U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

PubAg

Main content area

You searched for: Publication Year 2017 Remove constraint Publication Year: 2017 Subject term protein binding Remove constraint Subject term: protein binding
Start Over

Search

68  Search Results

« Previous | 1 - 20 of 68 |
Number of results to display per page

Search Results

1. 50th Anniversary Perspective: Polymer Brushes: Novel Surfaces for Future Materials

Author:
Chen Wei-Liang; Cordero Roselynn; Tran Hai; Ober Christopher K.
Source:
Macromolecules 2017 v.50 no.11 pp. 4089-4113
ISSN:
1520-5835
Subject:
bioadhesion; biosensors; polymerization; polymers; protein binding; theoretical models
Abstract:
... Polymer brushes have become a significant focus of polymer research with the need for straightforward and versatile surface modification. With the development of controlled radical polymerization from surfaces, new theoretical models, and sophisticated characterization tools, the resulting ability to control brush density and brush thickness gives unparalleled control over surface properties and f ...
DOI:
10.1021/acs.macromol.7b00450

2. ARID1A represses hepatocellular carcinoma cell proliferation and migration through lncRNA MVIH

Author:
Sheng Cheng; Lan Wang; Chuan-Huai Deng; Shi-Chun Du; Ze-Guang Han
Source:
Biochemical and biophysical research communications 2017 pp. -
ISSN:
0006-291X
Subject:
cell proliferation; disease course; hepatoma; mutation; neoplasm cells; non-coding RNA; nucleotides; protein binding
Abstract:
... ARID1A, encoding the BAF250a subunit of SWI/SNF complex, has a high mutation frequency in numerous types of cancer. LncRNAs, a type of non-coding RNAs longer than 200 nucleotides, have been reported to interplay with SWI/SNF complex during cancer progression. However, whether the interaction between ARID1A and lncRNA affects hepatocellular carcinoma (HCC) still needs to be investigated. Here, we r ...
DOI:
10.1016/j.bbrc.2017.07.072

3. BEESEM: estimation of binding energy models using HT-SELEX data

Author:
Shuxiang Ruan; S. Joshua Swamidass; Gary D. Stormo
Source:
Bioinformatics 2017 v.33 no.15 pp. 2288-2295
ISSN:
1460-2059
Subject:
algorithms; bioinformatics; confidence interval; energy; gene expression regulation; graphs; microarray technology; models; protein binding; risk; systematic evolution of ligands by exponential enrichment; transcription factors
Abstract:
... Motivation: Characterizing the binding specificities of transcription factors (TFs) is crucial to the study of gene expression regulation. Recently developed high-throughput experimental methods, including protein binding microarrays (PBM) and high-throughput SELEX (HT-SELEX), have enabled rapid measurements of the specificities for hundreds of TFs. However, few studies have developed efficient al ...
DOI:
10.1093/bioinformatics/btx191
PubMed:
28379348
PubMed Central:
PMC5860122

4. Chlorinated Polyfluoroalkyl Ether Sulfonic Acids in Matched Maternal, Cord, and Placenta Samples: A Study of Transplacental Transfer

Author:
Chen Fangfang; Yin Shanshan; Kelly Barry C.; Liu Weiping
Source:
Environmental Science & Technology 2017 v.51 no.11 pp. 6387-6394
ISSN:
1520-5851
Subject:
protein binding; blood serum; humans; blood proteins; placenta; quantitative analysis; women; umbilical cord; surveys; hydrophobicity; maternal exposure; sulfonic acids; binding capacity; perfluorooctane sulfonic acid; China
Abstract:
... Currently, information regarding concentrations of chlorinated polyfluoroalkyl ether sulfonic acids (Cl-PFESAs) in human placenta does not exist. The main objective of this study was to assess the occurrence and distribution of two Cl-PFESAs, 6:2 Cl-PFESA and 8:2 Cl-PFESA, in maternal serum, umbilical cord serum, and placenta to better assess the transport pathways related to human prenatal exposu ...
DOI:
10.1021/acs.est.6b06049

5. Controllable activation of nanoscale dynamics in a disordered protein alters binding kinetics

Author:
David J.E. Callaway; Tsutomu Matsui; Thomas Weiss; Laura R. Stingaciu; Christopher B. Stanley; William T. Heller; Zimei Bu
Source:
Journal of Molecular Biology 2017 pp. -
ISSN:
0022-2836
Subject:
amino acid sequences; electrostatic interactions; hydrophobicity; mutants; phosphorylation; protein binding; salt concentration; scaffolding proteins; signal transduction; spectroscopy; yields
Abstract:
... Phosphorylation of S339/S340 in the disordered tail of the multi-domain scaffolding protein NHERF1 affects the intracellular localization and trafficking of NHERF1 assembled signaling complexes. Using neutron spin echo spectroscopy (NSE), we show salt concentration dependent excitation of nanoscale motion at the tip of the C-terminal tail in the phosphomimic S339D/S340D mutant. The “tip of the whi ...
DOI:
10.1016/j.jmb.2017.03.003
PubMed:
28285124
PubMed Central:
PMC5399307

6. Covalent immobilization of Candida antarctica lipase on core-shell magnetic nanoparticles for production of biodiesel from waste cooking oil

Author:
Mohammad Reza Mehrasbi; Javad Mohammadi; Mazyar Peyda; Mehdi Mohammadi
Source:
Renewable energy 2017 v.101 pp. 593-602
ISSN:
0960-1481
Subject:
Pseudozyma antarctica; X-ray diffraction; adsorbents; biodiesel; carboxylic ester hydrolases; chemical bonding; coatings; cooking fats and oils; fuel production; iron oxides; methanol; nanoparticles; protein binding; scanning electron microscopy; silica; thermal stability; transesterification; transmission electron microscopy; wastes
Abstract:
... In the present work, lipase from Candida antarctica (CALB) was covalently immobilized on functionalized magnetic nanoparticles (MNPs) to catalyze biodiesel synthesis. Core-shell nanoparticles were synthesized by coating Fe3O4 core with silica shell (Fe3O4@SiO2). The nanoparticles functionalized with (3-glycidoxypropyl)trimethoxylsilane (GPTMS) were used as immobilization matrix. The protein bindin ...
DOI:
10.1016/j.renene.2016.09.022

7. A DEAD-Box Helicase Mediates an RNA Structural Transition in the HIV-1 Rev Response Element

Author:
John A. Hammond; Rajan Lamichhane; David P. Millar; James R. Williamson
Source:
Journal of Molecular Biology 2017 pp. -
ISSN:
0022-2836
Subject:
DEAD-box RNA helicases; Human immunodeficiency virus 1; dissociation; messenger RNA; models; molecular chaperones; oligomerization; physiological transport; protein binding; virion
Abstract:
... Nuclear export of partially spliced or unspliced HIV-1 RNA transcripts requires binding of the viral protein regulator of expression of virion (Rev) to the Rev response element (RRE) and subsequent oligomerization in a cooperative manner. Cellular DEAD-box helicase DEAD-box protein 1 (DDX1) plays a role in HIV replication, interacting with and affecting Rev-containing HIV transcripts in vivo, inte ...
DOI:
10.1016/j.jmb.2017.01.018
PubMed:
28153748
PubMed Central:
PMC5510989

8. DeepSite: protein-binding site predictor using 3D-convolutional neural networks

Author:
J. Jiménez; S. Doerr; G. Martínez-Rosell; A. S. Rose; G. De Fabritiis
Source:
Bioinformatics 2017 v.33 no.19 pp. 3036-3042
ISSN:
1460-2059
Subject:
algorithms; artificial intelligence; binding sites; bioinformatics; databases; drug design; drugs; geometry; neural networks; prediction; protein binding; proteins
Abstract:
... An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Here we present a novel knowledge-based approach that uses state-of-the-art ...
DOI:
10.1093/bioinformatics/btx350

9. ESI-IM-MS and Collision-Induced Unfolding That Provide Insight into the Linkage-Dependent Interfacial Interactions of Covalently Linked Diubiquitin

Author:
Wagner Nicole D.; Clemmer David E.; Russell David H.
Source:
Analytical chemistry 2017 v.89 no.18 pp. 10094-10103
ISSN:
1520-6882
Subject:
electrostatic interactions; gases; hydrophobic bonding; hydrophobicity; ionization; ions; post-translational modification; protein binding; protein unfolding; spectroscopy
Abstract:
... Understanding protein higher order structure and interfacial interactions is crucial to understanding protein binding motifs and cellular function, that is, an interactome. Polyubiquitylation is a post-translational modification that functions as a tag for a diverse array of cellular processes, wherein differences in chain length, branching, and linkage site encode different cellular functions. In ...
DOI:
10.1021/acs.analchem.7b02932

10. Effect of sample temperature, pH, and matrix on the percentage protein binding of protein-bound uraemic toxins

Author:
Olivier Deltombe; Annemieke Dhondt; Wim Van Biesen; Griet Glorieux; Sunny Eloot
Source:
Analytical methods 2017 v.9 no.12 pp. 1935-1940
ISSN:
1759-9679
Subject:
ambient temperature; blood serum; dialysis; fluorescence; hemodialysis; high performance liquid chromatography; hippuric acid; indole acetic acid; pH; patients; protein binding; sulfates; toxins; ultrafiltration
Abstract:
... While studying and trying to optimise dialysis clearances of protein-bound uraemic toxins (PBUTs), the percentage protein binding (% PB) may be an important parameter and can be calculated from measured free and total concentrations. Since different parameters may alter this % PB, we investigated whether the ultrafiltration temperature, sample pH, and sample matrix (i.e. serum or plasma) affects t ...
DOI:
10.1039/c7ay00054e

11. Exploring binding characteristics and the related competition of different protein-bound uremic toxins

Author:
Olivier Deltombe; Henriette de Loor; Griet Glorieux; Annemieke Dhondt; Wim Van Biesen; Björn Meijers; Sunny Eloot
Source:
Biochimie 2017 v.139 pp. 20-26
ISSN:
0300-9084
Subject:
albumins; binding capacity; blood serum; dialysis; hemodialysis; hippuric acid; indole acetic acid; patients; post-translational modification; protein binding; spectrometers; sulfates; toxins; ultra-performance liquid chromatography; uremia
Abstract:
... Little is known about potential differences in binding characteristics of protein-bound uremic toxins (PBUTs) in patients with chronic kidney disease (CKD) versus healthy controls. The question arises whether eventual differences are attributed to (i) the elevated levels of competing uremic toxins, and/or (ii) post-translational modifications of albumin.We evaluated the binding characteristics of ...
DOI:
10.1016/j.biochi.2017.05.010

12. Exploring the interaction of silver nanoparticles with lysozyme: Binding behaviors and kinetics

Author:
Gongke Wang; Huimin Hou; Shuangli Wang; Changling Yan; Yufang Liu
Source:
Colloids and surfaces 2017 v.157 pp. 138-145
ISSN:
0927-7765
Subject:
adsorption; circular dichroism spectroscopy; colloids; fluorescence; fluorescence emission spectroscopy; hydrophobic bonding; hysteresis; lysozyme; nanoparticles; nanosilver; protein binding; proteins; reaction kinetics; spectral analysis; thermodynamics; ultraviolet-visible spectroscopy
Abstract:
... The role of nanoparticle interaction with biomolecules to form a biocorona is the key to nanoparticle behavior and its consequences in the physiological environment. Since the adsorbed biocorona decides the fate of a nanomaterials in vivo, and thus a comprehensive understanding of the dynamic interactions of the proteins with the nanoparticle is imperative. Herein we investigate the interaction of ...
DOI:
10.1016/j.colsurfb.2017.05.071

13. Genome-wide identification of grain filling genes regulated by the OsSMF1 transcription factor in rice

Author:
Joung Sug Kim; Songhwa Chae; Kyong Mi Jun; Yoon-Mok Pahk; Tae-Ho Lee; Pil Joong Chung; Yeon-Ki Kim; Baek Hie Nahm
Source:
Rice 2017 v.10 no.1 pp. 16
ISSN:
1939-8425
Subject:
alpha-globulins; binding capacity; embryogenesis; filling period; gel electrophoresis; genes; leucine zipper; microarray technology; prolamins; promoter regions; protein binding; protein synthesis; rice; seed maturation; starch; transcription (genetics); transcription factors
Abstract:
... BACKGROUND: Spatial- and temporal-specific expression patterns are primarily regulated at the transcriptional level by gene promoters. Therefore, it is important to identify the binding motifs of transcription factors to better understand the networks associated with embryogenesis. RESULTS: Here, we used a protein-binding microarray (PBM) to identify the binding motifs of OsSMF1, which is a basic ...
DOI:
10.1186/s12284-017-0155-4
PubMed:
28444616
PubMed Central:
PMC5405039

14. How Fast Is Protein–Ligand Association?

Author:
Stefano Gianni; Per Jemth
Source:
Trends in biochemical sciences 2017 v.42 no.11 pp. 847-849
ISSN:
0968-0004
Subject:
cell biology; ligands; protein-protein interactions; proteins; reaction kinetics; terminology
Abstract:
... There is increasing interest in studying protein interactions and their role in cell biology using kinetics. However, there is confusion about the proper terminology in terms of the distinction between rates and rate constants. We recommend a more stringent use of the words speed, fast, slow, rate, and rate constant. ...
DOI:
10.1016/j.tibs.2017.08.007

15. Identification of repaglinide as a therapeutic drug for glioblastoma multiforme

Author:
Zui Xuan Xiao; Ruo Qiao Chen; Dian Xing Hu; Xiao Qiang Xie; Shang Bin Yu; Xiao Qian Chen
Source:
Biochemical and biophysical research communications 2017 pp. -
ISSN:
0006-291X
Subject:
antineoplastic activity; apoptosis; brain neoplasms; databases; diabetes mellitus; drugs; extracellular matrix; gene expression; genes; humans; in vitro studies; in vivo studies; longevity; mice; patients; protein binding; tissues
Abstract:
... Glioblastoma multiforme (GBM) is a highly aggressive brain tumor with a median survival time of only 14 months after treatment. It is urgent to find new therapeutic drugs that increase survival time of GBM patients. To achieve this goal, we screened differentially expressed genes between long-term and short-term survived GBM patients from Gene Expression Omnibus database and found gene expression ...
DOI:
10.1016/j.bbrc.2017.04.157

16. Impact of the biomolecular corona on the structure of PEGylated liposomes

Author:
Luca Digiacomo; Daniela Pozzi; Heinz Amenitsch; Giulio Caracciolo
Source:
Biomaterials science 2017 v.5 no.9 pp. 1884-1888
ISSN:
2047-4849
Subject:
blood; chemical bonding; gene therapy; protein binding
Abstract:
... Driven by the promises of gene therapy, PEGylated cationic liposomes (CLs) have been investigated for decades, but their use in the clinical setting is far from established. Such a dichotomy is due to several factors that have been ignored over the last two decades. The hardest challenge seems to occur when PEGylated CLs come into contact with a physiological environment (e.g. the blood). Recent e ...
DOI:
10.1039/c7bm00387k

17. Limitation of cellulose accessibility and unproductive binding of cellulases by pretreated sugarcane bagasse lignin

Author:
Germano Siqueira; Valdeir Arantes; Jack N. Saddler; André Ferraz; Adriane M. F. Milagres
Source:
Biotechnology for biofuels 2017 v.10 no.1 pp. 176
ISSN:
1754-6834
Subject:
binding capacity; catalytic activity; cell walls; cellulases; cellulose; economic sustainability; enzymatic hydrolysis; hydrolysis; lignin; protein binding; sodium hydroxide; sugarcane bagasse; sulfites
Abstract:
... BACKGROUND: The effectiveness of the enzymatic hydrolysis of cellulose in plant cell wall is strongly influenced by the access of enzymes to cellulose, which is at least in part limited by the presence of lignin. Although physicochemical treatments preceding the enzymatic catalysis significantly overcome this recalcitrance, the residual lignin can still play a role in the process. Lignin is sugges ...
DOI:
10.1186/s13068-017-0860-7
PubMed:
28702081
PubMed Central:
PMC5504807

18. Lipid droplet-associated gene expression and chromatin remodelling in LIPASE 5′-upstream region from beginning- to mid-endodormant bud in ‘Fuji’ apple

Author:
Takanori Saito; Shanshan Wang; Katsuya Ohkawa; Hitoshi Ohara; Hiromi Ikeura; Yukiharu Ogawa; Satoru Kondo
Source:
Plant molecular biology 2017 v.95 no.4-5 pp. 441-449
ISSN:
0167-4412
Subject:
Malus domestica; apples; binding sites; carboxylic ester hydrolases; chromatin; cold tolerance; esterification; fatty acids; gene expression; genes; gibberellins; histology; lipid bodies; meristems; protein binding; staining; transcription (genetics); transcription factors; trees; triacylglycerols; volatile compounds
Abstract:
... KEY MESSAGE: We found that lipid accumulation in the meristem region and the expression of MdLIP2A, which appears to be regulated by chromatin remodeling, coincided with endodormancy induction in the ‘Fuji’ apple. In deciduous trees, including apples (Malus × domestica Borkh.), lipid accumulation in the meristem region towards endodormancy induction has been thought to be an important process for ...
DOI:
10.1007/s11103-017-0662-0

19. MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Author:
Anthony O. Olarerin-George; Samie R. Jaffrey
Source:
Bioinformatics 2017 v.33 no.10 pp. 1563-1564
ISSN:
1460-2059
Subject:
bioinformatics; models; protein binding; transcriptome; transcriptomics
Abstract:
... Summary: An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites alon ...
DOI:
10.1093/bioinformatics/btx002
PubMed:
28158328
PubMed Central:
PMC5860047

20. On-line SPE sample treatment as a tool for method automatization and detection limits reduction: Quantification of 25-hydroxyvitamin D3/D2

Author:
Dimitrios Palaiogiannis; Evangelia Bekou; Kalliopi Pazaitou-Panayiotou; Victoria Samanidou; Andreas Tsakalof
Source:
Journal of chromatography 2017 v.1043 pp. 219-227
ISSN:
1570-0232
Subject:
blood serum; detection limit; humans; metabolites; patients; protein binding; ultra-performance liquid chromatography; vitamin D; vitamin status
Abstract:
... The development and approbation of new, automated UHPLC-DAD method for the quantification of 25-hydroxyvitamin D3/D2 (25OH-D3/D2) metabolites in plasma/serum for the evaluation of patient’s vitamin D status are presented. The method was developed on the Ultimate 3000 UHPLC dual gradient system supplied with the on-line SPE-concentration column coupled through six port switching valve to analytical ...
DOI:
10.1016/j.jchromb.2016.10.006