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Biopolymers

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https://www.readbyqxmd.com/read/28422272/modeling-interactions-between-a-%C3%AE-o-4-type-lignin-model-compound-and-1-allyl-3-methylimidazolium-chloride-ionic-liquid
#1
Youtao Zhu, Jing Yan, Chengbu Liu, Zhang Dongju
Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium-based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol-β-guaiacyl ether (VG) with 1-allyl-3-methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π-π stacking and intermolecular hydrogen bonding interactions...
April 19, 2017: Biopolymers
https://www.readbyqxmd.com/read/28406522/inhibition-of-polyglutamine-aggregation-by-similar-huntingtin-n-terminal-sequences-prospective-molecules-for-preclinical-evaluation-in-huntington-s-disease
#2
Gunasekhar Burra, Ashwani Kumar Thakur
The mutant huntingtin protein (mHtt) fragments with expanded polyglutamine sequence forms microscopically visible aggregates in neurons, a hallmark of Huntington's disease (HD). The aggregation process and aggregates are possible targets of therapeutic intervention in HD. Due to lack of treatment and cure, the patients die within 15-20 years after the disease onset. Therefore, discovering therapeutic molecules that may either inhibit the aggregation mechanism or downregulate the toxic effects of mhtt are highly needed...
April 12, 2017: Biopolymers
https://www.readbyqxmd.com/read/28387920/hydrophobic-hydrophilic-forces-in-protein-folding
#3
Stewart R Durell, Arieh Ben-Naim
The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (Direct forces), as well as from interactions with the solvent (Solvent-Induced forces). We present a statistical-mechanical formalism that describes both these Direct and indirect, Solvent-Induced thermodynamic forces on groups of the protein. We focus on two kinds of protein groups, commonly referred to as hydrophobic and hydrophilic...
April 7, 2017: Biopolymers
https://www.readbyqxmd.com/read/28369686/on-demand-tuned-hazard-free-elastomeric-composites-a-green-approach
#4
Partheban Manoharan, Narayan Chandra Das, Kinsuk Naskar
Rising ecological concerns and depletion of the potentially harmful environmental impacts caused by rubber products, are of prime importance in the industry. Therefore, implementation of sustainable greener materials is required to minimize the detrimental influences. In this research, we investigated the beneficial influence of naturally derived bio-resin towards the effects of association with Zinc Oxide Nanoparticles in highly dispersible silica (HDS) reinforced Natural rubber (NR)/Epoxidized Natural Rubber (ENR) based composites...
March 31, 2017: Biopolymers
https://www.readbyqxmd.com/read/28295161/magnesium-and-molecular-crowding-of-the-cosolutes-stabilize-the-i-motif-structure-at-physiological-ph
#5
Sarika Saxena, Savita Joshi, J Shankaraswamy, Shikhar Tyagi, Shrikant Kukreti
Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In the present study, we used three C-rich oligonucleotides (11Py, 21Py and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis...
March 14, 2017: Biopolymers
https://www.readbyqxmd.com/read/28224610/structural-changes-in-cartilage-and-collagen-studied-by-high-temperature-raman-spectroscopy
#6
Mark Fields, Nicholas Spencer, Jayesh Dudhia, Paul F McMillan
Understanding the high temperature behavior of collagen and collagenous tissue is important for surgical procedures and biomaterials processing for the food, pharmaceutical, and cosmetics industries. One primary event for proteins is thermal denaturation that involves unfolding the polypeptide chains while maintaining the primary structure intact. Collagen in the extracellular matrix of cartilage and other connective tissue is a hierarchical material containing bundles of triple-helical fibers associated with water and proteoglycan components...
June 2017: Biopolymers
https://www.readbyqxmd.com/read/28142189/mesoscopic-structure-of-pectin-in-solution
#7
K Alba, R J Bingham, V Kontogiorgos
Mesoscopic structure of pectin with different molecular characteristics was investigated by means of small angle X-ray scattering (SAXS), electrokinetic measurements and data modelling. The influence of a broad range of pH (2-7) on chain conformation in the dilute and semi-diluted regime was investigated. Scattering data and concomitant analysis revealed two length scales at all environmental conditions studied. pH showed greater influence at acidic values (pH 2.0) enhancing the globular component of the structure due to association of galacturonic acid residues...
June 2017: Biopolymers
https://www.readbyqxmd.com/read/28124375/dna-interaction-with-dapi-fluorescent-dye-force-spectroscopy-decouples-two-different-binding-modes
#8
L A Reis, M S Rocha
In this work, we use force spectroscopy to investigate the interaction between the DAPI fluorescent dye and the λ-DNA molecule under high (174 mM) and low (34 mM) ionic strengths. Firstly, we have measured the changes on the mechanical properties (persistence and contour lengths) of the DNA-DAPI complexes as a function of the dye concentration in the sample. Then, we use recently developed models in order to connect the behavior of both mechanical properties to the physical chemistry of the interaction. Such analysis has allowed us to identify and to decouple two main binding modes, determining the relevant physicochemical (binding) parameters for each of these modes: minor groove binding, which saturates at very low DAPI concentrations ( CT ∼ 0...
May 2017: Biopolymers
https://www.readbyqxmd.com/read/28035667/acceleration-of-protein-backbone-nmr-assignment-by-combinatorial-labeling-application-to-a-small-molecule-binding-study
#9
Christopher Hein, Frank Löhr, Daniel Schwarz, Volker Dötsch
Selective labeling with stable isotopes has long been recognized as a valuable tool in protein NMR to alleviate signal overlap and sensitivity limitations. In this study, combinatorial (15) N-, (13) C(α) -, and (13) C'-selective labeling has been used during the backbone assignment of human cyclophilin D to explore binding of an inhibitor molecule. Using a cell-free expression system, a scheme that involves (15) N, 1-(13) C, 2-(13) C, fully (15) N/(13) C, and unlabeled amino acids was optimized to gain a maximum of assignment information from three samples...
May 2017: Biopolymers
https://www.readbyqxmd.com/read/27997981/single-nucleotide-polymorphisms-and-domain-splice-variants-modulate-assembly-and-elastomeric-properties-of-human-elastin-implications-for-tissue-specificity-and-durability-of-elastic-tissue
#10
Ming Miao, Sean E Reichheld, Lisa D Muiznieks, Eva E Sitarz, Simon Sharpe, Fred W Keeley
Polymeric elastin provides the physiologically essential properties of extensibility and elastic recoil to large arteries, heart valves, lungs, skin and other tissues. Although the detailed relationship between sequence, structure and mechanical properties of elastin remains a matter of investigation, data from both the full-length monomer, tropoelastin, and smaller elastin-like polypeptides have demonstrated that variations in protein sequence can affect both polymeric assembly and tensile mechanical properties...
May 2017: Biopolymers
https://www.readbyqxmd.com/read/27875623/biophysical-characterization-of-quaternary-pyridinium-functionalized-polynorbornenes-for-dna-complexation-and-their-cellular-interactions
#11
Zeliha Guler Gokce, Semra Zuhal Birol, Tarık Eren, Sebnem Ercelen Ceylan
Cationic polymers with hydrophobic side chains have gained great interest as DNA carriers since they form a compact complex with negatively charged DNA phosphate groups and interact with the cell membrane. Amphiphilic polyoxanorbornenes with different quaternary alkyl pyridinium side chains with ethyl-p(OPy2) and hexyl units-p(OPy6) bearing 10 kDa MWT were synthesized by living Ring-Opening Metathesis Polymerization method. The physicochemical characteristics: critical micellar concentration, size distribution, surface charge, and condensation of polymer/DNA complex were investigated...
April 2017: Biopolymers
https://www.readbyqxmd.com/read/27861723/design-and-characterization-of-symmetric-nucleic-acids-via-molecular-dynamics-simulations
#12
Pradeep Pant, Saher Afshan Shaikh, B Jayaram
Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids...
April 2017: Biopolymers
https://www.readbyqxmd.com/read/27858985/analysis-of-ribosomal-inter-subunit-sites-as-targets-for-complementary-oligonucleotides
#13
Sapna G Thoduka, Paul A Zaleski, Zofia Dąbrowska, Marcin Równicki, Joanna Stróżecka, Anna Górska, Mikołaj Olejniczak, Joanna Trylska
The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Based on these properties we selected rRNA targets for hybridization with complementary 2'-O-methyl oligoribonucleotides (2'-OMe RNAs). Further, the inhibition efficiencies of the designed ribosome-interfering 2'-OMe RNAs were tested using a β-galactosidase assay in a translation system based on the E...
April 2017: Biopolymers
https://www.readbyqxmd.com/read/27813083/dbpa-is-a-region-specific-rna-helicase
#14
Anthony F T Moore, Riley C Gentry, Eda Koculi
DbpA is a DEAD-box RNA helicase implicated in RNA structural rearrangements in the peptidyl transferase center. DbpA contains an RNA binding domain, responsible for tight binding of DbpA to hairpin 92 of 23S ribosomal RNA, and a RecA-like catalytic core responsible for double-helix unwinding. It is not known if DbpA unwinds only the RNA helices that are part of a specific RNA structure, or if DbpA unwinds any RNA helices within the catalytic core's grasp. In other words, it is not known if DbpA is a site-specific enzyme or region-specific enzyme...
March 2017: Biopolymers
https://www.readbyqxmd.com/read/27718227/a-parallel-stranded-g-quadruplex-composed-of-threose-nucleic-acid-tna
#15
Jen-Yu Liao, Irina Anosova, Saikat Bala, Wade D Van Horn, John C Chaput
G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na(+) ) and potassium (K(+) ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-l-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif...
March 2017: Biopolymers
https://www.readbyqxmd.com/read/27718222/dna-doxorubicin-interaction-new-insights-and-peculiarities
#16
E F Silva, R F Bazoni, E B Ramos, M S Rocha
We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions...
March 2017: Biopolymers
https://www.readbyqxmd.com/read/27701729/optimization-of-a-%C3%AE-sheet-cap-for-long-loop-closure
#17
Jordan M Anderson, Alexander A Shcherbakov, Brandon L Kier, Jackson Kellock, Irene Shu, Aimee L Byrne, Lisa A Eidenschink, Niels H Andersen
Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable β-sheet structures, including features that allow us to probe these questions. Using paired Trp residues that form aromatic clusters on folding, we are able to stabilize two β-strands connected by varying loop lengths and composition (an example sequence: RWITVTI - loop - KKIRVWE)...
March 2017: Biopolymers
https://www.readbyqxmd.com/read/27706801/collision-induced-thermochemistry-of-reactions-of-dissociation-of-glycyl-homopeptides-an-experimental-and-theoretical-analysis
#18
Bojidarka Ivanova, Michael Spiteller
The research draws on experimental and theoretical data about energetics and kinetics of mass spectrometric (MS) reactions of glycyl homopenta- (G5) and glycyl homohexapeptides (G6). It shows the great applicability of the methods of quantum chemistry to predict MS profile of peptides using energetics of collision induced dissociation (CID) fragment species. Mass spectrometry is among irreplaceable methods, providing unambiguous qualitative, quantitative and structural information about analytes, applicable to many scientific areas like environmental chemistry; food chemistry; medicinal chemistry; and more...
February 2017: Biopolymers
https://www.readbyqxmd.com/read/27696370/nano-mechanical-characterization-of-disassembling-amyloid-fibrils-using-the-peak-force-qnm-method
#19
Wenpin Wang, Zongxia Guo, Jing Sun, Zhibo Li
The comprehensive understanding of disassembly mechanism of amyloid fibrils requires nano-scale characterization of the mechanical properties of amyloid fibrils during the disassembly process. In this work, gemini surfactant C12 C6 C12 Br2 micelles were used as a probe to disassemble Aβ(1-40) fibrils. The microstructure evolution and nano-mechanical properties of Aβ(1-40) fibrils during the disassembly process were systematically investigated by the Peak Force Quantitative Nano-mechanical (PF-QNM) technique...
February 2017: Biopolymers
https://www.readbyqxmd.com/read/27696356/investigation-of-an-alternate-water-supply-system-in-enzymatic-hydrolysis-in-the-processive-endocellulase-cel7a-from-rasamsonia-emersonii-by-molecular-dynamics-simulation
#20
Xun Sun, Meng-Dan Qian, Shan-Shan Guan, Ya-Ming Shan, Ying Dong, Hao Zhang, Song Wang, Wei-Wei Han
Cel7A from Rasamsonia emersonii is one of the processive endocellulases classified under family 7 glycoside hydrolase. Molecular dynamics simulations were carried out to obtain the optimized sliding and hydrolyzing conformations, in which the reducing ends of sugar chains are located on different sites. Hydrogen bonds are investigated to clarify the interactions between protein and substrate in either conformation. Nine hydrogen bonding interactions are identified in the sliding conformation, and six similar interactions are also found correspondingly in the hydrolyzing conformation...
February 2017: Biopolymers
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