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Protein Science: a Publication of the Protein Society

Smriti Sangwan, Michael R Sawaya, Kevin A Murray, MichaelP Hughes, David S Eisenberg
The aggregation cascade of disease-related amyloidogenic proteins, terminating in insoluble amyloid fibrils, involves intermediate oligomeric states. The structural and biochemical details of these oligomers have been largely unknown. Here we report crystal structures of variants of the cytotoxic oligomer-forming segment residues 28-38 of the ALS-linked protein, SOD1. The crystal structures reveal three different architectures: corkscrew oligomeric structure, non-twisting curved sheet structure and a steric zipper proto-filament structure...
February 17, 2018: Protein Science: a Publication of the Protein Society
N Connor Payne, Drew R Barber, Erik L Ruggles, Robert J Hondal
Dimedone is a widely used reagent to assess the redox state of cysteine-containing proteins as it will alkylate sulfenic acid residues, but not sulfinic acid residues. While it has been reported that dimedone can label selenenic acid residues in selenoproteins, we investigated the stability, and reversibility of this label in a model peptide system. We also wondered whether dimedone could be used to detect seleninic acid residues. We used benzenesulfinic acid, benzeneseleninic acid, and model selenocysteine-containing peptides to investigate possible reactions with dimedone...
February 16, 2018: Protein Science: a Publication of the Protein Society
Kazuhide Miyamoto, Ayumi Yamashita, Kazuki Saito
Cross-brace structural motifs are required as a scaffold to design artificial RING fingers (ARFs) that function as ubiquitin ligase (E3) in ubiquitination and have specific ubiquitin-conjugating enzyme (E2)-binding capabilities. The Simple Modular Architecture Research Tool database predicted the amino acid sequence 131-190 (KIAA1045ZF) of the human KIAA1045 protein as an unidentified structural region. Herein, the stoichiometry of zinc ions estimated spectrophotometrically by the metallochromic indicator revealed that the KIAA1045ZF motif binds to two zinc atoms...
February 12, 2018: Protein Science: a Publication of the Protein Society
Norbert E Juettner, Stefan Schmelz, Jan P Bogen, Dominic Happel, Wolf-Dieter Fessner, Felicitas Pfeifer, Hans-Lothar Fuchsbauer, Andrea Scrima
Transglutaminase from Streptomyces mobaraensis (MTG) has become a powerful tool to covalently and highly specifically link functional amines to glutamine donor sites of therapeutic proteins. However, details regarding the mechanism of substrate recognition and interaction of the enzyme with proteinaceous substrates still remain mostly elusive. We have determined the crystal structure of the Streptomyces papain inhibitory protein (SPIp ), a substrate of MTG, to study the influence of various substrate amino acids on positioning glutamine to the active site of MTG...
February 12, 2018: Protein Science: a Publication of the Protein Society
Joel W Francis, Christopher J Royer, Paul D Cook
Bacillithiol is a low-molecular weight thiol produced by many gram-positive organisms, including Staphylococcus aureus and Bacillus anthracis. It is the major thiol responsible for maintaining redox homeostasis and cellular detoxification, including inactivation of the antibiotic fosfomycin. The metal-dependent bacillithiol transferase BstA is likely involved in these sorts of detoxification processes, but the exact substrates and enzyme mechanism have not been identified. Here we report the 1.34 Å resolution X-ray crystallographic structure of BstA from S...
February 8, 2018: Protein Science: a Publication of the Protein Society
Ciaran P A Doherty, Lydia M Young, Theodoros K Karamanos, Hugh I Smith, Matthew P Jackson, Sheena E Radford, David J Brockwell
Protein aggregation is linked with the onset of several neurodegenerative disorders, including Parkinson's disease (PD), which is associated with the aggregation of α-synuclein (αSyn). The structural mechanistic details of protein aggregation, including the nature of the earliest protein:protein interactions, remain elusive. In this study we have used single molecule force spectroscopy (SMFS) to probe the first dimerisation events of the central aggregation-prone region of αSyn (residues 71-82) that may initiate aggregation...
February 8, 2018: Protein Science: a Publication of the Protein Society
Wai-Ming Yau, Robert Tycko
Aggregation of amyloid-β (Aβ) peptides in brain tissue leads to neurodegeneration in Alzheimer's disease (AD). Regardless of the kinetics or detailed mechanisms of Aβ aggregation, aggregation can only occur if Aβ concentrations exceed their local equilibrium solubility values. We propose that excess Aβ peptides can be removed from supersaturated solutions, including solutions in biological fluids, by the addition of hydrogels that are seeded with Aβ fibril fragments. Fibril growth within the hydrogels then sequesters excess peptides until equilibrium concentrations are reached...
February 8, 2018: Protein Science: a Publication of the Protein Society
Qiang Zhang, Yao-Wu Zheng, Shaun R Coughlin, Xiaokun Shu
Detection of protein-protein interactions involved in signal transduction in live cells and organisms has a variety of important applications. We report a fluorogenic assay for G protein-coupled receptor (GPCR) - β-arrestin interaction that is genetically encoded, generalizes to multiple GPCRs and features high signal-to-noise because fluorescence is absent until its components interact upon GPCR activation. Fluorescence after protease-activated receptor-1 activation developed in minutes and required specific serine-threonine residues in the receptor carboxyl tail, consistent with a classical G protein-coupled receptor kinase dependent β-arrestin recruitment mechanism...
February 7, 2018: Protein Science: a Publication of the Protein Society
Yanjie Liu, Xiaomeng Zhao, Muhammad Naeem, Jiandong An
Peptidoglycan recognition protein SA (PGRP-SA) is a key pattern recognition receptor in the insect innate immune system. PGRP-SA can bind to bacterial PGN and activate the Toll pathway, which triggers the expression and release of antimicrobial peptides to prevent bacterial infection. Here, we report the first structure of Apis mellifera PGRP-SA from Hymenoptera at 1.86 Å resolution. The overall architecture of Am-PGRP-SA was similar to the Drosophila PGRP-SA; however, the residues involved in PGN binding groove were not conserved, and the binding pocket was narrower...
February 2, 2018: Protein Science: a Publication of the Protein Society
Shuo Du, Li-Jia Qu, Junyu Xiao
Catharanthus roseus Receptor-Like Kinase 1-like (CrRLK1L) proteins contain two tandem malectin-like modules in their extracellular domains (ECDs) and function in diverse signaling pathways in plants. Malectin is a carbohydrate-binding protein in animals and recognizes a number of diglucosides; however, it remains unclear how the two malectin-like domains in the CrRLK1L proteins sense the ligand molecule. In this study, we reveal the crystal structures of the ECDs of ANXUR1 and ANXUR2, two CrRLK1L members in Arabidopsis thaliana that have critical functions in controlling pollen tube rupture during the fertilization process...
February 1, 2018: Protein Science: a Publication of the Protein Society
Lea L Sorret, Madison A DeWinter, Daniel K Schwartz, Theodore W Randolph
We investigated the effects of protein-protein interaction strength on interfacial viscoelastic properties and aggregation of recombinant human interleukin-1 receptor antagonist (rhIL-1ra) at silicone oil-water interfaces. Osmotic second virial coefficients determined by static light scattering were used to quantify protein-protein interactions in bulk solution. Attractive protein-protein interactions dominated at low ionic strengths and their magnitude decreased with increasing ionic strength, in contrast to repulsive interactions that would be expected based on uniformly charged sphere models...
February 1, 2018: Protein Science: a Publication of the Protein Society
Jillian E Smith-Carpenter, Benjamin J Alper
Here we report the enzymologic characterization of recombinant human pitrilysin metallopeptidase 1 (Pitrm1) and derivative mutants including the arginine-to-glutamine substitution mutant Pitrm1 R183Q, which has been implicated in inherited amyloidogenic neuropathy. Recombinant Pitrm1 R183Q was readily expressed in and purified from E. coli, but was less active than the recombinant wild-type enzyme against recombinant amyloid beta peptide (Aβ 1-40). A novel fluorogenic substrate derived from the reported Aβ 1-40 core peptide cleavage sequence, Mca-KLVFFAEDK-(Dnp)-OH, was synthesized and applied to real-time kinetic study of Pitrm1 and derivative mutants including Pitrm1 R183Q...
January 31, 2018: Protein Science: a Publication of the Protein Society
David D Boehr, Rebecca N D'Amico, Kathleen F O'Rourke
Enzymes undergo a range of internal motions from local, active site fluctuations to large-scale, global conformational changes. These motions are often important for enzyme function, including in ligand binding and dissociation and even preparing the active site for chemical catalysis. Protein engineering efforts have been directed towards manipulating enzyme structural dynamics and conformational changes, including targeting specific amino acid interactions and creation of chimeric enzymes with new regulatory functions...
January 30, 2018: Protein Science: a Publication of the Protein Society
Piotr Tokarz, Magdalena Wiśniewska, Marcin M Kamiński, Grzegorz Dubin, Przemysław Grudnik
ADP-dependent glucokinase (ADPGK) is an alternative novel glucose phosphorylating enzyme in a modified glycolysis pathway of hyperthermophilic Archaea. In contrast to classical ATP-dependent hexokinases, ADPGK utilizes ADP as a phosphoryl group donor. Here we present a crystal structure of archaeal ADPGK from Methanocaldococcus jannaschii in complex with an inhibitor, 5-iodotubercidin, D-glucose, inorganic phosphate and a magnesium ion. Detailed analysis of the architecture of the active site allowed for confirmation of the previously proposed phosphorylation mechanism and the crucial role of the invariant arginine residue (Arg197)...
January 20, 2018: Protein Science: a Publication of the Protein Society
David A Korasick, John J Tanner
Small-angle X-ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration, without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer...
January 20, 2018: Protein Science: a Publication of the Protein Society
Thanh D Do, Smriti Sangwan, Natália E C de Almeida, Alexandre I Ilitchev, Maxwell Giammona, Michael R Sawaya, Steven K Buratto, David S Eisenberg, Michael T Bowers
Amyloid formation is associated with devastating diseases such as Alzheimer's, Parkinson's and Type-2 diabetes. The large amyloid deposits found in patients suffering from these diseases have remained difficult to probe by structural means. Recent NMR models also predict heterotypic interactions from distinct peptide fragments but limited evidence of heterotypic packed sheets is observed in solution. Here we characterize two segments of the protein amyloid β (Aβ) known to form fibrils in Alzheimer's disease patients...
January 19, 2018: Protein Science: a Publication of the Protein Society
Claudia Alvarez-Carreño, Vikram Alva, Arturo Becerra, Antonio Lazcano
Hemerythrin-like proteins have generally been studied for their ability to reversibly bind oxygen through their binuclear non-heme iron centers. However, in recent years, it has become increasingly evident that some members of the hemerythrin-like superfamily also participate in many other biological processes. For instance, the binuclear non-heme iron site of YtfE, a hemerythrin-like protein involved in the repair of iron centers in Escherichia coli, catalyzes the reduction of nitric oxide to nitrous oxide, and the human F-box/LRR-repeat protein 5, which contains a hemerythrin-like domain, is involved in intracellular iron homeostasis...
January 13, 2018: Protein Science: a Publication of the Protein Society
Chad A Brautigam, Ranjit K Deka, Wei Z Liu, Michael V Norgard
Previously, we determined the crystal structure of apo-TpMglB-2, a D-glucose-binding component of a putative ABC transporter from the syphilis spirochete Treponema pallidum. The protein had an unusual topology for this class of proteins, raising the question of whether the D-glucose-binding mode would be different in TpMglB-2. Here, we present the crystal structures of a variant of TpMglB-2 with and without D-glucose bound. The structures demonstrate that, despite its aberrant topology, the protein undergoes conformational changes and binds D-glucose similarly to other Mgl-type proteins, likely facilitating D-glucose uptake in T...
January 10, 2018: Protein Science: a Publication of the Protein Society
Joseph S Xu, Madeleine N Hewitt, Jaskeerat S Gulati, Matthew A Cruz, Hongli Zhan, Shirley Liu, Kathleen S Matthews
The short 8-10 amino acid "hinge" sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer-binding domains. Structural studies of full-length or truncated LacI-operator DNA complexes demonstrate insertion of the dimeric helical "hinge" structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi-symmetric DNA sites for optimal contact by the N-terminal helix-turn helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences...
January 10, 2018: Protein Science: a Publication of the Protein Society
Douglas J Marcotte, Jean-Christophe Hus, Charles C Banos, Craig Wildes, Robert Arduini, Chris Bergeron, Catherine A Hession, Darren P Baker, Edward Lin, Kevin M Guckian, Anthone W Dunah, Laura F Silvian
The membrane protein interacting with kinase C1 (PICK1) plays a trafficking role in the internalization of neuron receptors such as the amino-3-hydroxyl-5-methyl-4-isoxazole-propionate (AMPA) receptor. Reduction of surface AMPA type receptors on neurons reduces synaptic communication leading to cognitive impairment in progressive neurodegenerative diseases such as Alzheimer disease. The internalization of AMPA receptors is mediated by the PDZ domain of PICK1 which binds to the GluA2 subunit of AMPA receptors and targets the receptor for internalization through endocytosis, reducing synaptic communication...
December 27, 2017: Protein Science: a Publication of the Protein Society
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