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https://www.readbyqxmd.com/read/28531185/thermal-stability-and-kinetic-constants-for-129-variants-of-a-family-1-glycoside-hydrolase-reveal-that-enzyme-activity-and-stability-can-be-separately-designed
#1
Dylan Alexander Carlin, Siena Hapig-Ward, Bill Wayne Chan, Natalie Damrau, Mary Riley, Ryan W Caster, Bowen Bethards, Justin B Siegel
Accurate modeling of enzyme activity and stability is an important goal of the protein engineering community. However, studies seeking to evaluate current progress are limited by small data sets of quantitative kinetic constants and thermal stability measurements. Here, we report quantitative measurements of soluble protein expression in E. coli, thermal stability, and Michaelis-Menten constants (kcat, KM, and kcat/KM) for 129 designed mutants of a glycoside hydrolase. Statistical analyses reveal that functional Tm is independent of kcat, KM, and kcat/KM in this system, illustrating that an individual mutation can modulate these functional parameters independently...
2017: PloS One
https://www.readbyqxmd.com/read/28513090/benchmarking-a-computational-design-method-for-the-incorporation-of-metal-ion-binding-sites-at-symmetric-protein-interfaces
#2
William A Hansen, Sagar D Khare
The design of novel metal-ion binding sites along symmetric axes in protein oligomers could provide new avenues for metalloenzyme design, construction of protein-based nanomaterials and novel ion transport systems. Here, we describe a computational design method, Symmetric Protein Recursive Ion-cofactor Sampling (SyPRIS), for locating constellations of backbone positions within oligomeric protein structures that are capable of supporting desired symmetrically coordinated metal ion(s) chelated by sidechains (chelant model)...
May 15, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28512576/applications-of-contact-predictions-to-structural-biology
#3
REVIEW
Felix Simkovic, Sergey Ovchinnikov, David Baker, Daniel J Rigden
Evolutionary pressure on residue interactions, intramolecular or intermolecular, that are important for protein structure or function can lead to covariance between the two positions. Recent methodological advances allow much more accurate contact predictions to be derived from this evolutionary covariance signal. The practical application of contact predictions has largely been confined to structural bioinformatics, yet, as this work seeks to demonstrate, the data can be of enormous value to the structural biologist working in X-ray crystallo-graphy, cryo-EM or NMR...
May 1, 2017: IUCrJ
https://www.readbyqxmd.com/read/28505339/labrs-a-rosetta-stone-for-retrospective-standardization-of-clinical-laboratory-test-results
#4
Ronald George Hauser, Douglas B Quine, Alex Ryder
Objective: Clinical laboratories in the United States do not have an explicit result standard to report the 7 billion laboratory tests results they produce each year. The absence of standardized test results creates inefficiencies and ambiguities for secondary data users. We developed and tested a tool to standardize the results of laboratory tests in a large, multicenter clinical data warehouse. Methods: Laboratory records, each of which consisted of a laboratory result and a test identifier, from 27 diverse facilities were captured from 2000 through 2015...
May 12, 2017: Journal of the American Medical Informatics Association: JAMIA
https://www.readbyqxmd.com/read/28501733/insomnia-in-adult-attention-deficit-hyperactivity-disorder-a-comparison-with-borderline-personality-disorder-population-in-a-clinical-setting-and-control-participants
#5
Sébastien Weibel, Françoise Jermann, Luisa Weiner, Rosetta Nicastro, Stefano Ardu, Eleonore Pham, Roland Hasler, Alexandre Dayer, Paco Prada, Nader Perroud
OBJECTIVES: Many adults with attention-deficit/hyperactivity disorder (ADHD) report sleeping difficulties. The relationship between sleep and ADHD is poorly understood, and shows discrepancies between subjective and objective measures. In order to determine the specificity of sleep-associated symptoms in ADHD, subjective sleep assessments among ADHD adult patients were compared with control subjects and with individuals suffering from borderline personality disorder (BPD). METHODS: 129 outpatients with ADHD, 70 with BPD (including 17 patients with BPD and ADHD comorbidity), and 65 control participants were assessed for sleep quality, insomnia, and sleepiness, using the Pittsburgh Sleep Quality Index (PSQI), the Insomnia Severity Index (ISI), and the Epworth Sleepiness Scale (ESS)...
May 5, 2017: Comprehensive Psychiatry
https://www.readbyqxmd.com/read/28501600/development-of-a-human-epidermal-growth-factor-derivative-with-egfr-blocking-and-depleted-biological-activities-a-comparative-in-vitro-study-using-egfr-positive-breast-cancer-cells
#6
Masomeh Mehrabi, Kamran Mansouri, Bijan Soleymani, Zohreh Hoseinkhani, Mohsen Shahlaie, Reza Khodarahmi
Epidermal growth factor (EGF) is a local growth factor that stimulates cell growth, proliferation, and differentiation by binding to its receptor EGFR. EGF and EGFR are involved in many aspects of the development of carcinomas. Because EGFR has been found to be over-expressed in many tumors of epithelial origin, it is a potential target for antitumor therapy. In this study we designed a mutated form of hEGF (mEGF) with a deletion of four amino acids residues (Gln(43), Tyr(44), Arg(45) and Asp(46)) in order to show importance of Leu spatial location for EGFR binding/activation...
May 10, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28481970/foldit-standalone-a-video-game-derived-protein-structure-manipulation-interface-using-rosetta
#7
Robert Kleffner, Jeff Flatten, Andrew Leaver-Fay, David Baker, Justin B Siegel, Firas Khatib, Seth Cooper
Summary: Foldit Standalone is an interactive graphical interface to the Rosetta molecular modeling package. In contrast to most command-line or batch interactions with Rosetta, Foldit Standalone is designed to allow easy, real-time, direct manipulation of protein structures, while also giving access to the extensive power of Rosetta computations. Derived from the user interface of the scientific discovery game Foldit (itself based on Rosetta), Foldit Standalone has added more advanced features and removed the competitive game elements...
May 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28470912/jumping-between-protein-conformers-using-normal-modes
#8
Swapnil Mahajan, Yves-Henri Sanejouand
The relationship between the normal modes of a protein and its functional conformational change has been studied for decades. However, using this relationship in a predictive context remains a challenge. In this work, we demonstrate that, starting from a given protein conformer, it is possible to generate in a single step model conformers that are less than 1 Å (Cα -RMSD) from the conformer which is the known endpoint of the conformational change, particularly when the conformational change is collective in nature...
May 3, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#9
Rebecca F Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram K Mulligan, Kalli Kappel, Jason W Labonte, Michael S Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15)...
May 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28416724/on-the-attempts-to-measure-water-and-other-volatiles-directly-at-the-surface-of-a-comet
#10
REVIEW
I P Wright, S Sheridan, G H Morgan, S J Barber, A D Morse
The Ptolemy instrument on the Philae lander (of the Rosetta space mission) was able to make measurements of the major volatiles, water, carbon monoxide and carbon dioxide, directly at the surface of comet 67P/Churyumov-Gerasimenko. We give some background to the mission and highlight those instruments that have already given insights into the notion of water in comets, and which will continue to do so as more results are either acquired or more fully interpreted. On the basis of our results, we show how comets may in fact be heterogeneous over their surface, and how surface measurements can be used in a quest to comprehend the daily cycles of processes that affect the evolution of comets...
May 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28412830/expression-and-immunogenicity-of-vp40-protein-of-zebov
#11
Yinbiao Wang, Xiao Liu, Ling Tao, Pengwei Xu, Xia Gao, Huijun Li, Zhongzhi Yang, Weidong Wu
BACKGROUND: EBOV outbreaks continue to threaten the world due to the absence of effective vaccines and therapeutics. Easy-to-use and rapid diagnostic tests for EBOV are highly desired for prevention and control of the EVD epidemic. METHODS: Escherichia coli expression system was used to express VP40 protein of Zaire Ebola virus (ZEBOV) as water-soluble protein upon optimization of temperature, time, and IPTG concentration. VP40 protein was purified through Ni-NTA affinity chromatography and applied to immunize rabbits for immunogenicity analysis...
April 2017: Archives of Iranian Medicine
https://www.readbyqxmd.com/read/28383276/predicting-the-initial-steps-of-salt-stable-cowpea-chlorotic-mottle-virus-capsid-assembly-with-atomistic-force-fields
#12
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsids, each protein unit is in contact with copies of itself through several interfaces. The relative strengths of the different contacts affect the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt-stable cowpea chlorotic mottle virus (CCMV) capsid protein using a combination of different computational tools. The best predictions of dimer configurations provided by blind docking with ZDOCK are rescored using geometry optimization with the Amber and Rosetta force fields...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28381558/gain-of-function-mutation-of-a-voltage-gated-sodium-channel-nav1-7-associated-with-peripheral-pain-and-impaired-limb-development
#13
Brian S Tanaka, Phuong T Nguyen, Eray Yihui Zhou, Yong Yang, Vladimir Yarov-Yarovoy, Sulayman D Dib-Hajj, Stephen G Waxman
Dominant mutations in voltage-gated sodium channel NaV1.7 cause inherited erythromelalgia (IEM), a debilitating pain disorder characterized by severe burning pain and redness of the distal extremities. NaV1.7 is preferentially expressed within peripheral sensory and sympathetic neurons. Here, we describe a novel NaV1.7 mutation in an 11-year old male with under-development of the limbs, recurrent attacks of burning pain with erythema and swelling in his feet and hands. Frequency and duration of the episodes gradually increased with age and relief by cooling became less effective...
April 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28349025/optimization-of-the-expression-of-dt386-br2-fusion-protein-in-escherichia-coli-using-response-surface-methodology
#14
Fatemeh Shafiee, Mohammad Rabbani, Ali Jahanian-Najafabadi
BACKGROUND: The aim of this study was to determine the best condition for the production of DT386-BR2 fusion protein, an immunotoxin consisting of catalytic and translocation domains of diphtheria toxin fused to BR2, a cancer specific cell penetrating peptide, for targeted eradication of cancer cells, in terms of the host, cultivation condition, and culture medium. MATERIALS AND METHODS: Recombinant pET28a vector containing the codons optimized for the expression of the DT386-BR2 gene was transformed to different strains of Escherichia coli (E...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28347235/selection-of-single-chain-antibody-fragments-binding-to-the-extracellular-domain-of-4-1bb-receptor-by-phage-display-technology
#15
Salman Bagheri, Mehdi Yousefi, Elmira Safaie Qamsari, Farhad Riazi-Rad, Mohsen Abolhassani, Vahid Younesi, Ruhollah Dorostkar, Ali Akbar Movassaghpour, Zahra Sharifzadeh
The 4-1BB is a surface glycoprotein that pertains to the tumor necrosis factor-receptor family. There is compelling evidence suggesting important roles for 4-1BB in the immune response, including cell activation and proliferation and also cytokine induction. Because of encouraging results of different agonistic monoclonal antibodies against 4-1BB in the treatment of cancer, infectious, and autoimmune diseases, 4-1BB has been suggested as an attractive target for immunotherapy. In this study, single chain variable fragment phage display libraries, Tomlinson I+J, were screened against specific synthetic oligopeptides (peptides I and II) designed from 4-1BB extracellular domain...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28325842/surface-changes-on-comet-67p-churyumov-gerasimenko-suggest-a-more-active-past
#16
M Ramy El-Maarry, O Groussin, N Thomas, M Pajola, A-T Auger, B Davidsson, X Hu, S F Hviid, J Knollenberg, C Güttler, C Tubiana, S Fornasier, C Feller, P Hasselmann, J-B Vincent, H Sierks, C Barbieri, P Lamy, R Rodrigo, D Koschny, H U Keller, H Rickman, M F A'Hearn, M A Barucci, J-L Bertaux, I Bertini, S Besse, D Bodewits, G Cremonese, V Da Deppo, S Debei, M De Cecco, J Deller, J D P Deshapriya, M Fulle, P J Gutierrez, M Hofmann, W-H Ip, L Jorda, G Kovacs, J-R Kramm, E Kührt, M Küppers, L M Lara, M Lazzarin, Z-Yi Lin, J J Lopez Moreno, S Marchi, F Marzari, S Mottola, G Naletto, N Oklay, A Pommerol, F Preusker, F Scholten, X Shi
The Rosetta spacecraft spent ~2 years orbiting comet 67P/Churyumov-Gerasimenko, most of it at distances that allowed surface characterization and monitoring at submeter scales. From December 2014 to June 2016, numerous localized changes were observed, which we attribute to cometary-specific weathering, erosion, and transient events driven by exposure to sunlight and other processes. While the localized changes suggest compositional or physical heterogeneity, their scale has not resulted in substantial alterations to the comet's landscape...
March 21, 2017: Science
https://www.readbyqxmd.com/read/28320259/levosimendan-for-hemodynamic-support-after-cardiac-surgery
#17
Giovanni Landoni, Vladimir V Lomivorotov, Gabriele Alvaro, Rosetta Lobreglio, Antonio Pisano, Fabio Guarracino, Maria G Calabrò, Evgeny V Grigoryev, Valery V Likhvantsev, Marcello F Salgado-Filho, Alessandro Bianchi, Vadim V Pasyuga, Massimo Baiocchi, Federico Pappalardo, Fabrizio Monaco, Vladimir A Boboshko, Marat N Abubakirov, Bruno Amantea, Rosalba Lembo, Luca Brazzi, Luigi Verniero, Pietro Bertini, Anna M Scandroglio, Tiziana Bove, Alessandro Belletti, Maria G Michienzi, Dmitriy L Shukevich, Tatiana S Zabelina, Rinaldo Bellomo, Alberto Zangrillo
Background Acute left ventricular dysfunction is a major complication of cardiac surgery and is associated with increased mortality. Meta-analyses of small trials suggest that levosimendan may result in a higher rate of survival among patients undergoing cardiac surgery. Methods We conducted a multicenter, randomized, double-blind, placebo-controlled trial involving patients in whom perioperative hemodynamic support was indicated after cardiac surgery, according to prespecified criteria. Patients were randomly assigned to receive levosimendan (in a continuous infusion at a dose of 0...
May 25, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28318014/-solvent-hydrogen-bond-occlusion-a-new-model-of-polar-desolvation-for-biomolecular-energetics
#18
Andrea Bazzoli, John Karanicolas
Water engages in two important types of interactions near biomolecules: it forms ordered "cages" around exposed hydrophobic regions, and it participates in hydrogen bonds with surface polar groups. Both types of interaction are critical to biomolecular structure and function, but explicitly including an appropriate number of solvent molecules makes many applications computationally intractable. A number of implicit solvent models have been developed to address this problem, many of which treat these two solvation effects separately...
June 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28302718/a-unique-choanoflagellate-enzyme-rhodopsin-exhibits-light-dependent-cyclic-nucleotide-phosphodiesterase-activity
#19
Kazuho Yoshida, Satoshi P Tsunoda, Leonid S Brown, Hideki Kandori
Photoactivated adenylyl cyclase (PAC) and guanylyl cyclase rhodopsin increase the concentrations of intracellular cyclic nucleotides upon illumination, serving as promising second-generation tools in optogenetics. To broaden the arsenal of such tools, it is desirable to have light-activatable enzymes that can decrease cyclic nucleotide concentrations in cells. Here, we report on an unusual microbial rhodopsin that may be able to meet the demand. It is found in the choanoflagellate Salpingoeca rosetta and contains a C-terminal cyclic nucleotide phosphodiesterase (PDE) domain...
May 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28300559/expression-purification-and-in-vitro-refolding-of-the-recombinant-truncated-saposin-like-protein-2-antigen-for-development-of-diagnosis-of-human-fascioliasis
#20
Abolfazl Mirzadeh, Zarrintaj Valadkhani, Asiyeh Yoosefy, Jalal Babaie, Majid Golkar, Ahmad Reza Esmaeili Rastaghi, Elham Kazemi-Rad, Keyhan Ashrafi
Early diagnosis of fascioliasis is critical in prevention of injury to the liver and bile ducts. Saposin-like protein (FhSAP-2) is probably the most ideal antigen of Fasciola hepatica for development of ELISA kits. SAP-2 has a conserved tertiary structure containing three disulfide bonds and conformational epitopes. Therefore, antigenicity of SAP-2 is greatly depends on disulfide bond formation and proper folding. We produced the recombinant truncated SAP-2 (rtSAP-2) in the SHuffle(®) T7 and Rosetta strain of Escherichia coli, in soluble and insoluble forms, respectively and purified by immobilized metal affinity chromatography (IMAC)...
March 11, 2017: Acta Tropica
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