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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)...
February 19, 2018: Biopolymers
Zhenxu Wu, Yulai Zhou, Li Chen, Mingxin Hu, Yu Wang, Linlong Li, Zongliang Wang, Peibiao Zhang
The recombinant basic fibroblast growth factor (bFGF) containing collagen-binding domain (CBD) has been found to be a potential therapeutic factor in tissue regeneration. However, its binding efficiency and quantification remain uncertain. In this research, massive recombinant bFGFs with good bioactivity for enhancing the proliferation of NIH-3T3 cells were achieved. An ELISA-based quantitative method was set up to investigate the binding efficiency of CBD-bFGFs on collagen films. It indicated that the CBDs significantly increased the collagen-binding ability of bFGF (P < ...
February 19, 2018: Biopolymers
Marilisa Vigorita, Serena Cozzolino, Rosario Oliva, Giuseppe Graziano, Pompea Del Vecchio
Differential scanning calorimetry measurements performed on RNase A in aqueous binary solutions containing different concentrations of urea, tetramethylurea, guanidinium chloride, and guanidinium thiocyanate, and in aqueous ternary solutions, containing the same denaturants plus 1 M trimethylamine N-oxide, TMAO, demonstrate that the latter has a general counteracting ability at pH 7.0, but not at pH 4.0. Experimental data rule out the idea that counteraction originates from direct interactions between TMAO molecules and denaturing agents...
February 7, 2018: Biopolymers
Wioleta Kowalczyk, Julie Sanchez, Phillipe Kraaz, Oliver E Hutt, David N Haylock, Peter J Duggan
A 54-member library of boronated octapeptides, with all but the boronated residue being proteinogenic, was tested for affinity to a set of saccharides commonly found on the terminus of mammalian glycans. After experimentation with a high-throughput dye-displacement assay, attention was focused on isothermal titration calorimetry as a tool to provide reliable affinity data, including enthalpy and entropy of binding. A small number of boronated peptides showed higher affinity and significant selectivity for N-acetylneuraminic acid over methyl-α-d-galactopyranoside, methyl-α/β-l-fucopyranoside and N-acetyl-d-glucosamine...
January 30, 2018: Biopolymers
Karoline Nordsieck, Lars Baumann, Vera Hintze, M Teresa Pisabarro, Matthias Schnabelrauch, Annette G Beck-Sickinger, Sergey A Samsonov
The chemokine interleukin-8 (IL-8, CXCL8) plays an important role in inflammatory processes and consecutive wound healing. It recruits primarily neutrophils to infection sites and stimulates their degranulation and phagocytosis in effector cells. IL-8 binds glycosaminoglycans (GAGs), a class of complex linear anionic polysaccharides often organized into diversely sulfated micro-domains, that enriches the protein concentration locally and so facilitate the formation of stable concentration gradients. In this study, we applied experimental and computational techniques to investigate the binding of wild type and truncated IL-8 variants to natural and chemically modified GAGs to gain further insight into the IL-8/GAG interaction...
January 27, 2018: Biopolymers
Vijay Kumar, Amresh Prakash, Andrew M Lynn
Alterations in the local dynamics of Cu/Zn Superoxide dismutase (SOD1) due to mutations affect the protein folding, stability, and function leading to misfolding and aggregation seen in amyotrophic lateral sclerosis (ALS). Here, we study the structure and dynamics of the most devastating ALS mutation, A4V SOD1 in aqueous trifluoroethanol (TFE) through experiments and simulation. Far-UV circular dichroism (CD) studies shows that TFE at intermediate concentrations (∼15% - 30%) induce partially unfolded β-sheet-rich extended conformations in A4V SOD1 which subsequently aggregates...
January 25, 2018: Biopolymers
Aline Lima de Oliveira, Eduardo Maffud Cilli, Uris Ros, Edson Crusca, María Eliana Lanio, Carlos Alvarez, Shirley Schreier, Thelma Aguiar Pertinhez, Alberto Spisni
Sticholysin II (StII) is a pore-forming actinoporin from the sea anemone Stichodactyla helianthus. A mechanistic model of its action has been proposed: proteins bind to cell membrane, insert their N-termini into the lipid core and assemble into homo-tetramer pores responsible for host-cell death. Because very likely the first 10 residues of StII N-terminus are critical for membrane penetration, to dissect the molecular details of that functionality, we studied two synthetic peptides: StII1-30 and StII16-35 ...
January 23, 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...
January 11, 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)...
January 10, 2018: Biopolymers
Ghufran Barnawi, Michael Noden, Robert Taylor, Chuda Lohani, David Beriashvili, Michael Palmer, Scott D Taylor
Daptomycin is an important Ca2+ -dependent cyclic lipodepsipeptide antibiotic used to treat serious gram-positive infections. The search for daptomycin analogs with improved activity and their application as tools for studying its mechanism of action has prompted us to develop an entirely Fmoc solid phase approach to the synthesis of daptomycin analogs. Key to the success of this approach was the development of conditions that allowed for the formation of the ester bond on resin-bound peptides consisting of residues 1-10 and the decanoyl lipid tail...
January 2, 2018: Biopolymers
Ria J Betush, Jennifer M Urban, Bradley L Nilsson
Amphipathic peptides with alternating polar and nonpolar amino acid sequences efficiently self-assemble into functional β-sheet fibrils as long as the nonpolar residues have sufficient hydrophobicity. For example, the Ac-(FKFE)2 -NH2 peptide rapidly self-assembles into β-sheet bilayer nanoribbons, while Ac-(AKAE)2 -NH2 fails to self-assemble under similar conditions due to the significantly reduced hydrophobicity and β-sheet propensity of Ala relative to Phe. Herein, we systematically explore the effect of substituting only two of the four Ala residues at various positions in the Ac-(AKAE)2 -NH2 peptide with amino acids of increasing hydrophobicity, β-sheet potential, and surface area (including Phe, 1-naphthylalanine (1-Nal), 2-naphthylalanine (2-Nal), cyclohexylalanine (Cha), and pentafluorophenylalanine (F5 -Phe)) on the self-assembly propensity of the resulting sequences...
January 2, 2018: Biopolymers
Sergei V Sychev, Stanislav V Sukhanov, Pavel V Panteleev, Zakhar O Shenkarev, Tatiana V Ovchinnikova
Arenicins are 21-residue β-hairpin antimicrobial peptides (AMPs) isolated from the marine lugworm Arenicola marina [Ovchinnikova et al., FEBS Lett. 2004;577:209-214]. The peptides have a high positive charge (+6) and display a broad spectrum of antimicrobial activities against bacteria and fungi. Arenicins adopt the monomeric highly twisted β-hairpin in water or planar β-structural dimers in anionic liposomes and detergent micelles. Until now, the interaction of cationic β-structural AMPs with zwitterionic phospholipid bilayers mimicking eukaryotic membranes is not well understood...
December 21, 2017: Biopolymers
Marco Cavaco, Miguel A R B Castanho, Vera Neves
Chimeric proteins composed of a biologically active peptide and a fragment crystallizable (Fc) domain of immunoglobulin G (IgG) are known as peptibodies. They present an extended half-life due to neonatal Fc receptor (FcRn) salvage pathway, a decreased renal clearance rate owing to its increased size (≈70 kDa) and, depending on the peptide used in the design of the peptibody, an active-targeting moiety. Also, the peptides therapeutic activity is boosted by the number of peptides in the fusion protein (at least two peptides) and to some peptides' alterations...
December 21, 2017: 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...
December 4, 2017: Biopolymers
Yinfeng Lyu, Ronald Domalaon, Xuan Yang, Frank Schweizer
Peptidomimetic modification is a common route of optimization for biologically active peptides. Previous studies in our group have shown that conjugation of amphiphilic tobramycin to other antibacterials enhance their latent outer membrane permeabilizing and efflux blocking activity toward Gram-negative pathogens including Pseudomonas aeruginosa. Herein, we describe the antimicrobial adjuvant properties of amphiphilic lysine ligated to tobramycin. The most potent amphiphilic lysine-tobramycin conjugate 3 potentiated the antibacterial efficacy of 8 clinically used antibiotics against wild type, multidrug- and extensively drug-resistant P...
December 4, 2017: Biopolymers
Liyang Shi, Yu Zhang, Dmitri Ossipov
In situ cross-linked hyaluronan (HA) hydrogels with different capacities for biomineralization were prepared and their enzymatic degradation was monitored. Covalent incorporation of bisphosphonates (BPs) into HA hydrogel results in the increased stiffness of the hydrogel in comparison with the unmodified HA hydrogel of the same cross-linking density. The rate of enzymatic degradation of HABP hydrogel was significantly lower than the rate of degradation of control HA hydrogel in vitro. This effect is observed only in the presence of calcium ions that strongly bind to the matrix-anchored BP groups and promote further mineralization of the matrix...
November 27, 2017: Biopolymers
Rossella De Marco, Arianna Greco, Natalia Calonghi, Samantha D Dattoli, Monica Baiula, Santi Spampinato, Pierre Picchetti, Luisa De Cola, Michele Anselmi, Francesca Cipriani, Luca Gentilucci
Persistent accumulation of immune cells mediated by α4β1 integrin (VLA-4) is a hallmark of the inflammatory diseases and of chronic inflammation observed in the affected tissues of autoimmune diseases. Aiming at exploring new methods for monitoring the course of the inflammatory processes, we designed the first peptide-functionalized nanostructured devices capable to mimic the high-density multivalency binding between the α4β1 integrin-expressing cells and the ligands overexpressed on the endothelial surfaces, in the proximity of the sites of inflammation...
November 27, 2017: Biopolymers
Andrea Pizzi, Valentina Dichiarante, Giancarlo Terraneo, Pierangelo Metrangolo
Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aβ16-20 ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments...
November 27, 2017: Biopolymers
Alessandro Contini, Nicola Ferri, Raffaella Bucci, Maria Giovanna Lupo, Emanuela Erba, Maria Luisa Gelmi, Sara Pellegrino
Rac1 GTPase interaction with guanine nucleotide exchange factor Tiam1 is involved in several cancer types and cardiovascular diseases. Although small molecules interfering with their protein-protein interaction (PPI) were identified and studied, the ability of small peptides and peptide mimics acting as Rac1/Tiam1 PPI inhibitors has not been yet explored. Using computational alanine scanning (CAS), the "hot" interfacial residues have been determined allowing the design of a small library of putative PPI inhibitors...
November 27, 2017: Biopolymers
H Ravishankar, A Barth, M Andersson
P-type ATPase proteins maintain cellular homeostasis and uphold critical concentration gradients by ATP-driven ion transport across biological membranes. Characterization of single-cycle dynamics by time-resolved X-ray scattering techniques in solution could resolve structural intermediates not amendable to for example crystallization or cryo-electron microscopy sample preparation. To pave way for such time-resolved experiments, we used biochemical activity measurements, Attenuated Total Reflectance (ATR) and time-dependent Fourier-Transform Infra-Red (FTIR) spectroscopy to identify optimal conditions for activating a Zn2+ -transporting Type-I ATPase from Shigella sonnei (ssZntA) at high protein concentration using caged ATP...
November 23, 2017: Biopolymers
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