scholarly journals Computational study of paroxetine-like inhibitors reveals new molecular insight to inhibit GRK2 with selectivity over ROCK1

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Seketoulie Keretsu ◽  
Swapnil P. Bhujbal ◽  
Seung Joo Cho
Keyword(s):  
Heart Failure ◽  
Computational Study ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Pyrazole Ring ◽  
3D Qsar ◽  
Free Energy Calculations ◽  
Piperidine Ring ◽  
High Sequence Similarity

Abstract The G-protein coupled receptor kinase 2 (GRK2) regulates the desensitization of beta-adrenergic receptors (β-AR), and its overexpression has been implicated in heart failure. Hence, the inhibition of GRK2 is considered to be an important drug target for the treatment of heart failure. Due to the high sequence similarity of GRK2 with the A, G, and C family (AGC family) of kinases, the inhibition of GRK2 also leads to the inhibition of AGC kinases such as Rho-associated coiled-coil kinase 1 (ROCK1). Therefore, unraveling the mechanisms to selectively inhibit GRK2 poses an important challenge. We have performed molecular docking, three dimensional quantitative structure activity relationship (3D-QSAR), molecular dynamics (MD) simulation, and free energy calculations techniques on a series of 53 paroxetine-like compounds to understand the structural properties desirable for enhancing the inhibitory activity for GRK2 with selectivity over ROCK1. The formation of stable hydrogen bond interactions with the residues Phe202 and Lys220 of GRK2 seems to be important for selective inhibition of GRK2. Electropositive substituents at the piperidine ring and electronegative substituents near the amide linker between the benzene ring and pyrazole ring showed a higher inhibitory preference for GRK2 over ROCK1. This study may be used in designing more potent and selective GRK2 inhibitors for therapeutic intervention of heart failure.

scholarly journals Cloning and Characterization of R3b; Members of the R3 Superfamily of Late Blight Resistance Genes Show Sequence and Functional Divergence

2011 ◽  
Vol 24 (10) ◽  
pp. 1132-1142 ◽  
Author(s):  
Guangcun Li ◽  
Sanwen Huang ◽  
Xiao Guo ◽  
Ying Li ◽  
Yu Yang ◽  
...  
Keyword(s):  
Late Blight ◽  
Positional Cloning ◽  
Sequence Similarity ◽  
Functional Divergence ◽  
Durable Resistance ◽  
Coiled Coil ◽  
Avirulence Gene ◽  
R Gene ◽  
Gene Stacking ◽  
High Sequence Similarity

Massive resistance (R) gene stacking is considered to be one of the most promising approaches to provide durable resistance to potato late blight for both conventional and genetically modified breeding strategies. The R3 complex locus on chromosome XI in potato is an example of natural R gene stacking, because it contains two closely linked R genes (R3a and R3b) with distinct resistance specificities to Phytophthora infestans. Here, we report about the positional cloning of R3b. Both transient and stable transformations of susceptible tobacco and potato plants showed that R3b conferred full resistance to incompatible P. infestans isolates. R3b encodes a coiled-coil nucleotide-binding site leucine-rich repeat protein and exhibits 82% nucleotide identity with R3a located in the same R3 cluster. The R3b gene specifically recognizes Avr3b, a newly identified avirulence factor from P. infestans. R3b does not recognize Avr3a, the corresponding avirulence gene for R3a, showing that, despite their high sequence similarity, R3b and R3a have clearly distinct recognition specificities. In addition to the Rpi-mcd1/Rpi-blb3 locus on chromosome IV, the R3 locus on chromosome XI is the second example of an R-gene cluster with multiple genes recognizing different races of P. infestans.

scholarly journals Investigation of a Direct Interaction between miR4749 and the Tumor Suppressor p53 by Fluorescence, FRET and Molecular Modeling

Biomolecules ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 346
Author(s):  
Anna Rita Bizzarri ◽  
Salvatore Cannistraro
Keyword(s):  
Tumor Suppressor ◽  
Computational Modeling ◽  
Binding Free Energy ◽  
Sequence Similarity ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Direct Interaction ◽  
Free Energy Calculations ◽  
Tumor Suppressor P53 ◽  
High Sequence Similarity

The interactions between the DNA binding domain (DBD) of the tumor suppressor p53 and miR4749, characterized by a high sequence similarity with the DNA Response Element (RE) of p53, was investigated by fluorescence spectroscopy combined with computational modeling and docking. Fluorescence quenching experiments witnessed the formation of a specific complex between DBD and miR4749 with an affinity of about 105 M. Förster Resonance Energy Transfer (FRET) allowed us to measure a distance of 3.9 ± 0.3 nm, between the lone tryptophan of DBD and an acceptor dye suitably bound to miR4749. Such information, combined with a computational modeling approach, allowed us to predict possible structures for the DBD-miR4749 complex. A successive docking refinement, complemented with binding free energy calculations, led us to single out a best model for the DBD-miR4749 complex. We found that the interaction of miR4749 involves the DBD L3 loop and the H1 helix, close to the Zn-finger motif; with this suggesting that miR4749 could directly inhibit the p53 interaction with DNA. These results might inspire new therapeutic strategies finalized to restore the p53 functional activity.

scholarly journals NuMA Influences Higher Order Chromatin Organization in Human Mammary Epithelium

2007 ◽  
Vol 18 (2) ◽  
pp. 348-361 ◽  
Author(s):  
Patricia C. Abad ◽  
Jason Lewis ◽  
I. Saira Mian ◽  
David W. Knowles ◽  
Jennifer Sturgis ◽  
...  
Keyword(s):  
Mammary Epithelial Cells ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Mammary Epithelium ◽  
Chromatin Organization ◽  
Mammary Epithelial ◽  
Cell Phenotype ◽  
Deoxyribonuclease I ◽  
C Terminus

The coiled-coil protein NuMA is an important contributor to mitotic spindle formation and stabilization. A potential role for NuMA in nuclear organization or gene regulation is suggested by the observations that its pattern of nuclear distribution depends upon cell phenotype and that it interacts and/or colocalizes with transcription factors. To date, the precise contribution of NuMA to nuclear function remains unclear. Previously, we observed that antibody-induced alteration of NuMA distribution in growth-arrested and differentiated mammary epithelial structures (acini) in three-dimensional culture triggers the loss of acinar differentiation. Here, we show that in mammary epithelial cells, NuMA is present in both the nuclear matrix and chromatin compartments. Expression of a portion of the C terminus of NuMA that shares sequence similarity with the chromatin regulator HPC2 is sufficient to inhibit acinar differentiation and results in the redistribution of NuMA, chromatin markers acetyl-H4 and H4K20m, and regions of deoxyribonuclease I-sensitive chromatin compared with control cells. Short-term alteration of NuMA distribution with anti-NuMA C-terminus antibodies in live acinar cells indicates that changes in NuMA and chromatin organization precede loss of acinar differentiation. These findings suggest that NuMA has a role in mammary epithelial differentiation by influencing the organization of chromatin.

scholarly journals The Rib43a Protein Is Associated with Forming the Specialized Protofilament Ribbons of Flagellar Microtubules inChlamydomonas

2000 ◽  
Vol 11 (1) ◽  
pp. 201-215 ◽  
Author(s):  
Jan M. Norrander ◽  
Aimee M. deCathelineau ◽  
Jennifer A. Brown ◽  
Mary E. Porter ◽  
Richard W. Linck
Keyword(s):  
Homo Sapiens ◽  
Sequence Similarity ◽  
Germ Cell Tumors ◽  
Three Dimensional ◽  
Coiled Coil ◽  
Dimensional Structure ◽  
Polymorphism Analysis ◽  
Basal Bodies ◽  
Coding Region ◽  
Expression Library

Ciliary and flagellar microtubules contain a specialized set of three protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. Previous studies of sea urchin sperm flagella identified three of the ribbon proteins astektins, which form coiled-coil filaments in doublet microtubules and which are associated with basal bodies and centrioles. To study the function of tektins and other ribbon proteins in the assembly of flagella and basal bodies, we have begun an analysis of ribbons from the unicellular biflagellate, Chlamydomonas reinhardtii, and report here the molecular characterization of the ribbon protein rib43a. Using antibodies against rib43a to screen an expression library, we recovered a full-length cDNA clone that encodes a 42,657-Da polypeptide. On Northern blots, the rib43a cDNA hybridized to a 1.7-kb transcript, which was up-regulated upon deflagellation, consistent with a role for rib43a in flagellar assembly. The cDNA was used to isolate RIB43a, an ∼4.6-kb genomic clone containing the complete rib43a coding region, and restriction fragment length polymorphism analysis placed the RIB43agene on linkage group III. Sequence analysis of theRIB43a gene indicates that the substantially coiled-coil rib43a protein shares a high degree of sequence identity with clones from Trypanosoma cruzi and Homo sapiens(genomic, normal fetal kidney, and endometrial and germ cell tumors) but little sequence similarity to other proteins including tektins. Affinity-purified antibodies against native and bacterially expressed rib43a stained both flagella and basal bodies by immunofluorescence microscopy and stained isolated flagellar ribbons by immuno-electron microscopy. The structure of rib43a and its association with the specialized protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilizing doublet and triplet microtubules and in organizing their three-dimensional structure.

scholarly journals Structural organization and evolution of the marsupial zona pellucida

Reproduction ◽  
2002 ◽  
pp. 13-21 ◽  
Author(s):  
WG Breed ◽  
RM Hope ◽  
OW Wiebkin ◽  
SC Spargo ◽  
JA Chapman
Keyword(s):  
Zona Pellucida ◽  
Structural Organization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Three Dimensional ◽  
Reducing Agents ◽  
Molecular Organization ◽  
Dimensional Structure ◽  
High Sequence Similarity ◽  
Lectin Staining

In this review, the biochemical composition and structural organization of the marsupial and eutherian zonae pellucidae are compared. Differences between the zonae from these two groups of mammals are observed in their response to dilute proteases and reducing agents, in their potential glycosylation patterns, and in some of their functions. However, studies on the glycoconjugates and polypeptides of the three zona pellucida genes have not explained these different responses to the proteases and reducing agents. There is high sequence similarity between the zona polypeptides of marsupials and eutherians, as well as a similarity in the oligosaccharides present, as demonstrated by lectin staining. As the marsupial and eutherian lineages diverged from a common ancestor over 100 million years ago, these observations indicate that the three-dimensional structure of these glycoproteins is highly conserved throughout all mammals, although the complexity of its molecular organization has yet to be resolved. Phylogenetic analyses indicate that there are at least four groups of paralogous zona pellucida genes in vertebrates. The marsupial ZPA and ZPB genes have been named in accordance with their orthologues but the phylogenetic relationships of the marsupial ZPC gene require further investigation.

scholarly journals Defensin-like peptide-2 from platypus venom: member of a class of peptides with a distinct structural fold

2000 ◽  
Vol 348 (3) ◽  
pp. 649-656 ◽  
Author(s):  
Allan M. TORRES ◽  
Greg M. DE PLATER ◽  
Magnus DOVERSKOG ◽  
Liesl C. BIRINYI-STRACHAN ◽  
Graham M. NICHOLSON ◽  
...  
Keyword(s):  
Tertiary Structure ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
High Sequence Similarity ◽  
Natural Function ◽  
Global Fold ◽  
Key Residues ◽  
Β Sheet

The venom of the male Australian duck-billed platypus contains a family of four polypeptides of appox. 5 kDa, which are referred to as defensin-like peptides (DLPs). They are unique in that their amino acid sequences have no significant similarities to those of any known peptides; however, the tertiary structure of one of them, DLP-1, has recently been shown to be similar to β-defensin-12 and to the sodium neurotoxin peptide ShI (Stichodactyla helianthus neurotoxin I). Although DLPs are the major peptides in the platypus venom, little is known about their biological roles. In this study, we determined the three-dimensional structure of DLP-2 by NMR spectroscopy, with the aim of gaining insights into the natural function of the DLPs in platypus venom. The DLP-2 structure was found to incorporate a short helix that spans residues 9-12, and an antiparallel β-sheet defined by residues 15-18 and 37-40. The overall fold and cysteine-pairing pattern of DLP-2 were found to be similar to those of DLP-1, and hence β-defensin-12; however, the sequence similarities between the three molecules are relatively small. The distinct structural fold of the DLP-1, DLP-2, and β-defensin-12 is based upon several key residues that include six cysteines. DLP-3 and DLP-4 are also likely to be folded similarly since they have high sequence similarity with DLP-2. The DLPs, and β-defensin-12 may thus be grouped together into a class of polypeptide molecules which have a common or very similar global fold. The fact that the DLPs did not display antimicrobial, myotoxic, or cell-growth-promoting activities implies that the nature of the side chains in this group of peptides is likely to play an important role in defining the biological function(s).

scholarly journals Biosynthesis of the Tricyclic Aromatic Type II Polyketide Rishirilide: New Potential Third Ring Oxygenation after Three Cyclization Steps

2021 ◽  
Author(s):  
Ahmad Alali ◽  
Lin Zhang ◽  
Jianyu Li ◽  
Chijian Zuo ◽  
Dimah Wassouf ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Three Dimensional ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Flavin Reductase ◽  
High Similarity ◽  
Dynamic Simulations ◽  
High Sequence Similarity ◽  
The Past ◽  
Biosynthetic Studies

AbstractRishirilides are a group of PKS II secondary metabolites produced by Streptomyces bottropensis Gö C4/4. Biosynthetic studies in the past have elucidated early and late steps of rishirilide biosynthesis. This work is aiming to solve the remaining steps in the rishirilide biosynthesis. Inactivation of the cyclase gene rslC3 in Streptomyces bottropensis resulted in an interruption of rishirilide production. Instead, accumulation of the tricyclic aromatic galvaquinones was observed. Similar results were observed after deletion of rslO4. Closer inspection into RslO4 crystal structure in addition to site-directed mutagenesis and molecular dynamic simulations revealed that RslO4 might be responsible for quinone formation on the third ring. The RslO1 three-dimensional structure shows a high similarity to FMN-dependent luciferase-like monooxygenases such as the epoxy-forming MsnO8 which acts with the flavin reductase MsnO3 in mensacarcin biosynthesis in the same strain. The high sequence similarity between RslO2 and MsnO3 suggests that RslO2 provides RslO1 with reduced FMN to form an epoxide that serves as substrate for RslO5.

Nocturnin in the demosponge Suberites domuncula: a potential circadian clock protein controlling glycogenin synthesis in sponges

2012 ◽  
Vol 448 (2) ◽  
pp. 233-242 ◽  
Author(s):  
Werner E. G. Müller ◽  
Xiaohong Wang ◽  
Vlad A. Grebenjuk ◽  
Michael Korzhev ◽  
Matthias Wiens ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Metabolic Enzyme ◽  
High Sequence Similarity ◽  
Suberites Domuncula ◽  
Light Supply ◽  
The Stability ◽  
Clock Protein

Sponges are filter feeders that consume a large amount of energy to allow a controlled filtration of water through their aquiferous canal systems. It has been shown that primmorphs, three-dimensional cell aggregates prepared from the demosponge Suberites domuncula and cultured in vitro, change their morphology depending on the light supply. Upon exposure to light, primmorphs show a faster and stronger increase in DNA, protein and glycogen content compared with primmorphs that remain in the dark. The sponge genome contains nocturnin, a light/dark-controlled clock gene, the protein of which shares a high sequence similarity with the related molecule of higher metazoans. The sponge nocturnin protein was found showing a poly(A)-specific 3′-exoribonuclease activity. In addition, the cDNA of the glycogenin gene was identified for subsequent expression studies. Antibodies against nocturnin were raised and used in parallel with the cDNA to determine the regional expression of nocturnin in intact sponge specimens; the highest expression of nocturnin was seen in the epithelial layer around the aquiferous canals. Quantitative PCR analyses revealed that primmorphs after transfer from light to dark show a 10-fold increased expression in the nocturnin gene. In contrast, the expression level of glycogenin decreases in the dark by 3– 4-fold. Exposure of primmorphs to light causes a decrease in nocturnin transcripts and a concurrent increase in glycogenin transcripts. It was concluded that sponges are provided with the molecular circadian clock protein nocturnin that is highly expressed in the dark where it controls the stability of a key metabolic enzyme, glycogenin.

Docking and 3D-QSAR Studies of Hydrazone and Triazole Derivatives for Selective Inhibition of GRK2 over ROCK2

2020 ◽  
Vol 17 (5) ◽  
pp. 618-632
Author(s):  
Seketoulie Keretsu ◽  
Swapnil Pandurang Bhujbal ◽  
Seung Joo Cho
Keyword(s):  
Heart Failure ◽  
Protein Kinase ◽  
Benzene Ring ◽  
Sequence Similarity ◽  
Triazole Ring ◽  
3D Qsar ◽  
Selective Inhibition ◽  
Structural Factors ◽  
Triazole Derivatives ◽  
Qsar Studies

Introduction: G protein-coupled receptor kinase 2 (GRK2) is known to be implicated in heart failure, and therefore serves as an important drug target. GRK2 belongs to the protein kinase A, G, and C family and shares high sequence similarity with its closely related protein, the Rhoassociated coiled-coil protein kinase 2 (ROCK2). Therefore, selective inhibition of GRK2 over ROCK2 is considered crucial for heart failure therapy. Objective: To understand the structural factors for enhancing the inhibitory activity for GRK2 and selectivity over ROCK2, we analyzed and compared molecular interactions using the same set of ligands against both receptors. Methods: We have performed molecular docking and three-dimensional quantitative structure activity relationship (3D-QSAR) studies on a series of hydrazone and triazole derivatives. Results: The presence of hydrophobic substituents at the triazole ring, electronegative substituents between the pyridine and triazole ring and hydrophobic substituents near the benzene ring increases the activity of both kinases. Whereas, having non-bulky substituents near the triazole ring, bulky and hydrophobic substations at the benzene ring and electronegative and H-bond acceptor substituents at the triazole ring showed a higher inhibitory preference for GRK2 over ROCK2. Conclusion: The outcome of this study may be used in the future development of potent GRK2 inhibitors having ROCK2 selectivity.

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