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Protein Science: a Publication of the Protein Society

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https://www.readbyqxmd.com/read/28643473/can-the-propensity-of-protein-crystallization-be-increased-by-using-systematic-screening-with-metals
#1
REVIEW
Raghurama P Hegde, Pavithra G Chinnaswamy, Debayan Dey, Steven C Almo, S Ramakumar, Udupi A Ramagopal
Protein crystallization is one of the major bottlenecks in protein structure elucidation with new strategies being constantly developed to improve the chances of crystallization. Generally, well-ordered epitopes possessing complementary-surface and capable of producing stable inter-protein interactions generate a regular three-dimensional arrangement of protein molecules which eventually results in a crystal lattice. Metals, when used for crystallization, with their various coordination numbers and geometries, can generate such epitopes mediating protein oligomerization and/or establish crystal contacts...
June 23, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28639381/elastin-like-polypeptide-switches-a-design-strategy-to-detect-multimeric-proteins
#2
Jugal Dhandhukia, Dab Brill, Aida Kouhi, Martha Pastuszka, John Andrew MacKay
Elastin-Like Polypeptides (ELPs) reversibly phase separate in response to changes in temperature, pressure, concentration, pH, and ionic species. While powerful triggers, biological microenvironments present a multitude of more specific biological cues, such as antibodies, cytokines, and cell-surface receptors. To develop better biosensors and bioresponsive drug carriers, rational strategies are required to sense and respond to these target proteins. We recently reported that non-covalent association of two ELP fusion proteins to a 'chemical inducer of dimerization' small molecule (1...
June 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28639341/rigidity-of-the-extracellular-part-of-her2-evidence-from-engineering-subdomain-interfaces-and-shared-helix-darpin-darpin-fusions
#3
Christian Jost, Jakob C Stüber, Annemarie Honegger, Yufan Wu, Alexander Batyuk, Andreas Plückthun
The second member of the human ErbB family of receptor tyrosine kinases, HER2/hErbB2, is regarded as an exceptional case: The four extracellular subdomains could so far only be found in one fixed overall conformation, designated "open" and resembling the ligand-bound form of the other ErbB receptors. It thus appears to be different from the extracellular domains of the other family members that show inter-subdomain flexibility and exist in a "tethered" form in the absence of ligand. For HER2, there was so far no direct evidence for such a tethered conformation on the cell surface...
June 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28608466/crystal-structure-of-human-wbscr16-an-rcc1-like-protein-in-mitochondria
#4
Masako Koyama, Taeko Sasaki, Narie Sasaki, Yoshiyuki Matsuura
WBSCR16 (Williams-Beuren Syndrome Chromosomal Region 16) gene is located in a large deletion region of Williams-Beuren syndrome (WBS), which is a neurodevelopmental disorder. Although the relationship between WBSCR16 and WBS remains unclear, it has been reported that WBSCR16 is a member of a functional module that regulates mitochondrial 16S rRNA abundance and intra-mitochondrial translation. WBSCR16 has RCC1 (Regulator of Chromosome Condensation 1)-like amino acid sequence repeats but the function of WBSCR16 appears to be different from that of other RCC1 superfamily members...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28608415/crystal-structural-characterization-reveals-novel-oligomeric-interactions-of-human-voltage-dependent-anion-channel-1
#5
Toshiaki Hosaka, Masateru Okazaki, Tomomi Kimura-Someya, Yoshiko Ishizuka-Katsura, Kaori Ito, Shigeyuki Yokoyama, Kosuke Dodo, Mikiko Sodeoka, Mikako Shirouzu
Voltage-dependent anion channel 1 (VDAC1), which is located in the outer mitochondrial membrane, plays important roles in various cellular processes. For example, oligomerization of VDAC1 is involved in the release of cytochrome c to the cytoplasm, leading to apoptosis. However, it is unknown how VDAC1 oligomerization occurs in the membrane. In the present study, we determined high-resolution crystal structures of oligomeric human VDAC1 (hVDAC1) prepared by using an Escherichia coli cell-free protein synthesis system, which avoided the need for denaturation and refolding of the protein...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28608407/disulfide-bonds-and-disorder-in-granulin-3-an-unusual-handshake-between-structural-stability-and-plasticity
#6
Gaurav Ghag, Christopher J Holler, Georgia Taylor, Thomas L Kukar, Vladimir N Uversky, Vijayaraghavan Rangachari
Granulins (GRNs) are a family of small (∼6 kDa) proteins generated by the proteolytic processing of their precursor, progranulin (PGRN), in many cell types. Both PGRN and GRNs are implicated in a plethora of biological functions, often in opposing roles to each other. Lately, GRNs have generated significant attention due to their implicated roles in neurodegenerative disorders. Despite their physiological and pathological significance, the structure-function relationships of GRNs are poorly defined. GRNs contain 12 conserved cysteines forming six intramolecular disulfide bonds, making them rather exceptional, even among a few proteins with high disulfide bond density...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28608391/the-chloroplast-localized-small-heat-shock-protein-hsp21-associates-with-the-thylakoid-membranes-in-heat-stressed-plants
#7
Katja Bernfur, Gudrun Rutsdottir, Cecilia Emanuelsson
The small heat shock protein (sHsp) chaperones are crucial for cell survival and can prevent aggregation of client proteins that partially unfold under destabilizing conditions. Most investigations on the chaperone activity sHsps are based on a limited set of thermosensitive model substrate client proteins since the endogenous targets are often not known. There is a high diversity among sHsps, with a single conserved β-sandwich fold domain defining the family, the α-crystallin domain, whereas the N-terminal and C-terminal regions are highly variable in length and sequence among various sHsps and conserved only within orthologues...
June 12, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28580734/sars-unique-fold-in-the-rousettus-bat-coronavirus-hku9
#8
Robert G Hammond, Xuan Tan, Margaret A Johnson
The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the "SARS-unique region" of the bat coronavirus HKU9. The protein contains a frataxin fold or double-wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding...
June 5, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28580679/dichromatch-at-the-protein-circular-dichroism-data-bank-dm-pcddb-a-web-based-tool-for-identifying-protein-nearest-neighbors-using-circular-dichroism-spectroscopy
#9
Lee Whitmore, Lazaros Mavridis, B A Wallace, Robert W Janes
Circular dichroism spectroscopy is a well-used, but simple method in structural biology for providing information on the secondary structure and folds of proteins. DichroMatch (DM@PCDDB) is an online tool that is newly available in the Protein Circular Dichroism Data Bank (PCDDB), which takes advantage of the wealth of spectral and metadata deposited therein, to enable identification of spectral nearest neighbours of a query protein based on six different methods of spectral matching. DM@PCDDB can potentially provide novel information about structural relationships between proteins and can be used in comparison studies of protein homologues and orthologues...
June 5, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28580643/insights-into-pg-binding-conformational-change-and-dimerization-of-the-ompa-c-terminal-domains-from-salmonella-enterica-serovar-typhimurium-and-borrelia-burgdorferi
#10
Kemin Tan, Brooke L Deatherage Kaiser, Ruiying Wu, Marianne Cuff, Yao Fan, Lance Bigelow, Robert P Jedrzejczak, Joshua N Adkins, John R Cort, Gyorgy Babnigg, Andrzej Joachimiak
S. Typhimurium can induce both humoral and cell-mediated responses when establishing itself in the host. These responses are primarily stimulated against the lipopolysaccharide and major outer membrane (OM) proteins. OmpA is one of these major OM proteins. It comprises a N-terminal eight-stranded β-barrel trans membrane domain and a C-terminal domain (OmpA(CTD) ). The OmpA(CTD) and its homologs are believed to bind to peptidoglycan (PG) within the periplasm, maintaining bacterial osmotic homeostasis and modulating the permeability and integrity of the OM...
June 5, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28571108/protein-quinary-interactions-with-an-unfolded-state-ensemble
#11
Rachel D Cohen, Gary J Pielak
Anfinsen's thermodynamic hypothesis states that the native three-dimensional fold of a protein represents the structure with the lowest Gibbs free energy. Changes in this energy can arise from changes to the folded state, the unfolded state, or both. It has been recently recognized that quinary interactions, transient contacts that take place only in cells, can modulate protein stability through interactions involving the folded state. Here we show that the cellular environment can also remodel the unfolded state ensemble...
June 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28556566/select-human-cancer-mutants-of-nrmt1-alter-its-catalytic-activity-and-decrease-n-terminal-trimethylation
#12
Kaitlyn M Shields, John G Tooley, Janusz J Petkowski, Daniel W Wilkey, Nichola C Garbett, Michael L Merchant, Alan Cheng, Christine E Schaner Tooley
A subset of B-cell lymphoma patients have dominant mutations in the histone H3 lysine 27 (H3K27) methyltransferase EZH2, which change it from a monomethylase to a trimethylase. These mutations occur in aromatic resides surrounding the active site and increase growth and alter transcription. We study the N-terminal trimethylase NRMT1 and the N-terminal monomethylase NRMT2. They are 50% identical, but differ in key aromatic residues in their active site. Given how these residues affect EZH2 activity, we tested whether they are responsible for the distinct catalytic activities of NRMT1/2...
May 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28556371/effects-of-aligned-%C3%AE-helix-peptide-dipoles-on-experimental-electrostatic-potentials
#13
Jimin Wang, Pablo E Videla, Victor S Batista
Aligned protein α-helix dipoles have been implicated in protein function and structure. The recent breakthroughs in high-resolution electron microscopy (EM) of macromolecules makes it possible to explore fundamental aspects of structural biology at the detailed molecular level. The electrostatic potential (ESP) generated by aligned protein α-helix dipole should be observable in high-resolution EM maps despite the fact that the effect may be partially screened by induced electric fields. Here, we show that aligned backbone dipoles in protein α-helices account for long-range features in the protein ESP functions...
May 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28556271/translocation-of-cell-penetrating-peptides-into-candida-fungal-pathogens
#14
Zifan Gong, Amy J Karlsson
Cell-penetrating peptides (CPPs) are small peptides capable of crossing cellular membranes while carrying molecular cargo. Although they have been widely studied for their ability to translocate nucleic acids, small molecules, and proteins into mammalian cells, studies of their interaction with fungal cells are limited. In this work, we evaluated the translocation of eleven fluorescently labeled peptides into the important human fungal pathogens Candida albicans and C. glabrata and explored the mechanisms of translocation...
May 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28547869/the-zinc-finger-domain-of-ring-finger-protein-141-reveals-a-unique-ring-fold
#15
Kazuhide Miyamoto, Airi Uechi, Kazuki Saito
Human RING finger protein 141 (RFP141) is a germ cell-specific transcription factor during spermatogenesis. We synthesized a compact construct encoding the C-terminal zinc finger of RFP141 (RFP141C peptide). Herein we determined the solution structure of the RFP141C peptide by nuclear magnetic resonance (NMR). Moreover, NMR data and the chemical modification of cysteine residues demonstrated that the RFP141C peptide binds to two zinc atoms in a cross-brace arrangement. The Simple Modular Architecture Research Tool database predicted the structure of RFP141C as a RING finger...
May 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28547763/new-approaches-towards-the-understanding-of-integral-membrane-proteins-a-structural-perspective-on-g-protein-coupled-receptors
#16
REVIEW
Reinhard Grisshammer
Three-dimensional structure determination of integral membrane proteins has advanced in unprecedented detail our understanding of mechanistic events of how ion channels, transporters, receptors, and enzymes function. This exciting progress required a tremendous amount of methods development, as exemplified here with G protein-coupled receptors (GPCRs): Optimizing the production of GPCRs in recombinant hosts; increasing the probability of crystal formation using high-affinity ligands, nanobodies, and minimal G proteins for co-crystallization, thus stabilizing receptors into one conformation; using the T4 lysozyme technology and other fusion partners to promote crystal contacts; advancing crystallization methods including the development of novel detergents, and miniaturization and automation of the lipidic cubic phase crystallization method; the concept of conformational thermostabilization of GPCRs; and developing microfocus X-ray synchrotron technologies to analyze small GPCR crystals...
May 25, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543850/structures-and-kinetics-for-plant-nucleoside-triphosphate-diphosphohydrolases-support-a-domain-motion-catalytic-mechanism
#17
Emma L Summers, Mathew H Cumming, Tifany Oulavallickal, Nicholas J Roberts, Vickery L Arcus
Extracellular nucleoside triphosphate diphosphohydrolases (NTPDases) are enzymes that hydrolyze extracellular nucleotides to the respective monophosphate nucleotides. In the past 20 years, NTPDases belonging to mammalian, parasitic and prokaryotic domains of life have been discovered, cloned and characterized. We reveal the first structures of NTPDases from the legume plant species Trifolium repens (7WC) and Vigna unguiculata subsp. cylindrica (DbLNP). Four crystal structures of 7WC and DbLNP were determined at resolutions between 1...
May 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543856/experimental-charge-density-from-electron-microscopic-maps
#18
Jimin Wang
The charge density (CD) distribution of an atom is the difference per unit volume between the positive charge of its nucleus and the distribution of the negative charges carried by the electrons that are associated with it. The CDs of the atoms in macromolecules are responsible for their electrostatic potential (ESP) distributions, which can now be visualized using cryo-electron microscopy at high resolution. CD maps can be recovered from experimental ESP density maps using the negative Laplacian operation...
May 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543811/the-structural-flexibility-of-the-human-copper-chaperone-atox1-insights-from-combined-pulsed-epr-studies-and-computations
#19
Ariel R Levy, Meital Turgeman, Lada Gevorkyan-Aiapetov, Sharon Ruthstein
Metallochaperones are responsible for shuttling metal ions to target proteins. Thus, a metallochaperone's structure must be sufficiently flexible both to hold onto its ion while traversing the cytoplasm and to transfer the ion to or from a partner protein. Here, we sought to shed light on the structure of Atox1, a metallochaperone involved in the human copper regulation system. Atox1 shuttles copper ions from the main copper transporter, Ctr1, to the ATP7b transporter in the Golgi apparatus. Conventional biophysical tools such as X-ray or NMR cannot always target the various conformational states of metallochaperones, owing to a requirement for crystallography or low sensitivity and resolution...
May 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28543736/a-rapid-expression-and-purification-condition-screening-protocol-for-membrane-protein-structural-biology
#20
Dan Sjöstrand, Riccardo Diamanti, Camilla A K Lundgren, Benjamin Wiseman, Martin Högbom
Membrane proteins control a large number of vital biological processes and are often medically important-not least as drug targets. However, membrane proteins are generally more difficult to work with than their globular counterparts, and as a consequence comparatively few high-resolution structures are available. In any membrane protein structure project, a lot of effort is usually spent on obtaining a pure and stable protein preparation. The process commonly involves the expression of several constructs and homologs, followed by extraction in various detergents...
May 20, 2017: Protein Science: a Publication of the Protein Society
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