A Complementation Assay for in Vivo Protein Structure/Function Analysis inPhyscomitrella patens(Funariaceae)

The formation of a gradient of nuclear Dorsal protein in the early Drosophila embryo is the last step in a maternally encoded dorsal-ventral signal transduction pathway. This gradient is formed in response to a ventral signal, which leads to the dissociation of cytoplasmic Dorsal from the I kappa B homolog Cactus. Free Dorsal is then targeted to the nucleus. Dorsal is a Rel-family transcription factor. Signal-dependent nuclear localization characterizes the regulation of Rel proteins. In order to identify regions of Dorsal that are essential for its homodimerization, nuclear targeting, and interaction with Cactus, we have performed an in vivo structure-function analysis. Our results show that all these functions are carried out by regions within the conserved Rel-homology region of Dorsal. The C-terminal divergent half of Dorsal is dispensable for its selective nuclear import. A basic stretch of 6 amino acids at the C terminus of the Rel-homology region is necessary for nuclear localization. This nuclear localization signal is not required for Cactus binding. Removal of the N-terminal 40 amino acids abolished the nuclear import of Dorsal, uncovering a potentially novel function for this highly conserved region.

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Development of new computational amino acid parameters for protein structure/function analysis within the resonant recognition model

2001 Conference Proceedings of the 23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society ◽

10.1109/iembs.2001.1017393 ◽

2005 ◽

Author(s):

E. Pirogova ◽

Irena ◽

Cosic

Keyword(s):

Protein Structure ◽

Amino Acid ◽

Structure Function ◽

Function Analysis ◽

Recognition Model ◽

Resonant Recognition Model

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Structure/Function Analysis of the Vaccinia Virus F18 Phosphoprotein, an Abundant Core Component Required for Virion Maturation and Infectivity

Journal of Virology ◽

10.1128/jvi.00399-10 ◽

2010 ◽

Vol 84 (13) ◽

pp. 6846-6860 ◽

Cited By ~ 15

Author(s):

Nadi T. Wickramasekera ◽

Paula Traktman

Keyword(s):

Amino Acids ◽

Structure Function ◽

Protein Interactions ◽

Function Analysis ◽

Aromatic Amino Acids ◽

Protein Protein Interactions ◽

Core Component ◽

Virion Morphogenesis

ABSTRACT Poxvirus virions, whose outer membrane surrounds two lateral bodies and a core, contain at least 70 different proteins. The F18 phosphoprotein is one of the most abundant core components and is essential for the assembly of mature virions. We report here the results of a structure/function analysis in which the role of conserved cysteine residues, clusters of charged amino acids and clusters of hydrophobic/aromatic amino acids have been assessed. Taking advantage of a recombinant virus in which F18 expression is IPTG (isopropyl-β-d-thiogalactopyranoside) dependent, we developed a transient complementation assay to evaluate the ability of mutant alleles of F18 to support virion morphogenesis and/or to restore the production of infectious virus. We have also examined protein-protein interactions, comparing the ability of mutant and WT F18 proteins to interact with WT F18 and to interact with the viral A30 protein, another essential core component. We show that F18 associates with an A30-containing multiprotein complex in vivo in a manner that depends upon clusters of hydrophobic/aromatic residues in the N′ terminus of the F18 protein but that it is not required for the assembly of this complex. Finally, we confirmed that two PSSP motifs within F18 are the sites of phosphorylation by cellular proline-directed kinases in vitro and in vivo. Mutation of both of these phosphorylation sites has no apparent impact on virion morphogenesis but leads to the assembly of virions with significantly reduced infectivity.

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A Rationally Designed Aminoacyl-tRNA Synthetase for Genetically Encoded Fluorescent Amino Acids

10.1101/065227 ◽

2016 ◽

Cited By ~ 1

Author(s):

Ximena Steinberg ◽

Jason Galpin ◽

Gibran Nasir ◽

Jose Sepulveda-Ugarte ◽

Romina V. Sepúlveda ◽

...

Keyword(s):

Amino Acids ◽

Protein Structure ◽

Structure Function ◽

Trna Synthetase ◽

Aminoacyl Trna Synthetase ◽

E Coli ◽

Promising Strategy ◽

Fluorescent Amino Acids

AbstractThe incorporation of non-canonical amino acids into proteins has emerged as a promising strategy to manipulate and study protein structure-function relationships with superior precision in vitro and in vivo. To date, fluorescent non-canonical amino acids (f-ncAA) have been successfully incorporated in proteins expressed in bacterial systems, Xenopus oocytes, and HEK-293T cells. Here, we describe the rational generation of an orthogonal aminoacyltRNA synthetase based on the E. coli tyrosine synthetase that is capable of encoding the f-ncAA tyr-coumarin in HEK-293T cells.

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Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome

10.1101/2020.05.05.20092452 ◽

2020 ◽

Cited By ~ 2

Author(s):

Vijendra Ramlall ◽

Phyllis M. Thangaraj ◽

Cem Meydan ◽

Jonathan Foox ◽

Daniel Butler ◽

...

Keyword(s):

Protein Structure ◽

Structure Function ◽

Function Analysis ◽

Transcriptional Profiling ◽

Public Health Intervention ◽

Virus Protein ◽

Type I ◽

Host Interactions ◽

History Of ◽

Viral Host Interactions

SummaryUnderstanding the pathophysiology of SARS-CoV-2 infection is critical for therapeutics and public health intervention strategies. Viral-host interactions can guide discovery of regulators of disease outcomes, and protein structure function analysis points to several immune pathways, including complement and coagulation, as targets of the coronavirus proteome. To determine if conditions associated with dysregulation of the complement or coagulation systems impact adverse clinical outcomes, we performed a retrospective observational study of 11,116 patients who presented with suspected SARS-CoV-2 infection. We found that history of macular degeneration (a proxy for complement activation disorders) and history of coagulation disorders (thrombocytopenia, thrombosis, and hemorrhage) are risk factors for morbidity and mortality in SARS-CoV-2 infected patients - effects that could not be explained by age, sex, or history of smoking. Further, transcriptional profiling of nasopharyngeal (NP) swabs from 650 control and SARS-CoV-2 infected patients demonstrated that in addition to innate Type-I interferon and IL-6 dependent inflammatory immune responses, infection results in robust engagement and activation of the complement and coagulation pathways. Finally, we conducted a candidate driven genetic association study of severe SARS-CoV-2 disease. Among the findings, our scan identified putative complement and coagulation associated loci including missense, eQTL and sQTL variants of critical regulators of the complement and coagulation cascades. In addition to providing evidence that complement function modulates SARS-CoV-2 infection outcome, the data point to putative transcriptional genetic markers of susceptibility. The results highlight the value of using a multi-modal analytical approach, combining molecular information from virus protein structure-function analysis with clinical informatics, transcriptomics, and genomics to reveal determinants and predictors of immunity, susceptibility, and clinical outcome associated with infection.

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