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https://www.readbyqxmd.com/read/28799215/secondary-structure-and-dynamics-study-of-the-intrinsically-disordered-silica-mineralizing-peptide-p5-s3-during-silicic-acid-condensation-and-silica-decondensation
#1
Christian Zerfaß, Garry W Buchko, Wendy J Shaw, Stephan Hobe, Harald Paulsen
The silica forming repeat R5 of sil1 from Cylindrotheca fusiformis was the blueprint for the design of P5 S3 , a 50-residue peptide which can be produced in large amounts by recombinant bacterial expression. It contains five protein kinase A target sites and is highly cationic due to 10 lysine and 10 arginine residues. In the presence of supersaturated orthosilicic acid P5 S3 enhances silica-formation whereas it retards the dissolution of amorphous silica (SiO2 ) at globally undersaturated concentrations. The secondary structure of P5 S3 during these two processes was studied by circular dichroism (CD) spectroscopy, complemented by nuclear magnetic resonance (NMR) spectroscopy of the peptide in the absence of silicate...
August 11, 2017: Proteins
https://www.readbyqxmd.com/read/28799176/the-molecular-mechanism-behind-resistance-of-the-kinase-flt3-to-the-inhibitor-quizartinib
#2
Ran Friedman
Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is a drug target for leukaemias. Several potent inhibitors of FLT3 exists, and bind to the inactive form of the enzyme. Unfortunately, resistance due to mutations in the kinase domain of FLT3 limits the therapeutic effects of these inhibitors. As in many other cases, it is not straightforward to explain why certain mutations lead to drug resistance. Extensive fully-atomistic molecular dynamics (MD) simulations of FLT3 were carried out with an inhibited form (FLT-quizartinib complex), a free (apo) form and an active conformation...
August 11, 2017: Proteins
https://www.readbyqxmd.com/read/28799172/protein-structure-prediction-making-awsem-awsem-er-by-adding-evolutionary-restraints
#3
Brian J Sirovetz, Nicholas P Schafer, Peter G Wolynes
Protein sequences have evolved to fold into functional structures, resulting in families of diverse protein sequences that all share the same overall fold. One can harness protein family sequence data to infer likely contacts between pairs of residues. In the current study, we combine this kind of inference from coevolutionary information with a coarse-grained protein force field ordinarily used with single sequence input, the Associative memory, Water mediated, Structure and Energy Model (AWSEM), to achieve improved structure prediction...
August 11, 2017: Proteins
https://www.readbyqxmd.com/read/28796342/elucidation-of-insulin-assembly-at-acidic-and-neutral-ph-characterization-of-low-molecular-weight-oligomers
#4
Matthew T Mawhinney, Thomas L Williams, James L Hart, Mitra L Taheri, Brigita Urbanc
Deficiency in insulin secretion and function that characterize type 2 diabetes often requires administration of extraneous insulin, leading to injection-site amyloidosis. Insulin aggregation at neutral pH is not well understood. Although oligomer formation is believed to play an important role, insulin oligomers have not been fully characterized yet. Here, we elucidate similarities and differences between in vitro insulin aggregation at acidic and neutral pH for a range of insulin concentrations (2.5-100 μM) by using kinetic thioflavin T fluorescence, circular dichroism, atomic force and electron microscopy imaging...
August 10, 2017: Proteins
https://www.readbyqxmd.com/read/28786199/deciphering-the-promiscuous-interactions-between-intrinsically-disordered-transactivation-domains-and-the-kix-domain
#5
Yongqi Huang, Meng Gao, Fei Yang, Lei Zhang, Zhengding Su
The kinase-inducible domain interacting (KIX) domain of the transcriptional coactivator CBP protein carries two isolated binding sites (designated as the c-Myb site and the MLL site) and is capable of binding numerous intrinsically disordered transactivation domains (TAD), including c-Myb and pKID via the c-Myb site, and MLL, E2A and c-Jun via the MLL site. In this study we compared the kinetics for binding of various disordered TADs to the KIX domain via computational biophysical analyses. We found that the binding rates are heavily affected by long-range electrostatic interactions...
August 8, 2017: Proteins
https://www.readbyqxmd.com/read/28779494/bending-of-the-bst-2-coiled-coil-during-viral-budding
#6
Kadir A Ozcan, Christopher E Berndsen
BST-2/tetherin is a human extracellular transmembrane protein that serves as a host defense factor against HIV-1 and other viruses by inhibiting viral spreading. Structurally, BST-2 is a homo-dimeric coiled-coil that is connected to the host cell membrane by N and C terminal transmembrane anchors. The C-terminal membrane anchor of BST-2 is inserted into the budding virus while the N-terminal membrane anchor remains in the host cell membrane creating a viral tether. The structural mechanism of viral budding and tethering as mediated by BST-2 is not clear...
August 4, 2017: Proteins
https://www.readbyqxmd.com/read/28762578/identification-and-functionality-prediction-of-pathogenesis-related-protein-1-from-legume-family
#7
Meenakshi Tellis, Monika Mathur, Gayatri Gurjar, Narendra Kadoo, Vidya Gupta
The production and accumulation of pathogenesis related (PR) proteins in plants is one of the important responses to biotic and abiotic stress. Large number of identified PR proteins has been categorized into 17 functional families based on their structure, phylogenetics and biological activities. However, they are not widely studied in legume crops. Using 29 PR1 proteins from Arabidopsis thaliana, as query, here we have predicted 92 candidate PR1 proteins through the PSI-BLAST and HMMER programs. These candidate proteins were comprehensively analysed with, multiple sequence alignment, domain architecture studies, signal peptide and motif extraction followed by phylogenetic analysis...
August 1, 2017: Proteins
https://www.readbyqxmd.com/read/28748648/accurate-template-based-modelling-in-casp12-using-the-intfold4-ts-modfold6-and-refold-methods
#8
Liam J McGuffin, Ahmad N Shuid, Robert Kempster, Ali H A Maghrabi, John O Nealon, Bajuna R Salehe, Jennifer D Atkins, Daniel B Roche
Our aim in CASP12 was to improve our Template Based Modelling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet these aims we developed two new automated methods, which we used to score, rank and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28748551/identification-of-a-dimeric-kdg-aldolase-from-agrobacterium-tumefaciens
#9
Tatiana P Soares da Costa, Madhvi Patel, Sebastien Desbois, Ruchi Gupta, Pierre Faou, Matthew A Perugini
Agrobacterium tumefaciens is a Gram-negative bacterium and causative agent of Crown Gall disease that infects a variety of economically-important plants. The annotated A. tumefaciens genome contains 10 putative dapA genes, which code for dihydrodipicolinate synthase (DHDPS). However, we have recently demonstrated that only one of these genes (dapA7) encodes a functional DHDPS. The function of the other nine putative dapA genes is yet to be determined. Here, we demonstrate using bioinformatics that the product of the dapA5 gene (DapA5) possesses all the catalytic residues canonical to 2-keto-3-deoxygluconate (KDG) aldolase, which is a class I aldolase involved in glucose metabolism...
July 27, 2017: Proteins
https://www.readbyqxmd.com/read/28745031/a-tale-of-two-tails-the-importance-of-unstructured-termini-in-the-aggregation-pathway-of-%C3%AE-2-microglobulin
#10
Rui J S Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I Shakhnovich, Patricia F N Faísca
The identification of intermediate states for folding and aggregation is important from a fundamental standpoint and for the design of novel therapeutic strategies targeted at conformational disorders. Protein human β2-microglobulin (HB2m) is classically associated with dialysis-related amyloidosis, but the single point mutant D76N was recently identified as the causative agent of a hereditary systemic amyloidosis affecting visceral organs. Here, we use D76N as a model system to explore the early stage of the aggregation mechanism of HB2m by means of an integrative approach framed on molecular simulations...
July 26, 2017: Proteins
https://www.readbyqxmd.com/read/28734034/protein-features-as-determinants-of-wild-type-glycoside-hydrolase-thermostability
#11
Henrik Marcus Geertz-Hansen, Lars Kiemer, Morten Nielsen, Kiril Stanchev, Nikolaj Blom, Søren Brunak, Thomas Nordahl Petersen
Thermostable enzymes for conversion of lignocellulosic biomass into biofuels have significant advantages over enzymes with more moderate themostability due to the challenging application conditions. Experimental discovery of thermostable enzymes is highly cost intensive, and the development of in-silico methods guiding the discovery process would be of high value. To develop such an in-silico method and provide the data foundation of it, we determined the melting temperatures of 602 fungal glycoside hydrolases from the families GH5, 6, 7, 10, 11, 43 and AA9 (formerly GH61)...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28734030/a-computational-method-for-selecting-short-peptide-sequences-for-inorganic-material-binding
#12
Niloofar Nayebi, Sibel Cetinel, Sara Ibrahim Omar, Jack A Tuszynski, Carlo Montemagno
Discovering or designing biofunctionalized materials with improved quality highly depends on the ability to manipulate and control the peptide-inorganic interaction. Various peptides can be used as assemblers, synthesizers, and linkers in the material syntheses. In another context, specific and selective material-binding peptides can be used as recognition blocks in mining applications. In this study, we propose a new in silico method to select short 4-mer peptides with high affinity and selectivity for a given target material...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28722205/temperature-stability-of-proteins-analysis-of-irreversible-denaturation-using-isothermal-calorimetry
#13
Arne Schön, Benjamin R Clarkson, Maria Jaime, Ernesto Freire
The structural stability of proteins has been traditionally studied under conditions in which the folding/unfolding reaction is reversible, since thermodynamic parameters can only be determined under these conditions. Achieving reversibility conditions in temperature stability experiments has often required performing the experiments at acidic pH or other non-physiological solvent conditions. With the rapid development of protein drugs, the fastest growing segment in the pharmaceutical industry, the need to evaluate protein stability under formulation conditions has acquired renewed urgency...
July 19, 2017: Proteins
https://www.readbyqxmd.com/read/28722183/a-rare-polyglycine-type-ii-like-helix-motif-in-naturally-occurring-proteins
#14
Eberhard Warkentin, Sina Weidenweber, Karola Schühle, Ulrike Demmer, Johann Heider, Ulrich Ermler
Common structural elements in proteins such as α-helices or β-sheets are characterized by uniformly repeating, energetically favorable main chain conformations which additionally exhibit a completely saturated hydrogen-bonding network of the main chain NH and CO groups. Although polyproline or polyglycine type II helices (PPII or PGII ) are frequently found in proteins, they are not considered as equivalent secondary structure elements because they do not form a similar self-contained hydrogen-bonding network of the main chain atoms...
July 19, 2017: Proteins
https://www.readbyqxmd.com/read/28718923/using-homology-modeling-to-interrogate-binding-affinity-in-neutralization-of-ricin-toxin-by-a-family-of-single-domain-antibodies
#15
Andrea Bazzoli, David J Vance, Michael J Rudolph, Yinghui Rong, Siva Krishna Angalakurthi, Ronald T Toth, C Russell Middaugh, David B Volkin, David D Weis, John Karanicolas, Nicholas J Mantis
In this report we investigated, within a group of closely related single domain camelid antibodies (VH Hs), the relationship between binding affinity and neutralizing activity as it pertains to ricin, a fast-acting toxin and biothreat agent. The V1C7-like VH Hs (V1C7, V2B9, V2E8, and V5C1) are similar in amino acid sequence, but differ in their binding affinities and toxin-neutralizing activities. Using the X-ray crystal structure of V1C7 in complex with ricin's enzymatic subunit (RTA) as a template, Rosetta-based homology modeling coupled with energetic decomposition led us to predict that a single pairwise interaction between Arg29 on V5C1 and Glu67 on RTA was responsible for the difference in ricin toxin binding affinity between V1C7, a weak neutralizer, and V5C1, a moderate neutralizer...
July 18, 2017: Proteins
https://www.readbyqxmd.com/read/28707342/ratio-of-ellipticities-between-192-and-208-nm-r1-an-effective-electronic-circular-dichroism-parameter-for-characterization-of-the-helical-components-of-proteins-and-peptides
#16
Raja Banerjee, Tridip Sheet
Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R2 ) ≅ [θ]222 /[θ]208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R1 ) ≅ [θ]192 /[θ]208 ), may be utilized towards identifying the peptide/protein conformation (especially 310 - and α-helices)...
July 13, 2017: Proteins
https://www.readbyqxmd.com/read/28707320/homology-model-of-the-human-trna-splicing-ligase-rtcb
#17
Argha Nandy, Patricia Saenz-Mendez, Adrienne M Gorman, Afshin Samali, Leif A Eriksson
RtcB is an essential human tRNA ligase required for ligating the 2',3'-cyclic phosphate and 5'-hydroxyl termini of cleaved tRNA halves during tRNA splicing and XBP1 fragments during endoplasmic reticulum stress. Activation of XBP1 has been implicated in various human tumors including breast cancer. Here we present, for the first time, a homology model of human RtcB (hRtcB) in complex with manganese and covalently bound GMP built from the Pyrococcus horikoshii RtcB (bRtcB) crystal structure, PDB ID 4DWQA. The structure is analyzed in terms of stereochemical quality, folding reliability, secondary structure similarity with bRtcB, druggability of the active site binding pocket and its metal-binding microenvironment...
July 13, 2017: Proteins
https://www.readbyqxmd.com/read/28688107/evaluating-amber-force-fields-using-computed-nmr-chemical-shifts
#18
David R Koes, John K Vries
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq and ff15ipq)...
July 8, 2017: Proteins
https://www.readbyqxmd.com/read/28681414/structure-and-catalytic-activation-of-the-trim23-ring-e3-ubiquitin-ligase
#19
Daria M Dawidziak, Jacint G Sanchez, Jonathan M Wagner, Barbie K Ganser-Pornillos, Owen Pornillos
Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2-ubiquitin conjugate...
July 6, 2017: Proteins
https://www.readbyqxmd.com/read/28677327/conformational-variability-of-the-stationary-phase-survival-protein-e-sure-from-xylella-fastidiosa-revealed-by-x-ray-crystallography-small-angle-x-ray-scattering-studies-and-normal-mode-analysis
#20
Agnes Thiane Pereira Machado, Emanuella Maria Barreto Fonseca, Marcelo Augusto Dos Reis, Antonio Marcos Saraiva, Clelton Aparecido Dos Santos, Marcelo Augusto Szymanski de Toledo, Igor Polikarpov, Anete Pereira de Souza, Ricardo Aparicio, Jorge Iulek
Xylella fastidiosa is a xylem-limited bacterium that infects a wide variety of plants. Stationary phase survival protein E is classified as a nucleotidase which is expressed when bacterial cells are in the stationary growth phase and subjected to environmental stresses. Here we report four refined X-ray structures of this protein from X. fastidiosa in four different crystal forms in the presence and/or absence of the substrate 3'-AMP. In all chains the conserved loop verified in family members assumes a closed conformation in either condition...
July 5, 2017: Proteins
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