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Yi Zhao, Marcus J C Long, Yiran Wang, Sheng Zhang, Yimon Aye
Posttranslational modifications (PTMs) are the lingua franca of cellular communication. Most PTMs are enzyme-orchestrated. However, the reemergence of electrophilic drugs has ushered mining of unconventional/non-enzyme-catalyzed electrophile-signaling pathways. Despite the latest impetus toward harnessing kinetically and functionally privileged cysteines for electrophilic drug design, identifying these sensors remains challenging. Herein, we designed "G-REX"-a technique that allows controlled release of reactive electrophiles in vivo...
February 28, 2018: ACS Central Science
Clement Chung, Shital Patel, Rosetta Lee, Lily Fu, Sean Reilly, Tuyet Ho, Jason Lionetti, Michael D George, Pam Taylor
PURPOSE: The development of a computerized prescriber order-entry (CPOE) system for chemotherapy in a multisite safety-net health system and the challenges to its successful implementation are described. SUMMARY: Before CPOE for chemotherapy was first implemented and embedded in the electronic medical record system of Harris Health System (HHS), pharmacy personnel relied on regimen-specific preprinted order sets. However, due to differences in practice styles and workflow logistics, the paper orders across the 3 facilities were mostly site specific, with varying clinical content...
March 15, 2018: American Journal of Health-system Pharmacy: AJHP
Vito Romano, Riccardo Vinciguerra, Esmaeil M Arbabi, Nick Hicks, Pietro Rosetta, Paolo Vinciguerra, Stephen B Kaye
PURPOSE: To assess topographical changes in patients with keratoconus while awaiting corneal cross-linking (CXL) treatment. METHODS: In this prospective, double-center, observational clinical study, patients with keratoconus were enrolled. Progression was defined as a change in the curvature within the cone area of at least 1.00 diopter (D) on tangential map and a thinning of 20 μm at the thinnest point after measurements taken at least 3 months apart. Morphological parameters were assessed at baseline (day of listing for CXL) and on the day of CXL treatment, including slit-lamp biomicroscopy, keratometry (maximum, minimum, and mean), and thinnest corneal thickness using corneal tomography (Pentacam; Oculus Optikgeräte GmbH, Wetzlar, Germany)...
March 1, 2018: Journal of Refractive Surgery
Jeanine F Amacher, Helen T Hobbs, Aaron C Cantor, Lochan Shah, Marco-Jose Rivero, Sarah A Mulchand, John Kuriyan
Cbl proteins are E3 ubiquitin ligases specialized for the regulation of tyrosine kinases by ubiquitylation. Human Cbl proteins are activated by tyrosine phosphorylation, thus setting up a feedback loop whereby the activation of tyrosine kinases triggers their own degradation. Cbl proteins are targeted to their substrates by a phosphotyrosine-binding SH2 domain. Choanoflagellates, unicellular eukaryotes that are closely related to metazoans, also contain Cbl. The tyrosine kinase complement of choanoflagellates is distinct from that of metazoans, and it is unclear if choanoflagellate Cbl is regulated similarly to metazoan Cbl...
March 2, 2018: Protein Science: a Publication of the Protein Society
Yuehui Tian, Shiqiang Gao, Shang Yang, Georg Nagel
It is since many years textbook knowledge that the concentration of the second messenger cGMP is regulated in animal rod and cone cells by type-II rhodopsins via a G protein signaling cascade. Microbial rhodopsins with enzymatic activity for regulation of cGMP concentration were only recently discovered: in 2014 light-activated guanylyl cyclase opsins in fungi and in 2017 a novel rhodopsin phosphodiesterase in the protist Salpingoeca rosetta ( Sr RhoPDE). The light-regulation of Sr RhoPDE however, seemed very weak or absent...
February 26, 2018: Biochemical Journal
Xiaohu Hao, Guijun Zhang, Xiaogen Zhou
Computing conformations which are essential to associate structural and functional information with gene sequences, is challenging due to the high dimensionality and rugged energy surface of the protein conformational space. Consequently, the dimension of the protein conformational space should be reduced to a proper level, and an effective exploring algorithm should be proposed. In this paper, a plug-in method for guiding exploration in conformational feature space with Lipschitz underestimation (LUE) for ab-initio protein structure prediction is proposed...
February 6, 2018: Computational Biology and Chemistry
Clément Viricel, Simon de Givry, Thomas Schiex, Sophie Barbe
Motivation: Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces...
February 20, 2018: Bioinformatics
Adarsh Kumar Chiranjivi, Vikash Kumar Dubey
Dihydrolipoamide dehydrogenase (DLDH) regulates many crucial metabolic pathways as a multi-enzyme complex. Leishmania donovani dihydrolipoamide dehydrogenase (LdDLDH) has two variants present on two different chromosomes with very less sequence similarities. In the current study, we cloned both the variants in pET28a (+) vector and expressed in Rosetta-gami (DE3) E. coli strain. Expressed proteins were finally purified from pellets using Ni-NTA affinity chromatography. Purified enzymes were biochemically characterized and different kinetic parameters were studied...
February 18, 2018: International Journal of Biological Macromolecules
Jan Ludwiczak, Adam Jarmula, Stanislaw Dunin-Horkawicz
Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time...
February 14, 2018: Journal of Structural Biology
Alexander M Sevy, Swetasudha Panda, James E Crowe, Jens Meiler, Yevgeniy Vorobeychik
Computational protein design has been successful in modeling fixed backbone proteins in a single conformation. However, when modeling large ensembles of flexible proteins, current methods in protein design have been insufficient. Large barriers in the energy landscape are difficult to traverse while redesigning a protein sequence, and as a result current design methods only sample a fraction of available sequence space. We propose a new computational approach that combines traditional structure-based modeling using the Rosetta software suite with machine learning and integer linear programming to overcome limitations in the Rosetta sampling methods...
February 16, 2018: PLoS Computational Biology
Robert L Chevalier
No abstract text is available yet for this article.
February 15, 2018: Journal of the American Society of Nephrology: JASN
Kristen L Partyka, Melissa L Randolph, Karen A Lawrence, Harvey Cramer, Howard H Wu
BACKGROUND: Ancillary molecular testing has been recommended for thyroid fine-needle aspirates (FNA) with indeterminate cytologic diagnoses. Rosetta Genomics and Interpace Diagnostics have developed assays that can utilize direct smears as the testing substrate. METHODS: A retrospective study of indeterminate thyroid FNAs with known histologic follow-up was performed. One Diff-Quik-stained smear and one Papanicolaou-stained smear with similar cellularity (at least 60-100 lesional cells) from each case were sent to Rosetta and Interpace, respectively, for analysis...
February 15, 2018: Diagnostic Cytopathology
Chuannan Long, Mengmeng Liu, Xia Chen, Xiaofang Wang, Mingqiang Ai, Jingjing Cui, Bin Zeng
The present study verified whether acyl-coenzyme A (acyl-CoA)-binding protein (ACBP) affected the production of Monascus pigments (MPs) in Monascus ruber CICC41233 (MrACBP). Phylogenetic analysis revealed that the cloned Mracbp gene, which encoded the MrACBP protein, exhibited the closest match (99% confidence level) to the gene from Penicilliopsis zonata . The MrACBP and maltose-binding protein (MBP) were simultaneously expressed in Escherichia coli Rosetta DE3 in the form of a fusion protein. The microscale thermophoresis binding assay revealed that the purified MBP-MrACBP exhibited a higher affinity for myristoyl-CoA (Kd = 88...
February 2018: 3 Biotech
Kyle A Barlow, Shane Ó Conchúir, Samuel Thompson, Pooja Suresh, James Lucas, Markus Heinonen, Tanja Kortemme
Computationally modeling changes in binding free energies upon mutation (interface ΔΔG) allows large-scale prediction and perturbation of protein-protein interactions. Additionally, methods that consider and sample relevant conformational plasticity should be able to achieve higher prediction accuracy over methods that do not. To test this hypothesis, we developed a method within the Rosetta macromolecular modeling suite (flex ddG) that samples conformational diversity using "backrub" to generate an ensemble of models, then applying torsion minimization, side chain repacking and averaging across this ensemble to estimate interface ΔΔG values...
February 5, 2018: Journal of Physical Chemistry. B
(no author information available yet)
No abstract text is available yet for this article.
February 2, 2018: European Journal of Contraception & Reproductive Health Care
Yue Liu, Zhonggen Zhan, Bing Zhu, Rongquan Zheng, Hongyi Cheng, Zuoming Nie
Antibacterial peptide can be easily degraded by protease and has the lethal effect on the host Escherichia coli. In order to solve these problems and further improve the expression ability of the Escherichia coli system, the antimicrobial peptide Spinosan-C of Paa spinosa was studied. First, the codon of Spinosan-C was optimized according to E. coli codon usage frequency. Then, the 8 multimeric Spinosan-C gene (8×Spinosan-C) was synthesized and cloned into prokaryotic expression vector pET-28a. The fusion antimicrobial peptide 8×Spinosan-C was further highly expressed in Escherichia coli strain Rosetta...
January 25, 2018: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E Brereton, P Andrew Karplus, Rochelle R Dotas, Vincenzo Venditti, Nikolaos G Sgourakis, Konstantinos Tripsianes
Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6-10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate...
January 26, 2018: Nature Communications
Wentao Shen, Jie Han, Pu Yan, Jiping Zhen, Lie Zhang, Xiaoying Li, Decai Tuo, Peng Zhou
Plant methionine sulfoxide reductase B1 (MsrB1) protects the photosynthetic apparatus from oxidative damage by scavenging reactive oxygen species to repair Met-oxidized proteins in response to abiotic stresses and biotic attack. Papaya MsrB1 (PaMsrB1) was identified previously to interact with papaya ringspot virus NIa-Pro, and this interaction inhibits the import of PaMsrB1 into the chloroplast. Further functional characterization of PaMsrB1 requires the production of a biologically active purified recombinant protein...
January 23, 2018: Protein Expression and Purification
Josephine Elia, Grace Ungal, Charlly Kao, Alexander Ambrosini, Nilsa De Jesus-Rosario, Lene Larsen, Rosetta Chiavacci, Tiancheng Wang, Christine Kurian, Kanani Titchen, Brian Sykes, Sharon Hwang, Bhumi Kumar, Jacqueline Potts, Joshua Davis, Jeffrey Malatack, Emma Slattery, Ganesh Moorthy, Athena Zuppa, Andrew Weller, Enda Byrne, Yun R Li, Walter K Kraft, Hakon Hakonarson
The glutamatergic neurotransmitter system may play an important role in attention-deficit hyperactivity disorder (ADHD). This 5-week, open-label, single-blind, placebo-controlled study reports the safety, pharmacokinetics and responsiveness of the metabotropic glutamate receptor (mGluR) activator fasoracetam (NFC-1), in 30 adolescents, age 12-17 years with ADHD, harboring mutations in mGluR network genes. Mutation status was double-blinded. A single-dose pharmacokinetic profiling from 50-800 mg was followed by a single-blind placebo at week 1 and subsequent symptom-driven dose advancement up to 400 mg BID for 4 weeks...
January 16, 2018: Nature Communications
Sepideh Shahbazi, Azam Bolhassani, Arash Arashkia, Esmaeil Sadroddiny
Immunotherapies targeting the human papillomavirus (HPV) oncogenic proteins, E6 and E7, are effective to treat HPV-associated cervical malignancies. In this study, two types of the fusion E7-GFP proteins (i.e., with or without linker) were expressed in different E. coli strains. Then, the efficiency of GFP and E7-GFP transfection was compared with FITC-antibody protein control using TurboFect reagent in the HEK-293T cell line. Our data indicated that both E7-GFP fusion proteins were efficiently produced in M15 E...
January 15, 2018: Protein and Peptide Letters
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