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    Protein purification by chemo-selective precipitation using thermoresponsive polymers.
    Biopolymers 2018 May 6:e23222. Epub 2018 May 6.
    College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350002, China.
    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. Read More

    Osteostimulation scaffolds of stem cells: BMP-7-derived peptide-decorated alginate porous scaffolds promote the aggregation and osteo-differentiation of human mesenchymal stem cells.
    Biopolymers 2018 May 6:e23223. Epub 2018 May 6.
    Department of Stomatology, Xuanwu Hospital, Capital Medical University, Beijing, 100053, China.
    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. Read More

    Dissecting the conformational determinants of chitosan and chitlac oligomers-REVISED.
    Biopolymers 2018 May 3:e23221. Epub 2018 May 3.
    Department of Life Sciences, University of Trieste, via L. Giorgieri 5, Trieste, 34127, Italy.
    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. Read More

    PHBV-TiO mats prepared by electrospinning technique: Physico-chemical properties and cytocompatibility.
    Biopolymers 2018 Apr 28:e23120. Epub 2018 Apr 28.
    Federal University of Jatai-BR 364, km 195, n° 3800, Jatai, Goias, 75801-615, Brazil.
    One of the most important challenges in tissue engineering research is the development of biomimetic materials. In this present study, we have investigated the effect of the titanium dioxide (TiO ) nanoparticles on the properties of electrospun mats of poly (hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), to be used as scaffold. The morphology of electrospun fibers was observed by scanning electron microscopy (SEM). Read More

    Synthetic polymers as substrates for a DNA-sliding clamp protein.
    Biopolymers 2018 Apr 26:e23119. Epub 2018 Apr 26.
    Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, Nijmegen, 6525, AJ, The Netherlands.
    The clamp protein (gp45) of the DNA polymerase III of the bacteriophage T4 is known to bind to DNA and stay attached to it in order to facilitate the process of DNA copying by the polymerase. As part of a project aimed at developing new biomimetic data-encoding systems we have investigated the binding of gp45 to synthetic polymers, that is, rigid, helical polyisocyanopeptides. Molecular modelling studies suggest that the clamp protein may interact with the latter polymers. Read More

    Formation of G-wires, bimolecular and tetramolecular quadruplex: Cation-induced structural polymorphs of G-rich DNA sequence of human SYTX gene.
    Biopolymers 2018 Apr 19:e23115. Epub 2018 Apr 19.
    Nucleic Acids Research Lab, Department of Chemistry, University of Delhi, Delhi, 110007, India.
    An exceptional property of auto-folding into a range of intra- as well as intermolecular quadruplexes by guanine-rich oligomers (GROs) of promoters, telomeres and various other genomic locations is still one of the most attractive areas of research at present times. The main reason for this attention is due to their established in vivo existence and biological relevance. Herein, the structural status of a 20-nt long G-rich sequence with two G5 stretches (SG20) is investigated using various biophysical and biochemical techniques. Read More

    Improvement of functional properties of a thermostable β-glycosidase for milk lactose hydrolysis.
    Biopolymers 2018 Apr 2:e23118. Epub 2018 Apr 2.
    Institute of Protein Biochemistry-Consiglio Nazionale delle Ricerche (CNR), via P. Castellino 111, Naples, 80131, Italy.
    In this work, a new exploitation of the thermostable β-glycosidase from Sulfolobus solfataricus expressed in Saccharomyces cerevisiae to create functional foods for low lactose diets was evaluated. For this purpose, the lactose hydrolysis reaction using immobilized and soluble enzymes was investigated. Activity and stability at different conditions of pH and temperature were tested. Read More

    Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes.
    Biopolymers 2018 Mar 30:e23114. Epub 2018 Mar 30.
    Dipartimento di Chimica "Ugo Schiff,", Università di Firenze, Via della Lastruccia 3-13, Sesto Fiorentino, 50019, Italy.
    The ligand binding characteristics of heme-containing proteins are determined by a number of factors, including the nature and conformation of the distal residues and their capability to stabilize the heme-bound ligand via hydrogen-bonding and electrostatic interactions. In this regard, the heme pockets of truncated hemoglobins (TrHbs) constitute an interesting case study as they share many common features, including a number of polar cavity residues. In this review, we will focus on three proteins of group II TrHbs, from Thermobifida fusca (Tf-HbO) and Pseudoalteromonas haloplanktis TAC125 (Ph-HbO). Read More

    Molecular determinants of the interaction of EGCG with ordered and disordered proteins.
    Biopolymers 2018 Mar 30:e23117. Epub 2018 Mar 30.
    Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom.
    The aggregation process of peptides and proteins is of great relevance as it is associated with a wide range of highly debilitating disorders, including Alzheimer's and Parkinson's diseases. The natural product (-)-epigallocatechin-3-gallate (EGCG) can redirect this process away from amyloid fibrils and towards non-toxic oligomers. In this study we used nuclear magnetic resonance (NMR) spectroscopy to characterize the binding of EGCG to a set of natively structured and unstructured proteins. Read More

    Thermodynamics of the pseudo-knot in helix 18 of 16S ribosomal RNA.
    Biopolymers 2018 Apr 23;109(4):e23116. Epub 2018 Mar 23.
    Centre of New Technologies, University of Warsaw, Banacha 2C, Warsaw, 02-09, Poland.
    A fragment of E. coli 16S rRNA formed by nucleotides 500 to 545 is termed helix 18. Nucleotides 505-507 and 524-526 form a pseudo-knot and its distortion affects ribosome function. Read More

    Understanding and designing head-to-tail cyclic peptides.
    Biopolymers 2018 Mar 12. Epub 2018 Mar 12.
    Department of Chemistry, Tufts University, Medford, Massachusetts.
    Cyclic peptides (CPs) are an exciting class of molecules with a variety of applications. However, design strategies for CP therapeutics, for example, are generally limited by a poor understanding of their sequence-structure relationships. This knowledge gap often leads to a trial-and-error approach for designing CPs for a specific purpose, which is both costly and time-consuming. Read More

    Bromotryptophans and their incorporation in cyclic and bicyclic privileged peptides.
    Biopolymers 2018 Mar 12. Epub 2018 Mar 12.
    Institute for Research in Biomedicine (IRB Barcelona), Chemistry and Molecular Pharmacology Program, Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.
    While revisiting biologically active natural peptides, the importance of the tryptophan residue became clear. In this article, the incorporation of this amino acid, brominated at different positions of the indole ring, into cyclic peptides was successfully achieved. These products demonstrated improved properties in terms of passive diffusion, permeability across membranes, biostability in human serum and cytotoxicity. Read More

    N-methylation in amino acids and peptides: Scope and limitations.
    Biopolymers 2018 Mar 12. Epub 2018 Mar 12.
    Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4001, South Africa.
    Active pharmaceutical ingredients (APIs) can be divided into two types, namely chemical and biological entities. Traditionally, the former has been associated with the so-called small molecules. The revival of peptides in pharmaceutical industry results from their importance in many biological roles. Read More

    Gold nanoparticles crosslinking by peptides and amino acids: A tool for the colorimetric identification of amino acids.
    Biopolymers 2018 Mar 12. Epub 2018 Mar 12.
    Department of Chemical Sciences, University of Padova, via Marzolo, 1, Padova, 35131, Italy.
    Gold nanoparticles are known to aggregate in the presence of proper multifunctional compounds. For those larger than 3 nm, the process can be followed with the naked eye because the surface plasmon absorption band of the particles shifts to longer wavelengths and the solution color changes from red to blue. To exploit this property, we have used amino acids and peptides as crosslinking agents in ethanol at low µM concentrations. Read More

    Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches.
    Biopolymers 2018 Mar 9. Epub 2018 Mar 9.
    Scuola Normale Superiore, Piazza dei Cavalieri 7, Pisa, 56126, Italy.
    Computational modeling involving Quantum Mechanics (QM) and Molecular Mechanics (MM) calculations are widely utilized to unveil the atomic-molecular properties that underpin their inherent characteristic features. The choice over the either of the QM and MM methods or a multiscale composite approach is driven by the target property of interest, and of course, the molecular size. Often, tailor-made schemes need to be devised to match the specific study purpose. Read More

    Exploring the structure characteristics and major channels of cytochrome P450 2A6, 2A13, and 2E1 with pilocarpine.
    Biopolymers 2018 Apr 27;109(4):e23108. Epub 2018 Feb 27.
    Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China.
    The majority of cytochromes P450 play a critical role in metabolism of endogenous and exogenous substrates, some of its products are carcinogens. Therefore, inhibition of P450 enzymes activity can promote the detoxification and elimination of chemical carcinogens. In this study, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed to explore the structure features and channel dynamics of three P450 isoforms 2A6, 2A13, and 2E1 bound with the common inhibitor pilocarpine. Read More

    Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages.
    Biopolymers 2018 Feb 22. Epub 2018 Feb 22.
    Department of Chemical Sciences, University of Napoli "Federico II," Via Cintia, Napoli, 80126, Italy.
    Inspired by natural heme-proteins, scientists have attempted for decades to design efficient and selective metalloporphyrin-based oxidation catalysts. Starting from the pioneering work on small molecule mimics in the late 1970s, we have assisted to a tremendous progress in designing cages of different nature and complexity, able to accommodate metalloporphyrins. With the intent of tuning and controlling their reactivity, more and more sophisticated and diverse environments are continuously exploited. Read More

    "Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams.
    Biopolymers 2018 Feb 19. Epub 2018 Feb 19.
    Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota.
    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). We resolve this thermodynamic conundrum using a Clausius-Clapeyron analysis of the urea-temperature phase diagram that defines how ΔH and the urea m-value interconvert through the slope of c versus T, (∂cm/∂T)=ΔH/(mT). Read More

    Binding efficiency of recombinant collagen-binding basic fibroblast growth factors (CBD-bFGFs) and their promotion for NIH-3T3 cell proliferation.
    Biopolymers 2018 Mar 19;109(3):e23105. Epub 2018 Feb 19.
    Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People's Republic of China.
    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. Read More

    Counteraction ability of TMAO toward different denaturing agents.
    Biopolymers 2018 Feb 7. Epub 2018 Feb 7.
    Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, Napoli, 80126, Italy.
    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. Read More

    The binding of boronated peptides to low affinity mammalian saccharides.
    Biopolymers 2018 Jan 30. Epub 2018 Jan 30.
    CSIRO Manufacturing, Bag 10, Clayton South, Victoria, 3169, Australia.
    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. Read More

    The effect of interleukin-8 truncations on its interactions with glycosaminoglycans.
    Biopolymers 2018 Jan 27. Epub 2018 Jan 27.
    Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, Gdańsk, 80-308, Poland.
    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. Read More

    Alterations in local stability and dynamics of A4V SOD1 in the presence of trifluoroethanol.
    Biopolymers 2018 Mar 25;109(3):e23102. Epub 2018 Jan 25.
    School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
    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. Read More

    Insights on the structure-activity relationship of peptides derived from Sticholysin II.
    Biopolymers 2018 Jan 23. Epub 2018 Jan 23.
    Department of Biochemistry and Chemical Technology, Institute of Chemistry, São Paulo State University, Araraquara, Brazil.
    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: StII and StII . Read More

    Impact of bistrand abasic sites and proximate orientation on DNA global structure and duplex energetics.
    Biopolymers 2018 Jan 11. Epub 2018 Jan 11.
    Department of Chemistry and Chemical Biology, Rutgers - The State University of New Jersey, Piscataway, New Jersey.
    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. Read More

    A long-lived Aβ oligomer resistant to fibrillization.
    Biopolymers 2018 Jan 10. Epub 2018 Jan 10.
    Department of Pharmaceutical Chemistry, University of California, San Francisco, California.
    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. Read More

    An entirely fmoc solid phase approach to the synthesis of daptomycin analogs.
    Biopolymers 2018 Jan 2. Epub 2018 Jan 2.
    Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada.
    Daptomycin is an important Ca -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. Read More

    Balancing hydrophobicity and sequence pattern to influence self-assembly of amphipathic peptides.
    Biopolymers 2018 Jan 2. Epub 2018 Jan 2.
    Department of Chemistry, University of Rochester, Rochester, New York.
    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) -NH peptide rapidly self-assembles into β-sheet bilayer nanoribbons, while Ac-(AKAE) -NH 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) -NH 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 (F -Phe)) on the self-assembly propensity of the resulting sequences. Read More

    Marine antimicrobial peptide arenicin adopts a monomeric twisted β-hairpin structure and forms low conductivity pores in zwitterionic lipid bilayers.
    Biopolymers 2017 Dec 21. Epub 2017 Dec 21.
    M.M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, Moscow, 117997, Russia.
    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]. Read More

    Peptibodies: An elegant solution for a long-standing problem.
    Biopolymers 2017 Dec 21. Epub 2017 Dec 21.
    Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa, 1649-028, Portugal.
    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. Read More

    Jack Aviv and brains of children.
    Biopolymers 2017 Dec 4. Epub 2017 Dec 4.
    Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, California.
    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. Read More

    Amphiphilic lysine conjugated to tobramycin synergizes legacy antibiotics against wild-type and multidrug-resistant Pseudomonas aeruginosa.
    Biopolymers 2017 Dec 4. Epub 2017 Dec 4.
    Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
    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. Read More

    Enzymatic degradation of hyaluronan hydrogels with different capacity for in situ bio-mineralization.
    Biopolymers 2018 Feb 27;109(2). Epub 2017 Nov 27.
    Science for Life Laboratory, Division of Polymer Chemistry, Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden.
    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. Read More

    Selective detection of α4β1 integrin (VLA-4)-expressing cells using peptide-functionalized nanostructured materials mimicking endothelial surfaces adjacent to inflammatory sites.
    Biopolymers 2017 Nov 27. Epub 2017 Nov 27.
    Department of Chemistry "G. Ciamician", University of Bologna, via Selmi 2, Bologna, 40126, Italy.
    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. Specifically, we describe the first examples of monolayers constituted by dye-loaded zeolite L crystals, coated with α4β1 integrin peptide ligands, and we analyze the adhesion of model Jurkat cells in comparison to non-α4β1 integrin-expressing cells. Read More

    Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides.
    Biopolymers 2017 Nov 27. Epub 2017 Nov 27.
    Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, Milano, I-20131, Italy.
    Amyloidogenic peptide fragment KLVFF (H N-Lys-Leu-Val-Phe-Phe-COOH, Aβ ), 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). Read More

    Peptide modulators of Rac1/Tiam1 protein-protein interaction: An alternative approach for cardiovascular diseases.
    Biopolymers 2017 Nov 27. Epub 2017 Nov 27.
    Department of Pharmaceutical Sciences, University of Milano, Milano, Italy.
    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. Read More

    Probing the activity of a recombinant Zn -transporting P-type ATPase.
    Biopolymers 2018 Feb 23;109(2). Epub 2017 Nov 23.
    Science for Life Laboratory, Department of Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, SE-171 21, Sweden.
    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 Zn -transporting Type-I ATPase from Shigella sonnei (ssZntA) at high protein concentration using caged ATP. Read More

    Design and development of low cost polyurethane biopolymer based on castor oil and glycerol for biomedical applications.
    Biopolymers 2018 Feb 21;109(2). Epub 2017 Nov 21.
    UCL Institute of Orthopaedics and Musculoskeletal Science, Division of Surgery & Interventional Science, University College London, London, United Kingdom.
    In the current study, we present the synthesis of novel low cost bio-polyurethane compositions with variable mechanical properties based on castor oil and glycerol for biomedical applications. A detailed investigation of the physicochemical properties of the polymer was carried out by using mechanical testing, ATR-FTIR, and X-ray photoelectron spectroscopy (XPS). Polymers were also tested in short term in-vitro cell culture with human mesenchymal stem cells to evaluate their biocompatibility for potential applications as biomaterial. Read More

    Structure-activity studies of peptidomimetics based on kinase-inhibitory region of suppressors of cytokine signaling 1.
    Biopolymers 2017 Nov 20. Epub 2017 Nov 20.
    Department of Pharmacy, CIRPEB: Centro Interuniversitario di Ricerca sui Peptidi Bioattivi- University of Naples "Federico II,", Naples, 80134, Italy.
    Suppressors of Cytokine Signaling (SOCS) proteins are negative regulators of JAK proteins that are receptor-associated tyrosine kinases, which play key roles in the phosphorylation and subsequent activation of several transcription factors named STATs. Unlike the other SOCS proteins, SOCS1 and 3 show, in the N-terminal portion, a small kinase inhibitory region (KIR) involved in the inhibition of JAK kinases. Drug discovery processes of compounds based on KIR sequence demonstrated promising in functional in vitro and in inflammatory animal models and we recently developed a peptidomimetic called PS5, as lead compound. Read More

    The burst-phase folding intermediate of ribonuclease H changes conformation over evolutionary history.
    Biopolymers 2017 Nov 20. Epub 2017 Nov 20.
    Department of Molecular and Cell Biology, University of California, Berkeley, California.
    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. Read More

    β-cyclodextrin encapsulated polyphenols as effective antioxidants.
    Biopolymers 2018 Jan 15;109(1). Epub 2017 Nov 15.
    Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
    Formation of dityrosine (DT) cross-linkages in proteins is one of the most widely used markers of oxidative stress. Ribonuclease A (RNase A) has 6 Tyr residues and shows a characteristic DT fluorescence peak upon oxidation in addition to major changes in its secondary structure. DT formation can be prevented by using polyphenols (GA, ECG, and EGCG) which are known to have strong antioxidant activity. Read More

    Differentiation potential of human adipose stem cells bioprinted with hyaluronic acid/gelatin-based bioink through microextrusion and visible light-initiated crosslinking.
    Biopolymers 2018 Feb 15;109(2). Epub 2017 Nov 15.
    Department of Materials Science and Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
    Bioprinting has a great potential to fabricate three-dimensional (3D) functional tissues and organs. In particular, the technique enables fabrication of 3D constructs containing stem cells while maintaining cell proliferation and differentiation abilities, which is believed to be promising in the fields of tissue engineering and regenerative medicine. We aimed to demonstrate the utility of the bioprinting technique to create hydrogel constructs consisting of hyaluronic acid (HA) and gelatin derivatives through irradiation by visible light to fabricate 3D constructs containing human adipose stem cells (hADSCs). Read More

    Conformational properties, membrane interaction, and antibacterial activity of the peptaibiotic chalciporin A: Multitechnique spectroscopic and biophysical investigations on the natural compound and labeled analogs.
    Biopolymers 2017 Nov 11. Epub 2017 Nov 11.
    Institute of Biomolecular, Chemistry, Padova Unit, CNR, Padova, 35131, Italy.
    In this work, an extensive set of spectroscopic and biophysical techniques (including FT-IR absorption, CD, 2D-NMR, fluorescence, and CW/PELDOR EPR) was used to study the conformational preferences, membrane interaction, and bioactivity properties of the naturally occurring synthetic 14-mer peptaibiotic chalciporin A, characterized by a relatively low (≈20%), uncommon proportion of the strongly helicogenic Aib residue. In addition to the unlabeled peptide, we gained in-depth information from the study of two labeled analogs, characterized by one or two residues of the helicogenic, nitroxyl radical-containing TOAC. All three compounds were prepared using the SPPS methodology, which was carefully modified in the course of the syntheses of TOAC-labeled analogs in view of the poorly reactive α-amino function of this very bulky residue and the specific requirements of its free-radical side chain. Read More

    Peptide strand length controls the energetics of self-assembly and morphology of β-sheet fibrils.
    Biopolymers 2017 Nov 11. Epub 2017 Nov 11.
    School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT.
    Self-assembling peptides can be used as versatile, natural, and multifunctional building blocks to produce a variety of well-defined nanostructures, materials and devices for applications in medicine and nanotechnology. Here, we concentrate on the 1D self-assembly of de novo designed Px-2 peptide β-strands into anti-parallel β-sheet tapes and higher order aggregates. We study six members of the Px-2 family, ranging from 3 amino acids (aa) to 13 aa in length, using a range of complementary experimental techniques, computer simulation and theoretical statistical mechanics. Read More

    Release kinetics of somatostatin from self-assembled nanostructured hydrogels.
    Biopolymers 2017 Nov 11. Epub 2017 Nov 11.
    Discipline of Pharmacy, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, 3083, Australia.
    Somatostatin-14 is a native neuropeptide with widespread functions in the body. Self-assembly of somatostatin-14 into amyloid-like nanofibrils has been previously demonstrated in aqueous media. We here hypothesize that the somatostatin nanofibrils can form a stable depot that release monomers in a controlled manner. Read More

    Enhanced tissue adhesiveness of injectable gelatin hydrogels through dual catalytic activity of horseradish peroxidase.
    Biopolymers 2018 Jan 6;109(1). Epub 2017 Nov 6.
    Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea.
    Development of bioadhesives with tunable mechanical strength, high adhesiveness, biocompatibility, and injectability is greatly desirable in all surgeries to replace or complement the sutures and staples. Herein, the dual catalytic activity of horseradish peroxidase is exploited to in situ form the hydroxyphenyl propionic acid-gelatin/thiolated gelatin (GH/GS) adhesive hydrogels including two alternative crosslinks (phenol-phenol and disulfide bonds) with fast gelation (few seconds - several minutes) and improved physicochemical properties. Their elastic moduli increase from 6. Read More

    Esculentin-1a derived peptides kill Pseudomonas aeruginosa biofilm on soft contact lenses and retain antibacterial activity upon immobilization to the lens surface.
    Biopolymers 2017 Oct 31. Epub 2017 Oct 31.
    Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.
    Contact lens (CL) wear is a risk factor for development of microbial keratitis, a vision threatening infection of the eye. Adverse events associated with colonization of lenses, especially by the multi-drug resistant and biofilm forming bacterium Pseudomonas aeruginosa remain a major safety issue. Therefore, novel strategies and compounds to reduce the onset of CL-associated ocular infections are needed. Read More

    The polypeptide biophysics of proline/alanine-rich sequences (PAS): Recombinant biopolymers with PEG-like properties.
    Biopolymers 2018 Jan 27;109(1). Epub 2017 Oct 27.
    Lehrstuhl für Biologische Chemie, Technische Universität München, 85354, Freising (Weihenstephan), Germany.
    PAS polypeptides comprise long repetitive sequences of the small L-amino acids proline, alanine and/or serine that were developed to expand the hydrodynamic volume of conjugated pharmaceuticals and prolong their plasma half-life by retarding kidney filtration. Here, we have characterized the polymer properties both of the free polypeptides and in fusion with the biopharmaceutical IL-1Ra. Data from size exclusion chromatography, dynamic light scattering, circular dichroism spectroscopy and quantification of hydrodynamic and polar properties demonstrate that the biosynthetic PAS polypeptides exhibit random coil behavior in aqueous solution astonishingly similar to the chemical polymer poly-ethylene glycol (PEG). Read More

    Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.
    Biopolymers 2017 Dec 27;107(12). Epub 2017 Oct 27.
    Institute of Physics, Center for Physical Sciences and Technology, Savanoriu 231, Vilnius, 02300, Lithuania.
    Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. Read More

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