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Zeliha Guler, 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...
November 22, 2016: Biopolymers
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...
November 17, 2016: Biopolymers
Jason L Heier, Dorian J Mikolajczak, Christoph Böttcher, Beate Koksch
No abstract text is available yet for this article.
November 16, 2016: Biopolymers
Pradeep Pant, Saher Afshan Shaikh, B Jayaram
Asymmetry (5'&cenveo_unknown_entity_wingdings_F0E0;3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential to 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...
November 9, 2016: Biopolymers
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...
November 4, 2016: Biopolymers
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...
October 7, 2016: Biopolymers
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. Firstly, 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...
October 7, 2016: Biopolymers
George Kubas, William Rees, Jonathan Caguiat, David Asch, Diana Fagan, Pedro Cortes
The present research investigates the identification of amino acid sequences that selectively bind to a pentaerythritol tetranitrate (PETN) explosive surrogate. Through the use of a phage display technique and enzyme-linked immunosorbent assays (ELISA), a peptide library was tested against PETNH (pentaerythritol trinitrate hemisuccinate), a surrogate of PETN, in order to screen for those with amino acids having affinity toward the explosive. The use of the PETN surrogate allowed the immobilization of the target during the screening process, while retaining a chemical profile similar to that of PETN...
October 6, 2016: Biopolymers
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...
October 5, 2016: Biopolymers
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)...
October 4, 2016: Biopolymers
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...
October 1, 2016: Biopolymers
Xun Sun, Meng-Dan Qian, Shan-Shan Guan, Ya-Ming Shan, Ying Dong, Hao Zhang, Song Wang, 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...
October 1, 2016: Biopolymers
Annada Rajbhandary, Bradley L Nilsson
Low molecular weight agents that undergo self-assembly into fibril networks with hydrogel properties are promising biomaterials. Most low molecular weight hydrogelators are discovered empirically or serendipitously due to imperfect understanding of the mechanisms of self-assembly, the packing structure of self-assembled materials, and how the self-assembly process corresponds to emergent hydrogelation. Herein, the mechanisms of self-assembly and hydrogelation of N-fluorenylmethoxycarbonyl diphenylalanine (Fmoc-PhePhe), a well-studied low molecular weight hydrogelator, is probed by systematic comparison with derivatives in which Phe residues are replaced by corresponding N-benzyl glycine peptoid (Nphe) analogs...
October 1, 2016: Biopolymers
Anne Bäcker, Olga Erhardt, Lukas Wietbrock, Natalia Schel, Bettina Göppert, Paul Abaffy, Thomas Sollich, Angelica Cecilia, Friederike J Gruhl
In the present work, different biopolymer blend scaffolds based on the silk protein fibroin from Bombyx mori (BM) were prepared via freeze-drying method. The chemical, structural and mechanical properties of the three dimensional (3D) porous silk fibroin (SF) composite scaffolds of gelatin, collagen and chitosan as well as SF from Antheraea pernyi (AP) and the recombinant spider silk protein spidroin (SSP1) have been systematically investigated, followed by cell culture experiments with epithelial prostate cancer cells (LNCaP) up to 14 days...
October 1, 2016: Biopolymers
D Reichert, S Gröger, C Hackel
To gain new insights into the interaction of proteins and disaccharides, we investigated the hydrodynamic radii, Rh(Prot) , of lysozyme molecules in solution and in a ternary protein-sugar-water system by PFG-NMR. Our approach is based on the assumption that the anhydrobiotic properties of disaccharides like trehalose are based on aggregation of sugar molecules to the proteins, i.e. accumulation of sugar molecules close to the protein, and that this process can be investigated by the experimentally detectable Rh(Prot) value of the protein...
September 28, 2016: Biopolymers
Magdalena Filipowicz, Natalia Ptaszyńska, Katarzyna Olkiewicz, Dawid Dębowski, Kamila Ćwikłowska, Timo Burster, Michał Pikuła, Adam Krzystyniak, Anna Łęgowska, Krzysztof Rolka
A series of analogues of trypsin inhibitor SFTI-1 were designed and synthesized to monitor peptide splicing. In the middle part of the SFTI-1 analogues, which is released upon incubation with proteinase, the RGD sequence or an acceptor of fluorescence for FRET was introduced. The results of studies with trypsin confirmed that the designed analogues underwent peptide splicing. Furthermore, we showed that a FRET displaying SFTI-1 analogue was internalized into the HaCaT keratinocytes, where it was degraded. Therefore, both proteolysis and the reduction of the disulfide bridge of the peptide took place...
September 14, 2016: Biopolymers
Marco Bortolus, Annalisa Dalzini, Anna Lisa Maniero, Giacomo Panighel, Alvaro Siano, Claudio Toniolo, Marta De Zotti, Fernando Formaggio
Trichogin GA IV is a short-length (10-amino acid long), mostly hydrophobic peptaibiotic with an N-terminal fatty acyl chain and a C-terminal 1,2-amino alcohol. A cardinal role of the terminal moieties in the cytotoxic activity of trichogin has been recently found. Previously, peptide orientation and dynamics of trichogin analogs in the membrane were studied using methyl ester derivatives. Therefore, in the present work we synthesized several trichogin analogs with naturally occurring terminal groups to verify whether these moieties have any effect on peptide-membrane interaction...
September 13, 2016: Biopolymers
Gerald S Manning
The dynamic process underlying muscle contraction is the parallel sliding of thin actin filaments along an immobile thick myosin fiber powered by oar-like movements of protruding myosin cross bridges (myosin heads). The free energy for functioning of the myosin nanomotor comes from the hydrolysis of ATP bound to the myosin heads. The unit step of translational movement is based on a mechanical-chemical cycle involving ATP binding to myosin, hydrolysis of the bound ATP with ultimate release of the hydrolysis products, stress-generating conformational changes in the myosin cross bridge, and relief of built-up stress in the myosin power stroke...
December 2016: Biopolymers
Kenneth A Rubinson, Yin Chen, Brady F Cress, Fuming Zhang, Robert J Linhardt
Heparin is a linear, anionic polysaccharide that is widely used as a clinical anticoagulant. Despite its discovery 100 years ago in 1916, the solution structure of heparin remains unknown. The solution shape of heparin has not previously been examined in water under a range of concentrations, and here is done so in D2 O solution using small-angle neutron scattering (SANS). Solutions of 10 kDa heparin-in the millimolar concentration range-were probed with SANS. Our results show that when sodium concentrations are equivalent to the polyelectrolyte's charge or up to a few hundred millimoles higher, the molecular structure of heparin is compact and the shape could be well modeled by a cylinder with a length three to four times its diameter...
December 2016: Biopolymers
Alessandro Grottesi, Simone Cecconi, Rafael Molina, Marco D'abramo
The conformational behavior of the wild-type endonucleases I-DmoI and two of its mutants has been studied in the presence and in the absence of DNA target sequences by means of extended molecular dynamics simulations. Our results show that in the absence of DNA, the three protein forms explore a similar essential conformational space, whereas when bound to the same DNA target sequence of 25 base pairs, they diversify and restrain the subspace explored. In addition, the differences in the essential subspaces explored by the residues near the catalytic site for both the bound and unbound forms are discussed in background of the experimental protein activity...
December 2016: Biopolymers
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