Extracellular Matrix Proteome of Chickpea (CicerarietinumL.) Illustrates Pathway Abundance, Novel Protein Functions and Evolutionary Perspect

2006 ◽  
Vol 5 (7) ◽  
pp. 1711-1720 ◽  
Author(s):  
Deepti Bhushan ◽  
Aarti Pandey ◽  
Arnab Chattopadhyay ◽  
Mani Kant Choudhary ◽  
Subhra Chakraborty ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: M319C, T431I, and K337D

2019 ◽  
Author(s):  
Peishan Huang ◽  
Stephanie C. Contreras ◽  
Eliana Bloomfield ◽  
Kristine Schmitz ◽  
Augustine Arredondo ◽  
...  
Keyword(s):  
Protein Function ◽  
Kinetic Data ◽  
Prediction Accuracy ◽  
Paenibacillus Polymyxa ◽  
Computational Algorithms ◽  
Enzyme Design ◽  
Data Set ◽  
Computational Tools ◽  
Protein Functions ◽  
Novel Protein

ABSTRACTThe use of computational tools has become an increasingly popular tool for engineering protein function. While there are numerous examples of computational tools enabling the design of novel protein functions, there remains room for improvement in both prediction accuracy and success. To improve algorithms for functional and stability predictions, we have initiated the development of a data set designed to be used for training new computational algorithms for enzyme design. To date our dataset is composed of over 129 mutants with associated expression levels, kinetic data, and thermal stability for the enzyme β-glucosidase B (BglB) from Paenibacillus polymyxa. In this study, we introduced three new variants (M319C, T431I, and K337D) to our existing dataset with the goal of cultivating a larger dataset to train new design algorithms and more broadly explore structure-function relationships in BglB.

scholarly journals Calpain A modulates Toll responses by limited Cactus/IκB proteolysis

2013 ◽  
Vol 24 (18) ◽  
pp. 2966-2980 ◽  
Author(s):  
Marcio Fontenele ◽  
Bomyi Lim ◽  
Danielle Oliveira ◽  
Márcio Buffolo ◽  
David H. Perlman ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Immune System ◽  
Cysteine Proteases ◽  
Proteolytic Cleavage ◽  
Terminal Region ◽  
Full Length ◽  
Calcium Dependent ◽  
Protein Functions ◽  
Novel Protein

Calcium-dependent cysteine proteases of the calpain family are modulatory proteases that cleave their substrates in a limited manner. Among their substrates, calpains target vertebrate and invertebrate IκB proteins. Because proteolysis by calpains potentially generates novel protein functions, it is important to understand how this affects NFκB activity. We investigate the action of Calpain A (CalpA) on the Drosophila melanogaster IκB homologue Cactus in vivo. CalpA alters the absolute amounts of Cactus protein. Our data indicate, however, that CalpA uses additional mechanisms to regulate NFκB function. We provide evidence that CalpA interacts physically with Cactus, recognizing a Cactus pool that is not bound to Dorsal, a fly NFκB/Rel homologue. We show that proteolytic cleavage by CalpA generates Cactus fragments lacking an N-terminal region required for Toll responsiveness. These fragments are generated in vivo and display properties distinct from those of full-length Cactus. We propose that CalpA targets free Cactus, which is incorporated into and modulates Toll-responsive complexes in the embryo and immune system.

scholarly journals Hypomorphic Sox10 alleles reveal novel protein functions and unravel developmental differences in glial lineages

Development ◽  
2007 ◽  
Vol 134 (18) ◽  
pp. 3271-3281 ◽  
Author(s):  
S. Schreiner ◽  
F. Cossais ◽  
K. Fischer ◽  
S. Scholz ◽  
M. R. Bosl ◽  
...  
Keyword(s):  
Developmental Differences ◽  
Protein Functions ◽  
Novel Protein

scholarly journals Selection and screening strategies in directed evolution to improve protein stability

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Chang Ren ◽  
Xin Wen ◽  
Jun Mencius ◽  
Shu Quan
Keyword(s):  
Systematic Review ◽  
Protein Stability ◽  
Directed Evolution ◽  
Rapid Development ◽  
Therapeutic Applications ◽  
Screening Strategies ◽  
Protein Functions ◽  
Novel Protein

AbstractProtein stability is not only fundamental for experimental, industrial, and therapeutic applications, but is also the baseline for evolving novel protein functions. For decades, stability engineering armed with directed evolution has continued its rapid development and inevitably poses challenges. Generally, in directed evolution, establishing a reliable link between a genotype and any interpretable phenotype is more challenging than diversifying genetic libraries. Consequently, we set forth in a small picture to emphasize the screening or selection techniques in protein stability-directed evolution to secure the link. For a more systematic review, two main branches of these techniques, namely cellular or cell-free display and stability biosensors, are expounded with informative examples.

scholarly journals Correction: A Viable Hypomorphic Allele of the Essential IMP3 Gene Reveals Novel Protein Functions in Saccharomyces cerevisiae

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
Author(s):  
Bruno Cosnier ◽  
Marta Kwapisz ◽  
Isabelle Hatin ◽  
Olivier Namy ◽  
Sylvie Hermann-Le Denmat ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Hypomorphic Allele ◽  
Protein Functions ◽  
Novel Protein

scholarly journals The Arabidopsis thaliana Chloroplast Proteome Reveals Pathway Abundance and Novel Protein Functions

2004 ◽  
Vol 14 (5) ◽  
pp. 354-362 ◽  
Author(s):  
Torsten Kleffmann ◽  
Doris Russenberger ◽  
Anne von Zychlinski ◽  
Wayne Christopher ◽  
Kimmen Sjölander ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Protein Functions ◽  
Chloroplast Proteome ◽  
Novel Protein

scholarly journals Genetic Diversity of Serine Protease Inhibitors in Myxozoan (Cnidaria, Myxozoa) Fish Parasites

2020 ◽  
Vol 8 (10) ◽  
pp. 1502
Author(s):  
Edit Eszterbauer ◽  
Dóra Sipos ◽  
Győző L. Kaján ◽  
Dóra Szegő ◽  
Ivan Fiala ◽  
...  
Keyword(s):  
Serine Protease ◽  
Protease Inhibitors ◽  
High Throughput Sequencing ◽  
Fish Parasites ◽  
Serine Protease Inhibitors ◽  
Animal Group ◽  
Protein Functions ◽  
First Time ◽  
Average Sequence Identity ◽  
Novel Protein

We studied the genetic variability of serine protease inhibitors (serpins) of Myxozoa, microscopic endoparasites of fish. Myxozoans affect the health of both farmed and wild fish populations, causing diseases and mortalities. Despite their global impact, no effective protection exists against these parasites. Serpins were reported as important factors for host invasion and immune evasion, and as promising targets for the development of antiparasitic therapies. For the first time, we identified and aligned serpin sequences from high throughput sequencing datasets of ten myxozoan species, and analyzed 146 serpins from this parasite group together with those of other taxa phylogenetically, to explore their relationship and origins. High intra- and interspecific variability was detected among the examined serpins. The average sequence identity was 25–30% only. The conserved domains (i.e., motif and signature) showed taxon-level differences. Serpins clustered according to taxonomy rather than to serpin types, and myxozoan serpins seemed to be highly divergent from that of other taxa. None of them clustered with their closest relative free-living cnidarians. The genetic distinction of myxozoan serpins further strengthens the idea of an independent origin of Myxozoa, and may indicate novel protein functions potentially related to parasitism in this animal group.

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