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Yanpeng Zheng, Lingwan Xu, Jingfa Yang, Xianglei Peng, He Wang, Na Yu, Ying Hua, Jiang Zhao, Jinsheng He, Tao Hong
Fluorescence-based methods are promising for measuring amyloid beta (Aβ) oligomers, given their capacity to analyse a sample at the single-molecule level. As the attachment of fluorescent labels may influence the biochemical properties of the Aβ oligomers, the effects of fluorescent labels on Aβ oligomers must be evaluated. In this paper, we compared the impacts of five different fluorescent dyes on the aggregation of Aβ42 oligomers using fluorescence correlation spectroscopy (FCS). We found that fluorescent labels of BODIPY® FL-C5 (BP), N-hydroxysuccinimide rhodamine B ester (RB) and rhodamine B isothiocyanate (RITC) increased the propensity of labelled Aβ42 oligomers to aggregate, whereas 6-(fluorescein-5-carboxamido) hexanoic acid succinimidyl ester (5-SFX) and fluorescein 5(6)-isothiocyanate (5(6)-FITC) decreased the propensity of labelled Aβ42 oligomers to aggregate...
October 11, 2018: Biopolymers
Ekaterina R Gasilova, Galina P Aleksandrova, Elena N Vlasova, Vadim A Baigildin
κ-carrageenan is a linear sulfated anionic gelling polysaccharide obtained from red seaweed algae by an alkaline hydrolysis. We applied static and dynamic light scattering (DLS), capillary viscometry, FT-IR, and electrophoretic DLS to gain insight into the effect of deep alkaline hydrolysis (95 °C, pH = 10 during Th = 60, 75, and 90 min) on κ-carrageenan macromolecules in a coil conformation. As DLS of coil-like κ-carrageenans is usually complicated by spurious permanent aggregates, the alkaline hydrolysis of κ-carrageenans has not been studied by DLS...
September 30, 2018: Biopolymers
Marco Chino, Shao-Qing Zhang, Fabio Pirro, Linda Leone, Ornella Maglio, Angela Lombardi, William F DeGrado
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters...
September 11, 2018: Biopolymers
Rafael Alcala-Torano, Mathieu Walther, Dayn J Sommer, Chad K Park, Giovanna Ghirlanda
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes...
September 6, 2018: Biopolymers
Fulvio Perrella, Umberto Raucci, Maria Gabriella Chiariello, Marco Chino, Ornella Maglio, Angela Lombardi, Nadia Rega
Fe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix-heme-α-helix "sandwich" motif. Up to now, no detailed MC6 structural characterization is available. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)-MC6 structural features and to validate the de novo designed fold...
August 9, 2018: Biopolymers
Zahra Ghassemi, Gymama Slaughter
With the rapid development of biomimetic polymers for cell-based assays and tissue engineering, crosslinking electrospun nanofibrous biopolymer constructs is of great importance for achieving sustainable and efficient three-dimensional scaffold constructs. Uncrosslinked electrospun gelatin nanofibrous constructs immediately and completely dissolved in aqueous solutions due to their aqueous solubility and poor storage stability. Here, a novel and versatile approach for the fabrication and crosslinking of electrospun gelatin construct with tunable porosity and high aspect ratio nanofibers is presented...
September 2018: Biopolymers
Shuguang Zhang
No abstract text is available yet for this article.
August 2018: Biopolymers
Shuguang Zhang
Circular dichroism (CD) spectroscopy is a useful technique to study the structure and dynamics of peptides, proteins and nucleic acids. CD is particularly useful because sample volumes may be as low as 50 μL, it provides high precision and sensitivity, and it achieves a good signal to noise ratio. CD characterizes molecular conformational changes in real time by finely controlling temperature, pH, and titrating urea and guanidine·HCl which is necessary for studying protein folding. Although CD does not provide detailed structure at the atomic level, it provides a global structural framework...
August 2018: Biopolymers
Kenneth J Breslauer
No abstract text is available yet for this article.
August 2018: Biopolymers
Alexander Tischer, Venkata R Machha, Jörg Rösgen, Matthew Auton
Protein phase diagrams have a unique potential to identify the presence of additional thermodynamic states even when non-2-state character is not readily apparent from the experimental observables used to follow protein unfolding transitions. Two-state analysis of the von Willebrand factor A3 domain has previously revealed a discrepancy in the calorimetric enthalpy obtained from thermal unfolding transitions as compared with Gibbs-Helmholtz analysis of free energies obtained from the Linear Extrapolation Method (Tischer and Auton, Prot Sci 2013; 22(9):1147-60)...
August 2018: Biopolymers
Conceição A Minetti, Jeffrey Y Sun, Daniel P Jacobs, Inkoo Kang, David P Remeta, Kenneth J Breslauer
Bistrand lesions embedded within a single helical turn of tridecameric deoxyoligonucleotide duplexes represent a model system for exploring the impact of clustered lesions that occur in vivo and pose a significant challenge to cellular repair machineries. Such investigations are essential for understanding the forces that dictate lesion-induced mutagenesis, carcinogenesis, and cytotoxicity within a context that mimics local helical perturbations caused by an ionizing radiation event. This study characterizes the structural and energy profiles of DNA duplexes harboring synthetic abasic sites (tetrahydrofuran, F) as models of clustered bistrand abasic (AP) lesions...
August 2018: Biopolymers
Mimi Nick, Yibing Wu, Nathan W Schmidt, Stanley B Prusiner, Jan Stöhr, William F DeGrado
The hydrophobic Aβ peptide is highly aggregation prone; it first forms soluble oligomers, which then convert into the amyloid fibrils found in the cerebral plaques of Alzheimer's disease. It is generally understood that as the peptide concentration of Aβ increases, the fibrillization process is accelerated, but we examine the limits on this phenomenon. We found that once a threshold concentration of Aβ is exceeded, a stable oligomer is formed at the expense of fibril formation. The suppression of fibril formation was observed by amyloid-binding dye Thioflavin T and solution nuclear magnetic resonance (NMR)...
August 2018: Biopolymers
Angelo A Lamola
Both lead intoxication in early childhood and deficient bilirubin-binding capacity (BBC) of blood in jaundiced neonates indicate risk for brain damage. Zinc protoporphyrin (ZPP) is a biomarker for lead intoxication (PbI) as well as well as for iron deficiency. Under the leadership of Jack Aviv, Aviv Biomedical, Inc. developed robust hematofluorometers for point-of-care assays of ZPP in blood and for the high-affinity BBC of blood. These assays use just drops of whole blood and are simple, fast and inexpensive...
August 2018: Biopolymers
Shion A Lim, Susan Marqusee
The amino acid sequence encodes the energy landscape of a protein. Therefore, we expect evolutionary mutations to change features of the protein energy landscape, including the conformations adopted by a polypeptide as it folds to its native state. Ribonucleases H (RNase H) from Escherichia coli and Thermus thermophilus both fold via a partially folded intermediate in which the core region of the protein (helices A-D and strands 4-5) is structured. Strand 1, however, uniquely contributes to the T. thermophilus RNase H folding intermediate (Icore+1 ), but not the E...
August 2018: Biopolymers
Sam M Ireland, Altin Sula, B A Wallace
Purified integral membrane proteins require amphipathic molecules to maintain their solubility in aqueous solutions. These complexes, in turn, are used in studies to characterise the protein structures by a variety of biophysical and structural techniques, including spectroscopy, crystallography, and cryo-electron microscopy. Typically the amphilphiles used have been detergent molecules, but more recently they have included amphipols, which are polymers of different sizes and compositions designed to create smaller, more well-defined solubilised forms of the membrane proteins...
August 2018: Biopolymers
Rebecca Strawn, FangFang Chen, Parminder Jeet Haven, Sam Wong, Anne Park-Arias, Monique De Leeuw, Yujia Xu
It has proven challenging to obtain collagen-mimetic fibrils by protein design. We recently reported the self-assembly of a mini-fibril showing a 35 nm, D-period like, axially repeating structure using the designed triple helix Col108. Peptide Col108 was made by bacterial expression using a synthetic gene; its triple helix domain consists of three pseudo-identical units of amino acid sequence arranged in tandem. It was postulated that the 35 nm d-period of Col108 mini-fibrils originates from the periodicity of the Col108 primary structure...
July 2018: Biopolymers
Yue Yang, Zuyuan Luo, Ying Zhao
The scaffolds for stem cell-based bone tissue engineering should hold the ability to guide stem cells osteo-differentiating. Otherwise, stem cells will differentiate into unwanted cell types or will form tumors in vivo. Alginate, a natural polysaccharide with great biocompatibility, was widely used in biomedical applications. However, the limited bioactivity and poor osteogenesis capability of pristine alginate hampered its further application in tissue engineering. In this work, a bone forming peptide-1 (BFP-1), derived from bone morphogenetic protein-7, was grafted to alginate polymer chains to prepare peptide-decorated alginate porous scaffolds (pep-APS) for promoting osteo-differentiation of human mesenchymal stem cells (hMSCs)...
July 2018: Biopolymers
D Galante, E Cavallo, A Perico, C D'Arrigo
Amyloid beta (Aβ) aggregation and oxidative stress are two of the central events in Alzheimer's Disease (AD). Both these phenomena can be caused by the interaction of Aβ with metal ions. In the last years the interaction between ZnII , CuII , and Aβ was much studied, but between iron and Aβ it is still little known. In this work we determine how three Aβ peptides, present in AD, interact with FeIII -citrate. The three Aβ peptides are: full length Aβ1-42, an isoform truncated at Glutamic acid in position three, Aβ3-42, and its pyroglutamated form AβpE3-42...
June 2018: Biopolymers
Yuanzi Wu, Zhen Cai, Shuigen Wu, Wenli Xiong, Shanyun Ma
A recoverable and thermoresponsive polymer-protein bioconjugate is synthesized and employed in the purification of protein with free sulfhydryl groups. Initiator with disulphide was modified on the cysteine residue of the target protein. Poly(N-isopropylacrylamide) exhibiting a lower critical solution temperature was grown from the protein. The resulting protein-polymer conjugate was successfully thermoprecipitated and separated from other proteins. The approach was demonstrated with bovine serum albumin with the recycling yield of 76...
June 2018: Biopolymers
Carmen Esteban, Ivan Donati, Sergio Pantano, Myriam Villegas, Julio Benegas, Sergio Paoletti
Chitosan and its highly hydrophilic 1-deoxy-lactit-1-yl derivative (Chitlac) are polysaccharides with increasing biomedical applications. Aimed to unravel their conformational properties we have performed a series of molecular dynamics simulations of Chitosan/Chitlac decamers, exploring different degrees of substitution (DS) of lactitol side chains. At low DS, two conformational regions with different populations are visited, while for DS ≥ 20% the oligomers remain mostly linear and only one main region of the glycosidic angles is sampled...
June 2018: Biopolymers
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