Top 3 Biorxiv Papers Today in Biochemistry


1.998 Mikeys
#1. Strategies to improve scFvs as crystallization chaperones suggested by analysis of a complex with the human PHD-bromodomain SP140
Michael Fairhead, Charlotta Preger, Edvard Wigren, Claire Strain-Damerell, Elena Ossipova, Mingda Ye, Mpho Makola, Nicola A Burgess-Brown, Helena Persson, Frank von Delft, Susanne Graslund
Antibody fragments have great potential as crystallization chaperones for structural biology due to their ability to either stabilise targets, trap certain conformations and/or promote crystal packing. Here we present an example of using a single-chain variable fragment (scFv) to determine the previously unsolved structure of the multidomain protein SP140. This nuclear leukocyte-specific protein contains domains related to chromatin-mediated gene expression and has been implicated in various disease states. The structure of two of the domains (PHD-bromodomain) was solved by crystallizing them as a complex with a scFv generated by phage display technology. SP140 maintains a similar overall fold to previous PHD-bromodomains and the scFv CDR loops predominately interact with the PHD, while the framework regions of the scFv makes numerous interactions with the bromodomain. Analysis of our and other complex structures suggest various protein engineering strategies that might be employed to improve the usefulness of scFvs as...
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Authors: 11
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1.997 Mikeys
#2. The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions
Maire Gavagan, Erin Fagnan, Elizabeth B Speltz, Jesse G Zalatan
GSK3β is a multifunctional kinase that phosphorylates β-catenin in the Wnt signaling network and also acts on other protein targets in response to distinct cellular signals. To test the long-standing hypothesis that the scaffold protein Axin specifically accelerates β-catenin phosphorylation, we measured GSK3β reaction rates with multiple substrates in a minimal, biochemically-reconstituted system. We observed an unexpectedly small, ~2-fold Axin-mediated rate increase for the β-catenin reaction. The much larger effects reported previously may have arisen because Axin can rescue GSK3β from an inactive state that occurs only under highly specific conditions. Surprisingly, Axin significantly slows the reaction of GSK3β with CREB, a non-Wnt pathway substrate. When both β-catenin and CREB are present, Axin accelerates the β-catenin reaction by preventing competition with CREB. Thus, while Axin alone does not markedly accelerate the β-catenin reaction, in physiological settings where multiple GSK3β substrates are present, Axin can...
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biorxivpreprint: The Wnt pathway scaffold protein Axin promotes signaling specificity by suppressing competing kinase reactions https://t.co/6kk9k1Ity9 #bioRxiv
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Authors: 4
Total Words: 8396
Unqiue Words: 2106

1.997 Mikeys
#3. Lipidomics analysis of juveniles’ blue mussels (Mytilus edulis L. 1758), a key economic and ecological species.
Vincenzo Alessandro Laudicella, Christine Beveridge, Stefano Carboni, Sofia Cota Franco, Mary K. Doherty, Nina Long, Elaine Mitchell, Michele S. Stanley, Philip D. Whitfield, Adam D. Hughes
Blue mussels (Mytilus edulis L.) are important components of coastal ecosystems functioning through benthopelagic coupling and ecosystem engineering. At the same time, mussel production is central in the economy of coastal areas. Therefore, understanding their nutritional, physiological and metabolic processes at key life stages is important for their management, both within food production systems and in wild populations. Lipids are crucial molecules for bivalve growth, but their diversity and roles have been considered from fatty acid (FA) perspective. In this paper, we applied lipidomics to bivalve nutrition. Lipidomics provides a holistic perspective on lipid patterns; by examining the lipidome, important physiological information can be acquired. Here, we use controlled laboratory experiments to elucidate the responses to changes in the diet of newly settled mussels juveniles, one of the most critical life stages. The diets considered in this study are single strains diet of Cylindrotheca fusiformis CCAP 1017/2 – CYL,...
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Sample Sizes : [30, 30, 3, 3, 3]
Authors: 10
Total Words: 20643
Unqiue Words: 6887

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