Computational Analysis of Spectroscopical Properties and Binding Affinities of Oxyluciferin Analogs in Firefly Luciferase Protein

The COVID-19 pandemic caused by SARS-CoV-2 is unprecedented in recent memory owing to the non-stop escalation in number of infections and deaths in almost every country of the world. The lack of treatment options further worsens the scenario, thereby necessitating the exploration of already existing US FDA-approved drugs for their effectiveness against COVID-19. In the present study, we have performed virtual screening of nutraceuticals available from DrugBank against 14 SARS-CoV-2 proteins. Molecular docking identified several inhibitors, two of which, rutin and NADH, displayed strong binding affinities and inhibitory potential against SARS-CoV-2 proteins. Further normal model-based simulations were performed to gain insights into the conformational transitions in proteins induced by the drugs. The computational analysis in the present study paves the way for experimental validation and development of multi-target guided inhibitors to fight COVID-19.

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A conserved tripeptide sorts proteins to peroxisomes.

The Journal of Cell Biology ◽

10.1083/jcb.108.5.1657 ◽

1989 ◽

Vol 108 (5) ◽

pp. 1657-1664 ◽

Cited By ~ 724

Author(s):

S J Gould ◽

G A Keller ◽

N Hosken ◽

J Wilkinson ◽

S Subramani

Keyword(s):

Protein Import ◽

Firefly Luciferase ◽

Site Directed Mutagenesis ◽

Directed Mutagenesis ◽

Luciferase Gene ◽

Luciferase Protein ◽

Peroxisomal Targeting ◽

Targeting Signal ◽

Peroxisomal Targeting Signal ◽

Made In

The firefly luciferase protein contains a peroxisomal targeting signal at its extreme COOH terminus (Gould et al., 1987). Site-directed mutagenesis of the luciferase gene reveals that this peroxisomal targeting signal consists of the COOH-terminal three amino acids of the protein, serine-lysine-leucine. When this tripeptide is appended to the COOH terminus of a cytosolic protein (chloramphenicol acetyltransferase), it is sufficient to direct the fusion protein into peroxisomes. Additional mutagenesis experiments reveal that only a limited number of conservative changes can be made in this tripeptide targeting signal without abolishing its activity. These results indicate that peroxisomal protein import, unlike other types of transmembrane translocation, is dependent upon a conserved amino acid sequence.

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Detection of Protein-Protein Interactions in Live Cells and Animals with Split Firefly Luciferase Protein Fragment Complementation

Methods in Molecular Biology - Genomics Protocols ◽

10.1007/978-1-59745-188-8_23 ◽

2008 ◽

pp. 339-352 ◽

Cited By ~ 15

Author(s):

Victor Villalobos ◽

Snehal Naik ◽

David Piwnica-Worms

Keyword(s):

Protein Interactions ◽

Firefly Luciferase ◽

Live Cells ◽

Protein Protein Interactions ◽

Protein Fragment ◽

Protein Fragment Complementation ◽

Luciferase Protein ◽

Fragment Complementation

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Computational analysis of the binding affinities of the natural-product cyclopentapeptides argifin and argadin to chitinase B from Serratia marcescens

Bioorganic & Medicinal Chemistry ◽

10.1016/j.bmc.2008.02.017 ◽

2008 ◽

Vol 16 (7) ◽

pp. 3565-3579 ◽

Cited By ~ 14

Author(s):

Hiroaki Gouda ◽

Yuichi Yanai ◽

Akihiro Sugawara ◽

Toshiaki Sunazuka ◽

Satoshi Ōmura ◽

...

Keyword(s):

Serratia Marcescens ◽

Natural Product ◽

Computational Analysis ◽

Binding Affinities

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Dissection of the molecular mechanisms of protein targeting to the peroxisome using immunofluorescence and immunocryoelectron microscopies

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100157760 ◽

1990 ◽

Vol 48 (3) ◽

pp. 44-45

Author(s):

G-A. Keller ◽

S. J. Gould ◽

S. Subramani ◽

S. Krisans

Keyword(s):

Mammalian Cells ◽

Molecular Mechanisms ◽

Protein Targeting ◽

Firefly Luciferase ◽

Peroxisomal Enzyme ◽

Transfected Cells ◽

Peroxisomal Targeting ◽

Targeting Signal ◽

Series Of Experiments ◽

Peroxisomal Targeting Signal

Subcellular compartments within eukaryotic cells must each be supplied with unique sets of proteins that must be directed to, and translocated across one or more membranes of the target organelles. This transport is mediated by cis- acting targeting signals present within the imported proteins. The following is a chronological account of a series of experiments designed and carried out in an effort to understand how proteins are targeted to the peroxisomal compartment.-We demonstrated by immunocryoelectron microscopy that the enzyme luciferase is a peroxisomal enzyme in the firefly lantern. -We expressed the cDNA encoding firefly luciferase in mammalian cells and demonstrated by immunofluorescence that the enzyme was transported into the peroxisomes of the transfected cells. -Using deletions, linker insertions, and gene fusion to identify regions of luciferase involved in its transport to the peroxisomes, we demonstrated that luciferase contains a peroxisomal targeting signal (PTS) within its COOH-terminal twelve amino acid.

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Specificity determinants of phosphoprotein phosphatases controlling kinetochore functions

Essays in Biochemistry ◽

10.1042/ebc20190065 ◽

2020 ◽

Vol 64 (2) ◽

pp. 325-336 ◽

Cited By ~ 1

Author(s):

Dimitriya H. Garvanska ◽

Jakob Nilsson

Keyword(s):

Spindle Assembly Checkpoint ◽

Activity Level ◽

Phosphorylation Sites ◽

Binding Affinities ◽

Mitotic Kinases ◽

Anaphase Onset ◽

Phosphoprotein Phosphatases ◽

Linear Motifs ◽

Temporal And Spatial ◽

Kinetochore Function

Abstract Kinetochores are instrumental for accurate chromosome segregation by binding to microtubules in order to move chromosomes and by delaying anaphase onset through the spindle assembly checkpoint (SAC). Dynamic phosphorylation of kinetochore components is key to control these activities and is tightly regulated by temporal and spatial recruitment of kinases and phosphoprotein phosphatases (PPPs). Here we focus on PP1, PP2A-B56 and PP2A-B55, three PPPs that are important regulators of mitosis. Despite the fact that these PPPs share a very similar active site, they target unique ser/thr phosphorylation sites to control kinetochore function. Specificity is in part achieved by PPPs binding to short linear motifs (SLiMs) that guide their substrate specificity. SLiMs bind to conserved pockets on PPPs and are degenerate in nature, giving rise to a range of binding affinities. These SLiMs control the assembly of numerous substrate specifying complexes and their position and binding strength allow PPPs to target specific phosphorylation sites. In addition, the activity of PPPs is regulated by mitotic kinases and inhibitors, either directly at the activity level or through affecting PPP–SLiM interactions. Here, we discuss recent progress in understanding the regulation of PPP specificity and activity and how this controls kinetochore biology.

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