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Protein Science: a Publication of the Protein Society

Masaru Yamanaka, Makoto Hoshizumi, Satoshi Nagao, Ryoko Nakayama, Naoki Shibata, Yoshiki Higuchi, Shun Hirota
The number of artificial protein supramolecules has been increasing, however control of protein oligomer formation remains challenging. Cytochrome c' from Allochromatium vinosum (AVCP) is a homo-dimeric protein in its native form, where its protomer exhibits a four-helix bundle structure containing a covalently bound five-coordinate heme as a gas binding site. AVCP exhibits a unique reversible dimer-monomer transition according to the absence and presence of CO. Herein, domain-swapped dimeric AVCP was constructed and utilized to form a tetramer and high-order oligomers...
November 24, 2016: Protein Science: a Publication of the Protein Society
Tetsuya Kadonosono, Wanaporn Yimchuen, Takuya Tsubaki, Tadashi Shiozawa, Yasuhiro Suzuki, Takahiro Kuchimaru, Yasufumi Sato, Shinae Kizaka-Kondoh
Vasohibins (VASH1 and VASH2) are recently identified regulators of angiogenesis and cancer cell functions. They are secreted proteins without any classical secretion signal sequences, and are thought to be secreted instead via an unconventional protein secretion (UPS) pathway in a small vasohibin-binding protein (SVBP)-dependent manner. However, the precise mechanism of SVBP-dependent UPS is poorly understood. In this study, we identified a novel UPS regulatory system in which essential domain architecture (VASH-PS) of VASHs, comprising regions VASH191-180 and VASH280-169 , regulate the cytosolic punctate structure formation in the absence of SVBP...
November 23, 2016: Protein Science: a Publication of the Protein Society
Sireesha Mamillapalli, Masaru Miyagi, James G Bann
The major immunogenic component of the current anthrax vaccine, anthrax vaccine adsorbed (AVA) is protective antigen (PA). We have shown recently that the thermodynamic stability of PA can be significantly improved by binding to the Von-Willebrand factor A (VWA) domain of capillary morphogenesis protein 2 (CMG2), and improvements in thermodynamic stability may improve storage and long-term stability of PA for use as a vaccine. In order to understand the origin of this increase in stability, we have isolated the receptor binding domain of PA, domain 4 (D4), and have studied the effect of the addition of CMG2 on thermodynamic stability...
November 22, 2016: Protein Science: a Publication of the Protein Society
Aiswarya Premchandar, Anna Kupniewska, Arkadiusz Bonna, Grazyna Faure, Tomasz Fraczyk, Ariel Roldan, Brice Hoffmann, Mélanie Faria da Cunha, Harald Herrmann, Gergely L Lukacs, Aleksander Edelman, Michał Dadlez
The intermediate filament protein keratin 8 (K8) interacts with the nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane regulator (CFTR) with phenylalanine 508 deletion (ΔF508), and this interaction hampers the biogenesis of functional ΔF508-CFTR and its insertion into the plasma membrane. Interruption of this interaction may constitute a new therapeutic target for cystic fibrosis patients bearing the ΔF508 mutation. Here we aimed to determine the binding surface between these two proteins, to facilitate the design of the interaction inhibitors...
November 21, 2016: Protein Science: a Publication of the Protein Society
Jochen Baßler, Yasar Luqman Ahmed, Martina Kallas, Markus Kornprobst, Fabiola R Calviño, Marén Gnädig, Matthias Thoms, Gunter Stier, Sherif Ismail, Satyavati Kharde, Nestor Castillo, Sabine Griesel, Sonja Bastuck, Bettina Bradatsch, Emma Thomson, Dirk Flemming, Irmgard Sinning, Ed Hurt
Ribosome biogenesis in eukaryotic cells is a highly dynamic and complex process innately linked to cell proliferation. The assembly of ribosomes is driven by a myriad of biogenesis factors that shape pre-ribosomal particles by processing and folding the ribosomal RNA and incorporating ribosomal proteins. Biochemical approaches allowed the isolation and characterization of pre-ribosomal particles from Saccharomyces cerevisiae, which lead to a spatiotemporal map of biogenesis intermediates along the path from the nucleolus to the cytoplasm...
November 18, 2016: Protein Science: a Publication of the Protein Society
Lorien J Parker, Alessio Bocedi, David B Ascher, Jade B Aitken, Hugh H Harris, Mario Lo Bello, Giorgio Ricci, Craig J Morton, Michael W Parker
Arsenic-based compounds are paradoxically both poisons and drugs. Glutathione transferase (GSTP1-1) is a major factor in resistance to such drugs. Here we describe using crystallography, X-ray absorption spectroscopy, mutagenesis, mass spectrometry and kinetic studies how GSTP1-1 recognizes the drug phenylarsine oxide (PAO). In conditions of cellular stress where glutathione (GSH) levels are low, PAO crosslinks C47 to C101 of the opposing monomer, a distance of 19.9 Å, and causes a dramatic widening of the dimer interface by ∼10 Å...
November 18, 2016: Protein Science: a Publication of the Protein Society
Ália Dos Santos, Andreas Hadjivasiliou, Felipe Ossa, Novandy K Lim, Aylin Turgut, Maureen E Taylor, Kurt Drickamer
Human dendritic cell-specific intercellular adhesion molecule-1 grabbing nonintegrin, DC-SIGN, and the sinusoidal endothelial cell receptor DC-SIGNR or L-SIGN, are closely related sugar-binding receptors. DC-SIGN acts both as a pathogen-binding endocytic receptor and as a cell adhesion molecule, while DC-SIGNR has only the pathogen-binding function. In addition to differences in the sugar-binding properties of the carbohydrate-recognition domains in the two receptors, there are sequence differences in the adjacent neck domains, which are coiled-coil tetramerization domains comprised largely of 23-amino acid repeat units...
November 17, 2016: Protein Science: a Publication of the Protein Society
Amanda Stratton, Matthew Ericksen, Travis V Harris, Nick Symmonds, Todd P Silverstein
The toxicity of mercury is often attributed to its tight binding to cysteine thiolate anions in vital enzymes. To test our hypothesis that Hg(II) binding to histidine could be a significant factor in mercury's toxic effects, we studied the enzyme chymotrypsin, which lacks free cysteine thiols; we found that chymotrypsin is not only inhibited, but also denatured by Hg(II). We followed the aggregation of denatured enzyme by the increase in visible absorbance due to light scattering. Hg(II)-induced chymotrypsin precipitation increased dramatically above pH 6...
November 17, 2016: Protein Science: a Publication of the Protein Society
Kanako Kuwasako, Nobukazu Nameki, Kengo Tsuda, Mari Takahashi, Atsuko Sato, Naoya Tochio, Makoto Inoue, Takaho Terada, Takanori Kigawa, Naohiro Kobayashi, Mikako Shirouzu, Takuhiro Ito, Taiichi Sakamoto, Kaori Wakamatsu, Peter Güntert, Seizo Takahashi, Shigeyuki Yokoyama, Yutaka Muto
The spliceosomal protein SF3b49, a component of the splicing factor 3b (SF3b) protein complex in the U2 small nuclear ribonucleoprotein, contains two RNA recognition motif (RRM) domains. In yeast, the first RRM domain (RRM1) of Hsh49 protein (yeast orthologue of human SF3b49) reportedly interacts with another component, Cus1 protein (orthologue of human SF3b145). Here, we solved the solution structure of the RRM1 of human SF3b49 and examined its mode of interaction with a fragment of human SF3b145 using NMR methods...
November 16, 2016: Protein Science: a Publication of the Protein Society
Subrata Paul, Sambuddha Banerjee, Hans J Vogel
The HisJ protein from Escherichia coli and related Gram negative bacteria is the periplasmic component of a bacterial ATP-cassette (ABC) transporter system. Together these proteins form a transmembrane complex that can take up L-histidine from the environment and translocate it into the cytosol. We have studied the specificity of HisJ for binding L-His and many related naturally occurring compounds. Our data confirm that L-His is the preferred ligand, but that 1-methyl-L-His and 3-methyl-L-His can also bind, while the dipeptide carnosine binds weakly and D-histidine and the histidine degradation products, histamine, urocanic acid and imidazole do not bind...
November 12, 2016: Protein Science: a Publication of the Protein Society
Pavel Klimeš, Pavel Mazura, Dušan Turek, Břetislav Brzobohatý
Enzyme kinetic measurements are important for the characterization and engineering of biocatalysts, with applications in a wide range of research fields. The measurement of initial reaction velocity is usually slow and laborious, which motivated us to explore the possibilities for automating this process. Our model enzyme is the maize β-glucosidase Zm-p60.1. Zm-p60.1 plays a significant role in plant growth and development by regulating levels of the active plant hormone cytokinin. Zm-p60.1 belongs to a wide group of hydrolytic enzymes...
November 12, 2016: Protein Science: a Publication of the Protein Society
Ismail A Ahmed, Feng Gai
The ester carbonyl stretching vibration has recently been shown to be a sensitive and convenient infrared (IR) probe of protein electrostatics due to the linear dependence of its frequency on local electric field. While an ester moiety can be easily incorporated into peptides via solid-phase synthesis, currently there is no method available to site-specifically incorporate it into a large protein. Herein, we show that it is possible to use a cysteine alkylation reaction to achieve this goal and demonstrate the feasibility of this simple method by successfully incorporating a methyl ester group (-CH2 COOCH3 ) into a model peptide (YGGCGG), two amyloid-forming peptides derived from the insulin B chain and Aβ, and bovine serum albumin (BSA)...
November 4, 2016: Protein Science: a Publication of the Protein Society
Ciara Kyne, Kiara Jordon, Dana I Filoti, Thomas M Laue, Peter B Crowley
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behavior under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis...
November 4, 2016: Protein Science: a Publication of the Protein Society
Rebekka Wild, Michael Hothorn
Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1.1. Initial crystals diffracted to 3.3 Å resolution. Reductive protein methylation of the fusion protein yielded a new crystal form diffracting to 2...
October 24, 2016: Protein Science: a Publication of the Protein Society
Kathleen M Clark, Jermaine L Jenkins, Nadia Fedoriw, Mark E Dumont
The function and localization of proteins and peptides containing C-terminal "CaaX" (Cys-aliphatic-aliphatic-anything) sequence motifs are modulated by post-translational attachment of isoprenyl groups to the cysteine sulfhydryl, followed by proteolytic cleavage of the aaX amino acids. The zinc metalloprotease ZMPSTE24 is one of two enzymes known to catalyze this cleavage. The only identified target of mammalian ZMPSTE24 is prelamin A, the precursor to the nuclear scaffold protein lamin A. ZMPSTE24 also cleaves prelamin A at a second site 15 residues upstream from the CaaX site...
October 24, 2016: Protein Science: a Publication of the Protein Society
Yang Yu, Igor Petrik, Kelly N Chacón, Parisa Hosseinzadeh, Honghui Chen, Ninian J Blackburn, Yi Lu
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, no report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions...
October 19, 2016: Protein Science: a Publication of the Protein Society
Zheng Liu, Cristina Gutierrez-Vargas, Jia Wei, Robert A Grassucci, Ming Sun, Noel Espina, Susan Madison-Antenucci, Liang Tong, Joachim Frank
With the advance of new instruments and algorithms, and the accumulation of experience over decades, single-particle cryo-EM has become a pivotal part of structural biology. Recently, we determined the structure of a eukaryotic ribosome at 2.5 Å for the large subunit. The ribosome was derived from Trypanosoma cruzi, the protozoan pathogen of Chagas disease. The high-resolution density map allowed us to discern a large number of unprecedented details including rRNA modifications, water molecules, and ions such as Mg(2+) and Zn(2+) ...
October 17, 2016: Protein Science: a Publication of the Protein Society
Joseph R Sachleben, Aashish N Adhikari, Grzegorz Gawlak, Robert J Hoey, Gaohua Liu, Andrzej Joachimiak, Gaetano T Montelione, Tobin R Sosnick, Shohei Koide
We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet with a novel fold that we have termed an Aromatic Claw...
October 17, 2016: Protein Science: a Publication of the Protein Society
Mikko Laitaoja, Sari Isoniemi, Jarkko Valjakka, István M Mándity, Janne Jänis
Small zinc finger (ZnF) motifs are promising molecular scaffolds for protein design owing to their structural robustness and versatility. Moreover, their characterization provides important insights into protein folding in general. ZnF motifs usually possess an exceptional specificity and high affinity towards Zn(II) ion to drive folding. While the Zn(II) ion is canonically coordinated by two cysteine and two histidine residues, many other coordination spheres also exist in small ZnFs, all having four amino acid ligands...
October 17, 2016: Protein Science: a Publication of the Protein Society
Martín Carballo-Pacheco, Birgit Strodel
Intrinsically disordered proteins are essential for biological processes such as cell signalling, but are also associated to devastating diseases including Alzheimers disease, Parkinsons disease or type II diabetes. Because of their lack of a stable threedimensional structure, molecular dynamics simulations are often used to obtain atomistic details that cannot be observed experimentally. The applicability of molecular dynamics simulations depends on the accuracy of the force field chosen to represent the underlying free energy surface of the system...
October 11, 2016: Protein Science: a Publication of the Protein Society
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