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Protein Science: a Publication of the Protein Society

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https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#1
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28340507/understanding-the-contribution-of-disulphide-bridges-to-the-folding-and-misfolding-of-an-anti-a%C3%AE-scfv
#2
Laia Montoliu-Gaya, Jose C Martínez, Sandra Villegas
ScFv-h3D6 is a single chain variable fragment that precludes Aβ peptide-induced cytotoxicity by withdrawing Aβ oligomers from the amyloid pathway to the worm-like pathway. Production of scFv molecules is not a straightforward procedure because of the occurrence of disulphide scrambled conformations generated in the refolding process. Here, we separately removed the disulphide bond of each domain and solved the scrambling problem; and then, we intended to compensate the loss of thermodynamic stability by adding three C-terminal elongation mutations previously described to stabilize the native fold of scFv-h3D6...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28329912/structural-and-mechanistic-insights-into-homocysteine-degradation-by-a-mutant-of-methionine-%C3%AE-lyase-based-on-substrate-assisted-catalysis
#3
Dan Sato, Tomoo Shiba, Shunsuke Yunoto, Kazuo Furutani, Mitsuki Fukumoto, Daizou Kudou, Takashi Tamura, Kenji Inagaki, Shigeharu Harada
Methionine γ-lyse (MGL) catalyzes the α, γ-elimination of l-methionine and its derivatives as well as the α, β-elimination of l-cysteine and its derivatives to produce α-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28329910/nucleosome-mobility-and-the-regulation-of-gene-expression-insights-from-single-molecule-studies
#4
REVIEW
Sergei Rudnizky, Omri Malik, Adaiah Bavly, Lilach Pnueli, Philippa Melamed, Ariel Kaplan
Nucleosomes at the promoters of genes regulate the accessibility of the transcription machinery to DNA, and function as a basic layer in the complex regulation of gene expression. Our understanding of the role of the nucleosome's spontaneous, thermally driven position changes in modulating expression is lacking. This is the result of the paucity of experimental data on these dynamics, at high-resolution, and for DNA sequences that belong to real, transcribed genes. We have developed an assay that uses partial, reversible unzipping of nucleosomes with optical tweezers to repeatedly probe a nucleosome's position over time...
March 22, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28295918/the-intrinsically-disordered-inhibitor-of-glutamine-synthetase-is-a-functional-protein-with-random-coil-like-pka-values
#5
Concetta Cozza, José L Neira, Francisco J Florencio, M Isabel Muro-Pastor, Bruno Rizzuti
The sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) in cyanobacteria allows the incorporation of ammonium into carbon skeletons. In the cyanobacterium Synechocystis sp. PCC 6803, the activity of GS is modulated by the interaction with proteins, which include a 65-residue-long intrinsically disordered protein (IDP), the inactivating factor IF7. This interaction is regulated by the presence of charged residues in both IF7 and GS. In order to understand how charged amino acids can affect the binding of an IDP with its target, and to provide clues on electrostatic interactions in disordered states of proteins, we measured the pKa values of all IF7 acidic groups (Glu32, Glu36, Glu38, Asp40, Asp58, and Ser65, the backbone C-terminus) at 100 mM NaCl concentration, by using NMR spectroscopy...
March 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28295806/proteins-mediating-dna-loops-effectively-block-transcription
#6
Zsuzsanna Vörös, Yan Yan, Daniel T Kovari, Laura Finzi, David Dunlap
Loops are ubiquitous topological elements formed when proteins simultaneously bind to two non-contiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM)...
March 14, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28276594/structural-and-functional-characterization-of-a-ubiquitin-variant-engineered-for-tight-and-specific-binding-to-an-alpha-helical-ubiquitin-interacting-motif
#7
Noah Manczyk, Bradley P Yates, Gianluca Veggiani, Andreas Ernst, Frank Sicheri, Sachdev S Sidhu
Ubiquitin interacting motifs (UIMs) are short α-helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N-terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin...
March 9, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28271570/single-domain-antibodies-for-the-knockdown-of-cytosolic-and-nuclear-proteins
#8
REVIEW
Thomas Böldicke
Single domain antibodies (sdAbs) from camels or sharks comprise only the variable heavy chain domain. Human sdAbs comprise the variable domain of the heavy chain (VH) or light chain (VL) and can be selected from human antibodies. SdAbs are stable, non aggregating molecules in vitro and in vivo compared to complete antibodies and scFv fragments. They are excellent novel inhibitors of cytosolic/nuclear proteins because they are correctly folded inside the cytosol in contrast to scFv fragments. SdAbs are unique because of their excellent specificity and possibility to target posttranslational modifications such as phosphorylation sites, conformers or interaction regions of proteins that cannot be targeted with genetic knockout techniques and are impossible to knockdown with RNAi...
March 8, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28263430/single-molecule-mechanochemical-characterization-of-e-coli-pol-iii-core-catalytic-activity
#9
M Nabuan Naufer, David A Murison, Ioulia Rouzina, Penny J Beuning, Mark C Williams
Pol III core is the three-subunit subassembly of the E. coli replicative DNA polymerase III holoenzyme. It contains the catalytic polymerase subunit α, the 3' → 5' proofreading exonuclease ε, and a subunit of unknown function, θ. We employ optical tweezers to characterize pol III core activity on a single DNA substrate. We observe polymerization at applied template forces F<25 pN and exonucleolysis at F>30 pN. Both polymerization and exonucleolysis occur as a series of short bursts separated by pauses...
March 6, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28263418/crystal-structure-of-human-proteasome-assembly-chaperone-pac4-involved-in-proteasome-formation
#10
Eiji Kurimoto, Tadashi Satoh, Yuri Ito, Eri Ishihara, Kenta Okamoto, Maho Yagi-Utsumi, Keiji Tanaka, Koichi Kato
The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not...
March 6, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28257598/structural-basis-for-dimerization-and-rna-binding-of-avian-infectious-bronchitis-virus-nsp9
#11
Tingting Hu, Cheng Chen, Huiyan Li, Yanshu Dou, Ming Zhou, Deren Lu, Qi Zong, Yulei Li, Cheng Yang, Zhihui Zhong, Namit Singh, Honggang Hu, Rundong Zhang, Haitao Yang, Dan Su
The potential for infection by coronaviruses (CoVs) has become a serious concern with the recent emergence of Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) in the human population. CoVs encode two large polyproteins, which are then processed into 15-16 nonstructural proteins (nsps) that make significant contributions to viral replication and transcription by assembling the RNA replicase complex. Among them, nsp9 plays an essential role in viral replication by forming a homodimer that binds single-stranded RNA...
March 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28257593/characterization-of-structural-and-immunological-properties-of-a-fusion-protein-between-flagellin-from-salmonella-and-lumazine-synthase-from-brucella
#12
Y Hiriart, A H Rossi, M E Biedma, A J Errea, G Moreno, D Cayet, J Rinaldi, B Blancá, J C Sirard, F Goldbaum, P Berguer, M Rumbo
Aiming to combine the flexibility of Brucella Lumazine synthetase (BLS) to adapt different protein domains in a decameric structure and the capacity of BLS and flagellin to enhance the immunogenicity of peptides that are linked to their structure, we generated a chimeric protein (BLS-FliC131) by fusing flagellin from Salmonella in the N-termini of BLS. The obtained protein was recognized by anti-flagellin and anti-BLS antibodies, keeping the oligomerization capacity of BLS, without affecting the folding of the monomeric protein components determined by circular dichroism...
March 3, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28249361/heparin-induced-amyloid-fibrillation-of-%C3%AE-2-microglobulin-explained-by-solubility-and-a-supersaturation-dependent-conformational-phase-diagram
#13
Masatomo So, Yasuko Hata, Hironobu Naiki, Yuji Goto
Amyloid fibrils are fibrillar deposits of denatured proteins associated with amyloidosis and are formed by a nucleation and growth mechanism. We revisited an alternative and classical view of amyloid fibrillation: amyloid fibrils are crystal-like precipitates of denatured proteins formed above solubility upon breaking supersaturation. Various additives accelerate and then inhibit amyloid fibrillation in a concentration-dependent manner, suggesting that the combined effects of stabilizing and destabilizing forces affect fibrillation...
March 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28249355/monobodies-and-other-synthetic-binding-proteins-for-expanding-protein-science
#14
REVIEW
Fern Sha, Gabriel Salzman, Ankit Gupta, Shohei Koide
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in-depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond...
March 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28247968/breaking-up-and-making-up-the-secret-life-of-the-vacuolar-h-atpase
#15
REVIEW
Rebecca A Oot, Sergio Couoh-Cardel, Stuti Sharma, Nicholas J Stam, Stephan Wilkens
The vacuolar ATPase (V-ATPase; V1 Vo -ATPase) is a large multisubunit proton pump found in the endomembrane system of all eukaryotic cells where it acidifies the lumen of subcellular organelles including lysosomes, endosomes, the Golgi apparatus and clathrin coated vesicles. V-ATPase function is essential for pH and ion homeostasis, protein trafficking, endocytosis, mechanistic target of rapamycin (mTOR) and Notch signaling, as well as hormone secretion and neurotransmitter release. V-ATPase can also be found in the plasma membrane of polarized animal cells where its proton pumping function is involved in bone remodeling, urine acidification and sperm maturation...
March 1, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28244185/systematic-analysis-of-residual-density-suggests-that-a-major-limitation-in-well-refined-x-ray-structures-of-proteins-is-the-omission-of-ordered-solvent
#16
Jimin Wang
In the residual electron density map of a fully-refined X-ray protein model, there should be no peaks arising from modeling errors or missing atoms. Any residual peaks that do occur should be contributed by random residual intensity differences between the model and the data. If the model is incomplete (i.e. some atoms are missing), there will be more positive peaks than negative ones. On the other hand, if the model includes inappropriately-located atoms, there will be an excess of negative peaks. In this study, random residual peaks are quantified using the probability density function P(x), which is defined as the probability for a peak having peak height between x and x+dx...
February 28, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28241402/de-novo-design-of-signal-sequences-to-localize-cargo-to-the-1-2-propanediol-utilization-microcompartment
#17
Christopher M Jakobson, Marilyn F Slininger Lee, Danielle Tullman-Ercek
Organizing heterologous biosyntheses inside bacterial cells can alleviate common problems owing to toxicity, poor kinetic performance, and cofactor imbalances. A subcellular organelle known as a bacterial microcompartment, such as the 1,2-propanediol utilization microcompartment of Salmonella, is a promising chassis for this strategy. Here we demonstrate de novo design of the N-terminal signal sequences used to direct cargo to these microcompartment organelles. We expand the native repertoire of signal sequences using rational and library-based approaches and show that a canonical leucine-zipper motif can function as a signal sequence for microcompartment localization...
February 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28241399/biolayer-interferometry-of-lipid-nanodisc-reconstituted-yeast-vacuolar-h-atpase
#18
Stuti Sharma, Stephan Wilkens
Vacuolar H(+) -ATPase (V-ATPase) is a large, multisubunit membrane protein complex responsible for the acidification of subcellular compartments and the extracellular space. V-ATPase activity is regulated by reversible disassembly, resulting in cytosolic V1 -ATPase and membrane-integral Vo proton channel sectors. Reversible disassembly is accompanied by transient interaction with cellular factors and assembly chaperones. Quantifying protein-protein interactions involving membrane proteins, however, is challenging...
February 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28218438/structural-and-biochemical-characterization-of-the-nucleoside-hydrolase-from-c-elegans-reveals-the-role-of-two-active-site-cysteine-residues-in-catalysis
#19
Ranjan Kumar Singh, Jan Steyaert, Wim Versées
Nucleoside hydrolases (NHs) catalyze the hydrolysis of the N-glycoside bond in ribonucleosides and are found in all three domains of life. Although in parasitic protozoa a role in purine salvage has been well established, their precise function in bacteria and higher eukaryotes is still largely unknown. NHs have been classified into three homology groups based on the conservation of active site residues. While many structures are available of representatives of group I and II, structural information for group III NHs is lacking...
February 20, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28218432/becn2-interacts-with-atg14-through-a-metastable-coiled-coil-to-mediate-autophagy
#20
Minfei Su, Yue Li, Shane Wyborny, David Neau, Srinivas Chakravarthy, Beth Levine, Christopher L Colbert, Sangita C Sinha
ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an anti-parallel, curved homodimer with seven pairs of non-ideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD...
February 20, 2017: Protein Science: a Publication of the Protein Society
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