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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
Nadja Berger, Fee Li, Bert Mallick, J Thomas Brüggemann, Wolfram Sander, Christian Merten
A set of cyclic tetrapeptides of the general form cyclo(Boc-Cys-Pro-X-Cys-OMe) with X being L-/D-Ala, L-/D-Val, and L-/D-Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs - namely a β-turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β-turn conformational preferences using NMR, VCD, and Raman spectroscopy...
September 8, 2016: Biopolymers
Erik Melander, Camilla Eriksson, Britt Jansson, Ulf Göransson, Margareta Hammarlund-Udenaes
This study provides a new method for quantifying the cyclotide kalata B1 in both plasma and brain homogenate. Cyclotides are ultra-stable peptides with three disulfide bonds that are interesting from a drug development perspective as they can be used as scaffolds. In this study we describe a new validated LC-MS/MS method with high sensitivity and specificity for kalata B1. The limit of quantification was 2 ng/mL in plasma and 5 ng/gmL in brain homogenate. The method was linear in the range 2 - 10 000 ng/mL for plasma and 5 - 2000 ng/g for brain...
September 7, 2016: Biopolymers
Chikara Fujimori, Jun Kumai, Kyotaro Nakamura, Yingzi Gu, Fumihiko Katagiri, Kentaro Hozumi, Yamato Kikkawa, Motoyoshi Nomizu
Peptide-conjugated polysaccharide matrices using bioactive laminin-derived peptides are useful biomaterials for tissue and cell engineering. Here, we demonstrate an easy handling preparation method for peptide-polysaccharide matrices using polyion complex with both alginate and chitosan. First, aldehyde-alginate was synthesized by oxidization of alginate using NaIO4 , and then, reacted with Cys-peptides. Next, the peptide-alginate solution was added to a chitosan-coated plate, and the peptide-polyion complex matrices (peptide-PCMs) were prepared...
September 7, 2016: Biopolymers
Nitin D Bansode, B Madhanagopal, Mahesh V Sonar, Krishna N Ganesh
It is shown that C4(S)-NH2 /OH/NHCHO-prolyl polypeptides exhibit PPII conformation in aqueous medium, but in a relatively hydrophobic solvent trifluoroethanol (TFE) transform into an unusual β-structure. The stereospecific directing effect of H-bonding in defining the specific structure is demonstrated by the absence of β-structure in the corresponding C4(S)-guanidinyl/(NH/O)-acetyl derivatives and retention of β-structure in C4(S)-(NHCHO)-prolyl polypeptides in TFE. The distinct conformations are identified by the characteristic CD patterns and supported by Raman spectroscopic data...
September 6, 2016: Biopolymers
Aparna Yerra, Danti Kumari Mysarla, Prasanthi Siripurapu, Anjali Jha, Satyavathi V Valluri, Anitha Mamillapalli
Silkworm, Bombyx mori belongs to the Lepidoptera family. The silk produced from this insect, mulberry silk, gained lot of importance as a fabric. Silk is being exploited as a biomaterial due to its surprising strength and biocompatibility. Polyamines are important cell growth regulators. In the present work the effect of treatment of polyamines, putrescine, spermidine and spermine on the quantity and quality of silk produced was assessed. Results showed that exogenous feeding of spermidine at a concentration of 50 µm increased fiber length significantly...
September 4, 2016: Biopolymers
Ghasem Bahlakeh, Mohammad Mahdi Hasani-Sadrabadi, Karl I Jacob
Chitosan biopolymer has been extensively applied in direct methanol fuel cells (DMFCs) as a potential replacement to conventional Nafion membrane for its considerably reduced methanol crossover. Here, we computationally explored the influences of methanol concentration, temperature and pH parameters upon the nanostructure and dynamics, particularly the methanol crossover, in chitosan proton-exchange membrane (PEM) through molecular dynamics simulations. Theoretical results demonstrated the increased swelling and radius of gyration of chitosan chains at higher concentrations...
September 2, 2016: Biopolymers
Ankita Malik, Mothukuri Ganesh Kumar, Anuapm Bandyopadhyay, Hosahudya N Gopi
β-Hydroxy-γ-amino acids (Statines) are a class of naturally occurring non-ribosomal amino acids frequently found in many peptide natural products. Peptidomimetics constituted with statines have been used as inhibitors for various aspartic acid proteases. In contrast to the synthetic γ-amino acids, very little is known about the folding behavior of these naturally occurring β-hydroxy γ-amino acids. To understand the folding behavior of statines, three α,γ-hybrid peptides P1 (Boc-Aib-γPhe-Aib-(R, S)Phesta-Aib-γPhe-Aib-CONH2 ), P2 (Boc-Aib-γPhe-Aib-(S, S)Phesta-Aib-γPhe-Aib-CONH2 ) and P3 (Boc-Aib-γPhe-Aib-(S, S)Phesta-Aib-(S, S)Phesta-Aib-CONH2 ) were synthesized on solid phase and their helical conformations in single crystals were studied...
August 26, 2016: Biopolymers
Norelle L Daly, Sunithi Gunasekera, Richard J Clark, Feng Lin, John D Wade, Marilyn A Anderson, David J Craik
Cyclotides are plant-derived, gene-encoded, circular peptides with a range of host-defense functions, including insecticidal activity. They also have potential as pharmaceutical scaffolds and understanding their biosynthesis is important to facilitate their large-scale production. Insights into the biosynthesis of cyclotides are emerging but there are still open questions, particularly regarding the influence of the structure of the precursor proteins on processing/biosynthetic pathways. The precursor protein of kalata B1, encoded by the plant Oldenlandia affinis, contains N- and C-terminal propeptides that flank the mature cyclotide domain...
August 26, 2016: Biopolymers
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