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Yanping Wang, Jin Li, Thomas F Kolon, Alicia Olivant Fisher, T Ernesto Figueroa, Ahmad H BaniHani, Jennifer A Hagerty, Ricardo Gonzalez, Paul H Noh, Rosetta M Chiavacci, Kisha R Harden, Debra J Abrams, Deborah Stabley, Cecilia E Kim, Katia Sol-Church, Hakon Hakonarson, Marcella Devoto, Julia Spencer Barthold
BACKGROUND: Copy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population. METHODS: Genome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1...
October 21, 2016: BMC Urology
Boris Redko, Helena Tuchinsky, Tamar Segal, Dror Tobi, Galia Luboshits, Osnat Ashur-Fabian, Albert Pinhasov, Gabi Gerlitz, Gary Gellerman
The newly discovered short (9 amino acid) non-RGD S-S bridged cyclic peptide ALOS-4 (H-cycl(Cys-Ser-Ser-Ala-Gly-Ser-Leu-Phe-Cys)-OH), which binds to integrin αvβ3 is investigated as peptide carrier for targeted drug delivery against human metastatic melanoma. ALOS4 binds specifically the αvβ3 overexpressing human metastatic melanoma WM-266-4 cell line both in vitro and in ex vivo assays. Coupling ALOS4 to the topoisomerase I inhibitor Camptothecin (ALOS4-CPT) increases the cytotoxicity of CPT against human metastatic melanoma cells while reduces dramatically the cytotoxicity against non-cancerous cells as measured by the levels of γH2A...
October 19, 2016: Oncotarget
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Obdulia Rabal, Fernando Pastor, Helena Villanueva, Mario M Soldevilla, Sandra Hervas-Stubbs, Julen Oyarzabal
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX) technologies with in silico prediction of aptamer binders has attracted a lot of interest in the recent years. We propose a workflow involving 2D structure prediction, 3D RNA modeling using Rosetta and docking to the target protein with 3dRPC for: (i) prediction of the binding mode of our two previously reported potent (Kd < 50 nmol/l) murine TIM3 aptamers, and (ii) the prioritization of TIM3 aptamers that were enriched in the SELEX workflow...
October 18, 2016: Molecular Therapy. Nucleic Acids
Ji-Hua Yu, Yang-Yang Li, Mian Xiang, Jian-Quan Zhu, Xin-He Huang, Wan-Jun Wang, Rui Tan, Jia-Yu Zhou, Hai Liao
OBJECTIVES: To clone and characterize a novel bi-functional α-amylase/subtilisin inhibitor (LASI) from the rhizome of Ligusticum chuanxiong, a traditional Chinese medicine. RESULTS: The LASI showed strong homology with members of the Kunitz trypsin inhibitor family. Its putative amino acid sequence has a 40 % identity with that of the α-amylase/subtilisin inhibitor from rice. LASI gene without signal peptide was expressed in E. coli Rosetta. After purification, the recombinant LASI protein was inhibitory against not only α-amylase from porcine pancreas, Helicoverpa armigera, Spodoptera litura and Plutella xylostella, but also subtilisin A, but not against trypsin or chymotrypsin...
October 17, 2016: Biotechnology Letters
Anderson H Lima, Alberto M Dos Santos, Cláudio Nahum Alves, Jerônimo Lameira
UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) is one of the key enzymes involved in peptidoglycan biosynthesis. The peptide HESFWYLPHQSY (called PEP 1354) is an inhibitor of MurA with an IC50 value of 200 μM. In this paper, we have used the FlexPepDock ab-initio protocol from the Rosetta program Homology Modeling and Molecular dynamics simulations to analyze, for the first time, the interaction of the PEP 1354 peptide with MurA enzyme from Pseudomonas aeruginosa (MurA-PA). Our modeling results suggest that the peptide binds to the same active site as the natural substrate UDP-N-acetylglucosamine (UNAG)...
October 13, 2016: Chemical Biology & Drug Design
Leah D McGurn, Maryam Moazami-Goudarzi, Sean A White, Tannu Suwal, Beant Brar, Jason Q Tang, George S Espie, Matthew S Kimber
CcaA is a b-carbonic anhydrase that is a component of the carboxysomes of a subset of b-cyanobacteria. This protein, which has a characteristic C-terminal extension of unknown function, is recruited to the carboxysome via interactions with CcmM, which is itself a γ-carbonic anhydrase homolog with enzymatic activity in many, but not all cyanobacteria. We have determined the structure of CcaA from Synechocystis sp. PCC 6803 at 1.45 Å. In contrast to the dimer of dimers organization of most bacterial β-carbonic anhydrases, or the loose dimer-of-dimers-of-dimers organization found in the plant enzymes, CcaA shows a well-packed trimer-of-dimers organization...
October 11, 2016: Biochemical Journal
Paolo Vinciguerra, Vito Romano, Pietro Rosetta, Emanuela F Legrottaglie, Raffaele Piscopo, Claudia Fabiani, Claudio Azzolini, Riccardo Vinciguerra
PURPOSE: To compare 1-year transepithelial corneal collagen cross-linking with iontophoresis (I-CXL) outcomes with standard CXL (S-CXL) epithelium-off for progressive keratoconus. METHODS: Forty eyes of 40 patients with progressive keratoconus were included in this comparative, prospective clinical study. Corrected distance visual acuity (CDVA), spherical equivalent, cylinder refraction, corneal topography, Scheimpflug tomography, aberrometry, and endothelial cell count were assessed at baseline and at 1, 3, 6, and 12 months of follow-up...
October 1, 2016: Journal of Refractive Surgery
Jian Ping Wang, Jun Dong, Chang Fei Duan, Hui Cai Zhang, Xin He, Geng Nan Wang, Guo Xian Zhao, Jing Liu
A recombinant anti-sarafloxacin ScFv antibody was produced by direct transformation of its gene into Rosetta-gami(DE3) for expression, and then its recognition mechanisms for 12 fluoroquinolones were studied by using molecular docking method. Based on the results of virtual mutation, the ScFv antibody was evolved by directional mutagenesis of contact amino acid residue Tyr99 to His. The ScFv mutant showed highly increased affinity for the 12 drugs with up to 7-folds improved sensitivity. Finally, the mutant was used to develop an indirect competitive enzyme linked immunosorbent assay for determination of the 12 drugs in milk...
October 10, 2016: Journal of Agricultural and Food Chemistry
Andrew A White
No abstract text is available yet for this article.
November 2016: Immunology and Allergy Clinics of North America
Elizabeth Gibney
No abstract text is available yet for this article.
September 30, 2016: Nature
Daniel Clery
No abstract text is available yet for this article.
September 30, 2016: Science
Jinchao Yu, Jessica Andreani, Françoise Ochsenbein, Raphaël Guerois
Computational protein-protein docking is of great importance for understanding protein interactions at the structural level. CAPRI (Critical Assessment of PRediction of Interactions) experiments provide the protein docking community with a unique opportunity to blindly test methods based on real-life cases and help accelerate methodology development. For CAPRI rounds 28-35, we used an automatic docking pipeline integrating the coarse-grained co-evolution-based potential InterEvScore. This score was developed to exploit the information contained in the multiple sequence alignments of binding partners and selectively recognize co-evolved interfaces...
October 4, 2016: Proteins
Caitlin A Kowalsky, Timothy A Whitehead
The comprehensive sequence determinants of cohesin to binding affinity towards type I dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2,970 and 2,778 single point mutants of C.thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with three independent experimental methods...
October 3, 2016: Proteins
Karolis Uziela, Nanjiang Shu, Björn Wallner, Arne Elofsson
Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function...
October 4, 2016: Scientific Reports
Giovanni Landoni, Antonio Pisano, Vladimir Lomivorotov, Gabriele Alvaro, Ludhmila Hajjar, Gianluca Paternoster, Caetano Nigro Neto, Nicola Latronico, Evgeny Fominskiy, Laura Pasin, Gabriele Finco, Rosetta Lobreglio, Maria Luisa Azzolini, Giuseppe Buscaglia, Alberto Castella, Marco Comis, Adele Conte, Massimiliano Conte, Francesco Corradi, Erika Dal Checco, Giovanni De Vuono, Marco Ganzaroli, Eugenio Garofalo, Gordana Gazivoda, Rosalba Lembo, Daniele Marianello, Martina Baiardo Redaelli, Fabrizio Monaco, Valentina Tarzia, Marta Mucchetti, Alessandro Belletti, Paolo Mura, Mario Musu, Giovanni Pala, Massimiliano Paltenghi, Vadim Pasyuga, Desiderio Piras, Claudio Riefolo, Agostino Roasio, Laura Ruggeri, Francesco Santini, Andrea Székely, Luigi Verniero, Antonella Vezzani, Alberto Zangrillo, Rinaldo Bellomo
OBJECTIVE: Of the 230 million patients undergoing major surgical procedures every year, more than 1 million will die within 30 days. Thus, any nonsurgical interventions that help reduce perioperative mortality might save thousands of lives. The authors have updated a previous consensus process to identify all the nonsurgical interventions, supported by randomized evidence, that may help reduce perioperative mortality. DESIGN AND SETTING: A web-based international consensus conference...
August 2, 2016: Journal of Cardiothoracic and Vascular Anesthesia
Ray Yu-Ruei Wang, Yifan Song, Benjamin A Barad, Yifan Cheng, James S Fraser, Frank DiMaio
Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models manually built in near-atomic-resolution cryo-EM maps...
September 26, 2016: ELife
Joseph D Yesselman, Rhiju Das
Noncanonical RNA motifs help define the vast complexity of RNA structure and function, and in many cases, these loops and junctions are on the order of only ten nucleotides in size. Unfortunately, despite their small size, there is no reliable method to determine the ensemble of lowest energy structures of junctions and loops at atomic accuracy. This chapter outlines straightforward protocols using a webserver for Rosetta Fragment Assembly of RNA with Full Atom Refinement (FARFAR) ( http://rosie.rosettacommons...
2016: Methods in Molecular Biology
Pierre Cole, Sebastien Weibel, Rosetta Nicastro, Roland Hasler, Alexandre Dayer, Jean-Michel Aubry, Paco Prada, Nader Perroud
BACKGROUND: Attention deficit hyperactivity disorder (ADHD) is associated with marked impairments in familial, social, and professional functioning. Although stimulant treatments can be effective in adult ADHD, some patients will respond poorly or not at all to medication. Previous studies demonstrated that cognitive behavioural therapy- (CBT) and dialectical behavior therapy- (DBT) oriented interventions are effective in reducing the burden of the disease, which is mainly marked by depression, interpersonal difficulties, low self-esteem, and low quality of life...
September 2016: Psychiatria Danubina
Kristoffer E Johansson, Nicolai Tidemand Johansen, Signe Christensen, Scott Horowitz, James C A Bardwell, Johan G Olsen, Martin Willemoës, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg, Thomas Hamelryck, Jakob R Winther
Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria...
October 23, 2016: Journal of Molecular Biology
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