking the natural hormone best and was found to be in vitro at least five times more potent than LG190178. In living cells, CD4528 was only two times less potent than 1α,25(OH)2D3 and induced mRNA expression of the VDR target gene CYP24 in a comparable fashion. At a noncalcemic dose of 150 μg/kg, CD4528 showed in vivo a clear induction of CYP24 expression and therefore may be used as a lead compound for the development of therapeutics against psoriasis, osteoporosis, and cancer.

scholarly journals Glycine activated ion channel subunits encoded by ctenophore glutamate receptor genes

2015 ◽  
Vol 112 (44) ◽  
pp. E6048-E6057 ◽  
Author(s):  
Robert Alberstein ◽  
Richard Grey ◽  
Austin Zimmet ◽  
David K. Simmons ◽  
Mark L. Mayer
Keyword(s):  
Ligand Binding ◽  
Salt Bridge ◽  
Binding Pocket ◽  
Kainate Receptors ◽  
Mnemiopsis Leidyi ◽  
Binding Assays ◽  
Sequence Alignments ◽  
Binding Domains ◽  
Binding Cavity ◽  
Future Work

Recent genome projects for ctenophores have revealed the presence of numerous ionotropic glutamate receptors (iGluRs) in Mnemiopsis leidyi and Pleurobrachia bachei, among our earliest metazoan ancestors. Sequence alignments and phylogenetic analysis show that these form a distinct clade from the well-characterized AMPA, kainate, and NMDA iGluR subtypes found in vertebrates. Although annotated as glutamate and kainate receptors, crystal structures of the ML032222a and PbiGluR3 ligand-binding domains (LBDs) reveal endogenous glycine in the binding pocket, whereas ligand-binding assays show that glycine binds with nanomolar affinity; biochemical assays and structural analysis establish that glutamate is occluded from the binding cavity. Further analysis reveals ctenophore-specific features, such as an interdomain Arg-Glu salt bridge, present only in subunits that bind glycine, but also a conserved disulfide in loop 1 of the LBD that is found in all vertebrate NMDA but not AMPA or kainate receptors. We hypothesize that ctenophore iGluRs are related to an early ancestor of NMDA receptors, suggesting a common evolutionary path for ctenophores and bilaterian species, and suggest that future work should consider both glycine and glutamate as candidate neurotransmitters in ctenophore species.

scholarly journals The Phytoestrogen Coumestrol Is a Naturally Occurring Antagonist of the Human Pregnane X Receptor

2008 ◽  
Vol 22 (4) ◽  
pp. 838-857 ◽  
Author(s):  
Hongwei Wang ◽  
Hao Li ◽  
Linda B. Moore ◽  
Michael D. L. Johnson ◽  
Jodi M. Maglich ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Drug Interactions ◽  
Target Genes ◽  
Pregnane X Receptor ◽  
Binding Pocket ◽  
Human Hepatocytes ◽  
Primary Human Hepatocytes ◽  
Naturally Occurring ◽  
Binding Cavity ◽  
Transcription Data

Antagonizing the action of the human nuclear xenobiotic receptor pregnane X receptor (PXR) may have important clinical implications in preventing drug-drug interactions and improving therapeutic efficacy. We provide evidence that a naturally occurring phytoestrogen, coumestrol, is an antagonist of the nuclear receptor PXR (NR1I2). In transient transfection assays, coumestrol was able to suppress the agonist effects of SR12813 on human PXR activity. PXR activity was assessed and correlated with effects on the metabolism of the anesthetic tribromoethanol and on gene expression in primary human hepatocytes. We found that coumestrol was able to suppress the effects of PXR agonists on the expression of the known PXR target genes, CYP3A4 and CYP2B6, in primary human hepatocytes as well as inhibit metabolism of tribromoethanol in humanized PXR mice. Coumestrol at concentrations above 1.0 μm competed in scintillation proximity assays with a labeled PXR agonist for binding to the ligand-binding cavity. However, mammalian two-hybrid assays and transient transcription data using ligand-binding-cavity mutant forms of PXR show that coumestrol also antagonizes coregulator recruitment. This effect is likely by binding to a surface outside the ligand-binding pocket. Taken together, these data imply that there are antagonist binding site(s) for coumestrol on the surface of PXR. These studies provide the basis for development of novel small molecule inhibitors of PXR with the ultimate goal of clinical applications toward preventing drug-drug interactions.

scholarly journals The first plant acyl-CoA-binding protein structures: the close homologues OsACBP1 and OsACBP2 from rice

2017 ◽  
Vol 73 (5) ◽  
pp. 438-448 ◽  
Author(s):  
Ze-Hua Guo ◽  
Wallace H. Y. Chan ◽  
Geoffrey K. W. Kong ◽  
Quan Hao ◽  
Mee-Len Chye
Keyword(s):  
Arabidopsis Thaliana ◽  
Binding Affinity ◽  
Protein Structures ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Titration Calorimetry ◽  
Binding Modes ◽  
High Sequence Identity ◽  
Sequence Identity ◽  
Chain Acyl

Acyl-CoA-binding proteins (ACBPs) are a family of proteins that facilitate the binding of long-chain acyl-CoA esters at a conserved acyl-CoA-binding domain. ACBPs act to form intracellular acyl-CoA pools, transport acyl-CoA esters and regulate lipid metabolism. In the model plantArabidopsis thaliana, a family of six ACBPs has been demonstrated to function in stress and development. Six ACBPs (OsACBPs) have also been identified inOryza sativa(rice), but they are not as well characterized as those inArabidopsis thaliana. To understand the need in rice for the two 10 kDa ACBPs, namely OsACBP1 and OsACBP2, which share 79% sequence identity, their crystal structures were elucidated and their affinities toward acyl-CoA esters were compared using isothermal titration calorimetry. OsACBP2 was found to display a higher binding affinity for unsaturated acyl-CoA esters than OsACBP1. A difference between the two proteins is observed at helix 3 and is predicted to lead to different ligand-binding modes in terms of the shape of the binding pocket and the residues that are involved. OsACBP1 thus resembles bovine ACBP, while OsACBP2 is similar to human liver ACBP, in both structure and binding affinity. This is the first time that ACBP structures have been reported from plants, and suggests that OsACBP1 and OsACBP2 are not redundant in function despite their high sequence identity and general structural similarity.

Structural Insights into Azole-based Inhibitors of Heme Oxygenase-1: Development of Selective Compounds for Therapeutic Applications

2019 ◽  
Vol 25 (42) ◽  
pp. 5803-5821 ◽  
Author(s):  
Mona N. Rahman ◽  
Dragic Vukomanovic ◽  
Jason Z. Vlahakis ◽  
Walter A. Szarek ◽  
Kanji Nakatsu ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Competitive Inhibition ◽  
Cytochromes P450 ◽  
Structural Similarity ◽  
Binding Pocket ◽  
Initial Study ◽  
Structural Basis ◽  
Heme Oxygenase 1 ◽  
Design Strategies ◽  
Inhibitor Binding

The development of isozyme-selective heme oxygenase (HO) inhibitors promises powerful pharmacological tools to elucidate the regulatory characteristics of the HO system. It is already known that HO has cytoprotective properties with a role in several disease states; thus, it is an enticing therapeutic target. Historically, the metalloporphyrins have been used as competitive HO inhibitors based on their structural similarity to the substrate, heme. However, heme’s important role in several other proteins (e.g. cytochromes P450, nitric oxide synthase), results in non-selectivity being an unfortunate side effect. Reports that azalanstat and other non-porphyrin molecules inhibited HO led to a multi-faceted effort over a decade ago to develop novel compounds as potent, selective inhibitors of HO. The result was the creation of the first generation of non-porphyrin based, non-competitive inhibitors with selectivity for HO, including a subset with isozyme selectivity for HO-1. Using X-ray crystallography, the structures of several complexes of HO-1 with novel inhibitors have been elucidated and provided insightful information regarding the salient features required for inhibitor binding. This included the structural basis for non-competitive inhibition, flexibility and adaptability of the inhibitor binding pocket, and multiple, potential interaction subsites, all of which can be exploited in future drug-design strategies. Notably, HO-1 inhibitors are of particular interest for the treatment of hyperbilirubinemia and certain types of cancer. Key features based on this initial study have already been used by others to discover additional potential HO-1 inhibitors. Moreover, studies have begun to use selected compounds and determine their effects in some disease models.

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