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https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#1
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven 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 parameterized 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, REF15...
April 21, 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
#2
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
#3
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-ccmv-capsid-assembly-with-atomistic-force-fields
#4
Zoltan Antal, Janos Szoverfi, Szilard N Fejer
Computational prediction of native protein-protein interfaces still remains a challenging task. In virus capsid proteins, each protein unit is in contact with copies of itself through several interfaces. The relative strength of the different contacts affects the dynamics of the assembly, especially if the process is hierarchical. We investigate the dimerization of the salt stable 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 6, 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
#5
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
#6
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
#7
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
#8
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
#9
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...
March 21, 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
#10
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...
March 20, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28302718/a-unique-choanoflagellate-enzyme-rhodopsin-with-cyclic-nucleotide-phosphodiesterase-activity
#11
Kazuho Yoshida, Satoshi P Tsunoda, Leonid S Brown, Hideki Kandori
Photoactivated adenylyl cyclase (PAC) and guanylyl cyclase rhodopsin (Rh-GC) increase the concentrations of intracellular cyclic nucleotides upon illumination, serving as promising second-generation tools in optogenetics. To broaden arsenal of such tools, it is desirable to have light-activatable enzymes which can decrease cyclic nucleotide concentrations in cells. Here, we report on an unusual microbial rhodopsin which 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...
March 16, 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
#12
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
https://www.readbyqxmd.com/read/28286974/natural-radioactivity-levels-and-associated-health-hazards-from-the-terrestrial-ecosystem-in-rosetta-branch-of-the-river-nile-egypt
#13
W M Abdellah, H M Diab, S U El-Kameesy, E Salama, S El-Framawy
Twenty soil and 25 sediment samples were collected from the banks and bottom of the River Nile in the surroundings of biggest cities located close to it. Natural radioactivity concentrations of (226)Ra, (232)Th and (40)K have been evaluated for all samples by means of γ spectrometric analysis. The radioactivity levels of soil and sediment samples fall within the internationally recommended values. Nevertheless, high natural background radiation zones are detected in the Kafr El-Zayat region due to the presence of a fertilizer factory, and in the Rosetta region due to the presence of black sand deposits...
March 13, 2017: Isotopes in Environmental and Health Studies
https://www.readbyqxmd.com/read/28282854/systematic-design-of-trypsin-cleavage-site-mutated-exendin4-cysteine-1-an-orally-bioavailable-glucagon-like-peptide-1-receptor-agonist
#14
Wenbo Sai, Hong Tian, Kangmin Yang, Daoqi Tang, Jinxiao Bao, Yang Ge, Xiaoda Song, Yu Zhang, Cheng Luo, Xiangdong Gao, Wenbing Yao
Exendin-4 is a strong therapeutic candidate for the treatment of metabolic syndrome. Related receptor agonist drugs have been on the market since 2005. However, technical limitations and the pain caused by subcutaneous injection have severely limited patient compliance. The goal of the study is to investigate a biologically active exendin-4 analog could be administered orally. Using intraperitoneal glucose tolerance tests, we discovered that exendin4-cysteine administered by oral gavage had a distinct hypoglycemic effect in C57BL/6J mice...
March 8, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28279194/crispr-targeted-genome-editing-of-mesenchymal-stem-cell-derived-therapies-for-type-1-diabetes-a-path-to-clinical-success
#15
REVIEW
Dario Gerace, Rosetta Martiniello-Wilks, Najah Therese Nassif, Sara Lal, Raymond Steptoe, Ann Margaret Simpson
Due to their ease of isolation, differentiation capabilities, and immunomodulatory properties, the therapeutic potential of mesenchymal stem cells (MSCs) has been assessed in numerous pre-clinical and clinical settings. Currently, whole pancreas or islet transplantation is the only cure for people with type 1 diabetes (T1D) and, due to the autoimmune nature of the disease, MSCs have been utilised either natively or transdifferentiated into insulin-producing cells (IPCs) as an alternative treatment. However, the initial success in pre-clinical animal models has not translated into successful clinical outcomes...
March 9, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28274612/effects-of-obesity-on-il-33-st2-system-in-heart-adipose-tissue-and-liver-study-in-the-experimental-model-of-zucker-rats
#16
Rosetta Ragusa, Manuela Cabiati, Maria Angela Guzzardi, Andrea D'Amico, Daniela Giannessi, Silvia Del Ry, Chiara Caselli
Suppression of tumorigenicity 2 (ST2) mediates the effect of Interleukin-33 (IL-33). Few data are reported on the relationship between IL-33/ST2 and obesity. We aimed to investigate effects of obesity on IL-33/ST2 system in heart, adipose tissue and liver in a rodent model of obesity. The relationship of cardiac expression of IL-33/ST2 system with natriuretic peptides (NPs) system and inflammatory mediators was also studied. mRNA expression of IL-33/ST2 system was evaluated in cardiac, adipose and hepatic biopsies from obese Zucker rats (O) and controls (CO)...
March 6, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28263091/attachment-and-reflective-functioning-in-women-with-borderline-personality-disorder
#17
Deborah Badoud, Paco Prada, Rosetta Nicastro, Charlotte Germond, Patrick Luyten, Nader Perroud, Martin Debbané
Insecure attachment and impairments in reflective functioning (RF) are thought to play a critical role in borderline personality disorder (BPD). In particular, the mentalization-based model argues that insecure attachment indirectly accounts for increased BPD features, notably via disruption of RF capacities. Although the mediation relationship between attachment, RF, and BPD is supported by previous evidence, it remains to be directly tested in adults with BPD. In the current study, a sample of 55 female adult BPD patients and 105 female healthy controls completed a battery of self-report measures to investigate the interplay between attachment, RF capacities, and BPD clinical status...
March 6, 2017: Journal of Personality Disorders
https://www.readbyqxmd.com/read/28243985/efficient-synthesis-of-s-n-boc-3-hydroxypiperidine-using-an-r-specific-carbonyl-reductase-from-candida-parapsilosis
#18
Jingjing Chen, Ming Yan, Lin Xu
(S)-N-Boc-3-hydroxypiperidine (S-NBHP) is a critical chiral intermediate in the synthesis of pharmaceuticals, including ibrutinib, the active pharmaceutical ingredient of the new drug Imbruvica approved for the treatment of lymphoma. An (R)-specific carbonyl reductase from Candida parapsilosis (CprCR, also known as R-specific alcohol dehydrogenase) that catalyzes asymmetric reduction to produce (S)-N-Boc-3-hydroxypiperidine (S-NBHP) was identified for the first time. When co-expressed with a glucose dehydrogenase from Bacillus megaterium in Escherichia coli Rosetta (DE3), recombinant crude enzyme exhibited an activity of 9 U/mg with N-Boc-3-piperidone as the substrate and 12 U/mg with glucose as the substrate...
March 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28238619/application-of-the-rosetta-stone-to-understand-how-much-mvpa-preschoolers-accumulate-a-systematic-review
#19
REVIEW
Fabricio C P Ravagnani, Christianne F Coelho-Ravagnani, Keith Brazendale, Robert G Weaver, Daniel B Bornstein, Michael W Beets
OBJECTIVES: This study illustrates the utility of the Rosetta Stone equations for comparing estimates of preschool-age children's moderate-to-vigorous physical activity (MVPA) across studies utilizing different cutpoints. DESIGN: Systematic review. METHODS: A search of online databases was conducted to identify studies that reported daily minutes of MVPA in preschoolers using the cutpoints from which Rosetta Stone equations have been developed...
February 23, 2017: Journal of Science and Medicine in Sport
https://www.readbyqxmd.com/read/28236237/modeling-peptide-protein-structure-and-binding-using-monte-carlo-sampling-approaches-rosetta-flexpepdock-and-flexpepbind
#20
Nawsad Alam, Ora Schueler-Furman
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding...
2017: Methods in Molecular Biology
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