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Protein Science: a Publication of the Protein Society

Dejan M Petrovi, Bastien Bissaro, Piotr Chylenski, Morten Skaugen, Morten Sørlie, Marianne S Jensen, Finn L Aachmann, Gaston Courtade, Anikó Várnai, Vincent G H Eijsink
The catalytically crucial N-terminal histidine (His1) of fungal lytic polysaccharide monooxygenases (LPMOs) is post-translationally modified to carry a methylation. The functional role of this methylation remains unknown. We have carried out an in-depth functional comparison of two variants of a family AA9 LPMO from Thermoascus aurantiacus (TaLPMO9A), one with, and one without the methylation on His1. Various activity assays showed that the two enzyme variants are identical in terms of substrate preferences, cleavage specificities and the ability to activate molecular oxygen...
July 4, 2018: Protein Science: a Publication of the Protein Society
Jian Hu, Hui-Fang Liu, Jun Sun, Jia Wang, Rong Liu
It remains challenging to accurately discriminate between biological and crystal interfaces. Most existing analyses and algorithms focused on the features derived from a single side of the interface. However, less attention has been paid to the properties of residue pairs across protein interfaces. To address this problem, we defined a novel co-evolutionary feature for homodimers through integrating direct coupling analysis and image processing techniques. The residue pairs across biological homodimeric interfaces were significantly enriched in co-evolving residues compared to those across crystal contacts, resulting in a promising classification accuracy with area under the curves (AUCs) of more than 0...
June 22, 2018: Protein Science: a Publication of the Protein Society
Josep Rizo
Research for three decades and major recent advances have provided crucial insights into how neurotransmitters are released by Ca2+ -triggered synaptic vesicle exocytosis, leading to reconstitution of basic steps that underlie Ca2+ -dependent membrane fusion and yielding a model that assigns defined functions for central components of the release machinery. The SNAREs syntaxin-1, SNAP-25 and synaptobrevin-2 form a tight SNARE complex that brings the vesicle and plasma membranes together and is key for membrane fusion...
June 12, 2018: Protein Science: a Publication of the Protein Society
Marie S Prevost, Gabriel Waksman
Human infections by the intracellular bacterial pathogen Legionella pneumophila result in a severe form of pneumonia, the Legionnaire's disease. L. pneumophila utilises a type IVb secretion (T4bS) system termed "dot/icm" to secrete protein effectors to the host cytoplasm. The dot/icm system is powered at least in part by a functionally critical AAA+ ATPase, a protein called DotB, thought to belong to the VirB11 family of proteins. Here we present the crystal structure of DotB at 3.19 Å resolution, in its hexameric form...
May 17, 2018: Protein Science: a Publication of the Protein Society
Haley A Brown, Evgeny Vinogradov, Michel Gilbert, Hazel M Holden
Recent studies have demonstrated that the O-antigens of some pathogenic bacteria such as Brucella abortus, Francisella tularensis, and Campylobacter jejuni contain quite unusual N-formylated sugars (3-formamido-3,6-dideoxy-d-glucose or 4-formamido-4,6-dideoxy-d-glucose). Typically, four enzymes are required for the formation of such sugars: a thymidylyltransferase, a 4,6-dehydratase, a pyridoxal 5'-phosphate or PLP-dependent aminotransferase, and an N-formyltransferase. To date, there have been no published reports of N-formylated sugars associated with Mycobacterium tuberculosis...
May 15, 2018: Protein Science: a Publication of the Protein Society
Kemin Tan, Christine Tesar, Rosemarie Wilton, Robert P Jedrzejczak, Andrzej Joachimiak
Carbohydrate hydrolyzing α-glucosidases are commonly found in microorganisms present in the human intestine microbiome. We have previously reported crystal structures of an α-glucosidase from the human gut bacterium Blaubia (Ruminococcus) obeum (Ro-αG1) and its substrate preference/specificity switch. This novel member of the GH31 family is a structural homolog of human intestinal maltase-glucoamylase (MGAM) and sucrase-isomaltase (SI) with a highly conserved active site that is predicted to be common in Ro-αG1 homologs among other species that colonize the human gut...
May 15, 2018: Protein Science: a Publication of the Protein Society
Ping Wang, Babykumari Chitramuthu, Andrew Bateman, Hugh P J Bennett, Ping Xu, Feng Ni
The ancient and pluripotent progranulins contain multiple repeats of a cysteine-rich sequence motif of ∼60 amino acids, called the granulin/epithelin module (GEM) with a prototypic structure of four β-hairpins zipped together by six inter-hairpin disulfide bonds. Prevalence of this disulfide-enforced structure is assessed here by an expression screening of 19 unique GEM sequences of the four progranulins in the zebrafish genome, progranulins 1, 2, A and B. While a majority of the expressed GEM peptides did not exhibit uniquely-folded conformations, module AaE from progranulin A and AbB from progranulin B were found to fold into the protopypic 4-hairpin structure along with disulfide formation...
May 7, 2018: Protein Science: a Publication of the Protein Society
Maria-Armineh Tossounian, Khadija Wahni, Inge Van Molle, Didier Vertommen, Leonardo Astolfi Rosado, Joris Messens
Glutathione transferase enzymes help plants to cope with biotic and abiotic stress. They mainly catalyse the conjugation of glutathione (GSH) onto xenobiotics, and some act as glutathione peroxidase. With X-ray crystallography, kinetics and thermodynamics, we studied the impact of oxidation on Arabidopsis thaliana glutathione transferase Phi 9 (GSTF9). GSTF9 has no cysteine in its sequence, and it adopts a universal GST structural fold characterized by a typical conserved GSH-binding site (G-site) and a hydrophobic co-substrate-binding site (H-site)...
May 7, 2018: Protein Science: a Publication of the Protein Society
Ingvild Gudim, Marie Lofstad, Wouter van Beek, Hans-Petter Hersleth
Flavodoxins are small proteins that shuttle electrons in a range of reactions in microorganisms. Flavodoxins contain a redox-active cofactor, a flavin mononucleotide (FMN), and it is well established that when flavodoxins are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilising the one-electron reduced state. Here we present high-resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidised (ox) and one-electron reduced (semiquinone, sq) state...
May 3, 2018: Protein Science: a Publication of the Protein Society
Zhiqiang Yao, Shuiqin Jiang, Lujia Zhang, Bei Gao, Xiao He, John Z H Zhang, Dongzhi Wei
The study of enzyme substrate specificity is vital for developing potential applications of enzymes. However, the routine experimental procedures require lot of resources in the discovery of novel substrates. This article reports an in silico structure-based algorithm called Crius, which predicts substrates for enzyme. The results of this fragment-based algorithm show good agreements between the simulated and experimental substrate specificities, using a lipase from Candida antarctica (CALB), a nitrilase from Cyanobacterium syechocystis sp...
May 3, 2018: Protein Science: a Publication of the Protein Society
Kirill E Medvedev, Lisa N Kinch, Nick V Grishin
Viruses are the most abundant life form and infect practically all organisms. Consequently, these obligate parasites are a major cause of human suffering and economic loss. Rossmann-like fold is the most populated fold among α/β-folds in the Protein Data Bank and proteins containing Rossmann-like fold constitute 22% of all known proteins 3D structures. Thus, analysis of viral proteins containing Rossmann-like domains could provide an understanding of viral biology and evolution as well as could propose possible targets for antiviral therapy...
May 3, 2018: Protein Science: a Publication of the Protein Society
Diana Gomes, Rebecca K Kalman, Rebecca K Pagels, Miguel A Rodrigues, Christopher J Roberts
Protein aggregation can follow different pathways, and these can result in different net aggregation rates and kinetic profiles. α-chymotypsinogen A (aCgn) was used as a model system to quantitatively and qualitatively assess an approach that combines ex situ size-exclusion chromatography (SEC) with in situ laser scattering (LS) to monitor aggregation vs. time. Aggregation was monitored for a series of temperatures and initial dimer (ID) levels for starting conditions that were primarily (> 97%) monomer, and under initial-rate conditions (limited to low monomer conversion-less than 20% monomer mass loss), as these conditions are of most to interest to many pharmaceutical and biotechnology applications...
May 1, 2018: Protein Science: a Publication of the Protein Society
Xinke Yu, Eric Y Hayden, Ming Xia, Owen Liang, Lisa Cheah, David B Teplow, Ya-Hong Xie
Amyloid β-protein (Aβ) self-association is one process linked to the development of Alzheimer's disease (AD). Aβ peptides, including its most abundant forms, Aβ40 and Aβ42, are associated with the two predominant neuropathologic findings in AD, vascular and parenchymal amyloidosis, respectively. Efforts to develop therapies for AD often have focused on understanding and controlling the assembly of these two peptides. An obligate step in these efforts is the monitoring of assembly state. We show here that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) readily distinguishes Aβ40 and Aβ42...
April 26, 2018: Protein Science: a Publication of the Protein Society
Tiantian Yu, Joanna R Laird, Jennifer A Prescher, Colin Thorpe
Gaussia princeps luciferase (GLuc) generates an intense burst of blue light when exposed to coelenterazine in the absence of ATP. Here we show that this 5-disulfide containing enzyme can be used as a facile and convenient substrate for studies of oxidative protein folding. Reduced GLuc (rGLuc), with 10 free cysteine residues, is completely inactive as a luciferase but more than 60% bioluminescence activity compared to controls can be recovered using a range of oxidizing regimens in the absence of the exogenous shuffling activity of protein disulfide isomerase (PDI)...
April 26, 2018: Protein Science: a Publication of the Protein Society
Nathalie Casanova-Morales, Diego Quiroga-Roger, Hilda M Alfaro-Valdés, Zahra Alavi, Miguel I A Lagos-Espinoza, Giovanni Zocchi, Christian A M Wilson
Immunoglobulin Binding Protein (BiP) is a chaperone and molecular motor belonging to the Hsp70 family, involved in the regulation of important biological processes such as synthesis, folding and translocation of proteins in the Endoplasmic Reticulum. BiP has two highly conserved domains: the N-terminal Nucleotide-Binding Domain (NBD), and the C-terminal Substrate-Binding Domain (SBD), connected by a hydrophobic linker. ATP binds and it is hydrolyzed to ADP in the NBD, and BiP's extended polypeptide substrates bind in the SBD...
April 26, 2018: Protein Science: a Publication of the Protein Society
David J Pagliarini
The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology...
April 20, 2018: Protein Science: a Publication of the Protein Society
Michael L Barta, Shoichi Tachiyama, Meenakumari Muthuramalingam, Olivia Arizmendi, Cecilia E Villanueva, Kasra X Ramyar, Brian V Geisbrecht, Scott Lovell, Kevin P Battaile, Wendy L Picking, William D Picking
Bacterial type III secretion systems (T3SS) are used to inject proteins into mammalian cells to subvert cellular functions. The Shigella T3SS apparatus (T3SA) is comprised of a basal body, cytoplasmic sorting platform and exposed needle with needle "tip complex" (TC). TC maturation occurs when the translocator protein IpaB is recruited to the needle tip where both IpaD and IpaB control secretion induction. IpaB insertion into the host membrane is the first step of translocon pore formation and secretion induction...
April 19, 2018: Protein Science: a Publication of the Protein Society
Kathryn M Schultz, Matthew A Fischer, Elizabeth L Noey, Candice S Klug
Lipopolysaccharide (LPS) is an essential element of nearly all Gram-negative bacterial outer membranes and serves to protect the cell from adverse environmental stresses. Seven members of the lipopolysaccharide transport (Lpt) protein family function together to transport LPS from the inner membrane (IM) to the outer leaflet of the outer membrane of bacteria such as Escherichia coli. Each of these proteins has a solved crystal structure, including LptC, which is a largely periplasmic protein that is associated with the IM LptB2 FG complex and anchored to the membrane by an N-terminal helix...
April 19, 2018: Protein Science: a Publication of the Protein Society
Andisheh Abedini, Julia Derk, Ann Marie Schmidt
Proteotoxicity plays a key role in many devastating human disorders, including Alzheimer's, Huntington's and Parkinson's diseases; type 2 diabetes; systemic amyloidosis; and cardiac dysfunction, to name a few. The cellular mechanisms of proteotoxicity in these disorders have been the focus of considerable research, but their role in prevalent and morbid disorders, such as diabetes, is less appreciated. There is a large body of literature on the impact of glucotoxicity and lipotoxicity on insulin-producing pancreatic β-cells, and there is increasing recognition that proteotoxicty plays a key role...
April 17, 2018: Protein Science: a Publication of the Protein Society
Jean Baum, Daniel Raleigh
No abstract text is available yet for this article.
July 2018: Protein Science: a Publication of the Protein Society
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