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    Β-cyclodextrin encapsulated polyphenols as effective antioxidants.
    Biopolymers 2017 Nov 15. 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 2017 Nov 15. 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 2017 Nov 6. 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 2017 Oct 27. 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

    Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation.
    Biopolymers 2017 Oct 25. Epub 2017 Oct 25.
    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 hyperthermophilic Ssh10b from Sulfolobus shibatae is a member of the Sac10b family, which binds RNA in vivo as a physiological substrate, and it has been postulated to play a key role in chromosomal organization in Archaea. Even though the crystal structure of Ssh10b-RNA was resolved successively by X-ray diffraction (Protein Data Bank [PDB] code: 3WBM), the detailed dynamic characteristics of Ssh10b-RNA are still unclear. In this study, molecular dynamics (MDs) simulations at 6 temperatures (300, 350, 375, 400, 450, and 500 K) and molecular mechanics Generalized-Born surface area (MM-GB/SA) free energy calculations were performed to investigate the mechanism of how Ssh10b protects and stabilizes RNA. Read More

    Effect of heavy water on the conformational stability of globular proteins.
    Biopolymers 2017 Oct 25. Epub 2017 Oct 25.
    Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, Benevento, 82100, Italy.
    It is well established from the experimental point of view that the native state of globular proteins is more stable in heavy water than in water. No robust explanation, however, has been provided up to now. The application of the theoretical approach, originally devised to rationalize the general occurrence of cold denaturation, indicates that the magnitude of the solvent-excluded volume effect is slightly smaller in heavy water than in water and cannot explain the observed protein stabilization. Read More

    Polypeptoid polymers: Synthesis, characterization, and properties.
    Biopolymers 2017 Oct 25. Epub 2017 Oct 25.
    Department of Chemistry and Macromolecular Studies Group, Louisiana State University, Baton Rouge, 70803, Los Angeles.
    Polypeptoids, a class of peptidomimetic polymers, have emerged at the forefront of macromolecular and supramolecular science and engineering as the technological relevance of these polymers continues to be demonstrated. The chemical and structural diversity of polypeptoids have enabled access to and adjustment of a variety of physicochemical and biological properties (eg, solubility, charge characteristics, chain conformation, HLB, thermal processability, degradability, cytotoxicity and immunogenicity). These attributes have made this synthetic polymer platform a potential candidate for various biomedical and biotechnological applications. Read More

    Synthesis and structure analysis of ferrocene-containing pseudopeptides.
    Biopolymers 2017 Oct 23. Epub 2017 Oct 23.
    Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna - Via Selmi, 2, Bologna, 40126, Italy.
    Ferrocene with its aromaticity and facile redox properties is an attractive moiety to be incorporated into functional moieties. Medicinal applications of ferrocene are well known and ferrocene itself shows cytotoxic and antianemic properties. In this article, we will describe the synthesis and the structure analysis of two pseudopeptides containing a ferrocene moiety as N-terminal group. Read More

    Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA).
    Biopolymers 2017 Dec 23;107(12). Epub 2017 Oct 23.
    Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
    In this work, we have studied the interaction between the anticancer drug doxorubicin (doxo) and condensed DNA, using optical tweezers. To perform this task, we use the protein bovine serum albumin (BSA) in the working buffer to mimic two key conditions present in the real intracellular environment: the condensed state of the DNA and the abundant presence of charged macromolecules in the surrounding medium. In particular, we have found that, when doxo is previously intercalated in disperse DNA, the drug hinders the DNA condensation process upon the addition of BSA in the buffer. Read More

    Process development of a FGF21 protein-antibody conjugate.
    Biopolymers 2017 Sep 26. Epub 2017 Sep 26.
    Pfizer Inc.-BioTherapeutics Pharmaceutical Sciences: Bioprocess R&D, 700 Chesterfield Parkway West, Chesterfield, Missouri, 63017.
    A scalable, viable process was developed for the Fibroblast Growth Factor 21 (FGF21) protein-antibody conjugate, CVX-343, an extended half-life therapeutic for the treatment of metabolic disease. CVX-343 utilizes the CovX antibody scaffold technology platform that was specifically developed for peptide and protein half-life extension. CVX-343 is representative of a growing number of complex novel peptide- and protein-based bioconjugate molecules currently being explored as therapeutic candidates. Read More

    Antimicrobial activity of lysozyme isoforms: Key molecular features.
    Biopolymers 2017 Dec 25;107(12). Epub 2017 Sep 25.
    STLO, UMR1253, Agrocampus Ouest, INRA, Rennes, F-35, France.
    Increasing bacterial resistance towards antibiotics has stimulated research for novel antimicrobials. Proteins acting on bacterial membranes could be a solution. Lysozyme has been proven active against E. Read More

    Highly efficient antibacterial diblock copolypeptides based on lysine and phenylalanine.
    Biopolymers 2017 Nov 19;107(11). Epub 2017 Sep 19.
    School of Materials Science and Engineering, Tongji University, 4800 Caoan Road, Shanghai, 201804, China.
    A series of amphiphilic diblock copolypeptides (K30 -b-F15 , K30 -b-F30 , and K30 -b-F45 ) were synthesized via N-carboxy-α-amino-anhydride ring-opening polymerization. The copolypeptides had excellent antibacterial efficacy to both Gram positive (S. aureus) and Gram negative (E. Read More

    Thermal melt circular dichroism spectroscopic studies for identifying stabilising amphipathic molecules for the voltage-gated sodium channel NavMs.
    Biopolymers 2017 Sep 19. Epub 2017 Sep 19.
    Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom.
    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. Read More

    Structural insight into the XTACC3/XMAP215 interaction from CD and NMR studies on model peptides.
    Biopolymers 2017 Nov 18;107(11). Epub 2017 Sep 18.
    Department of Biological Physical Chemistry, IQFR-CSIC, Madrid, 28006, Spain.
    TACC3 is a centrosomal adaptor protein that plays important roles during mitotic spindle assembly. It interacts with chTOG/XMAP215, which catalyzes the addition of tubulin dimers during microtubule growth. A 3D coiled-coil model for this interaction is available but the structural details are not well described. Read More

    Synthesis and gelation of copolypept(o)ides with random and block structure.
    Biopolymers 2017 Oct 18;107(10). Epub 2017 Aug 18.
    Shanghai Key Laboratory of Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai, 200237, China.
    Copolypept(o)ides of polysarcosine (PSar) and poly(N-isopropyl-L-glutamine) (PIGA) with random and block sequence structures were synthesized by ring-opening polymerization (ROP) of sarcosine N-carboxyanhydrides (Sar-NCA) and γ-benzyl-l-glutamate N-carboxyanhydrides (BLG-NCA) and post modification. With different distribution of Sar along the main chain, H-bonding pattern and secondary structure of polypeptides were turned, as well as aggregation and gelation behavior. Both copolypept(o)ides formed hydrogels above their critical gelation concentrations (CGCs) without thermo-sensitivity, which was normally reserved for PEG copolypeptides (eg, PEG-b-PIGA). Read More

    Design of modular dual enzyme-responsive peptides.
    Biopolymers 2017 Sep 11;108(5). Epub 2017 Aug 11.
    Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, 607 Charles E. Young Drive East, Los Angeles, California, 90095.
    Dual enzyme-responsive peptides were synthesized by masking the ɛ-amine of lysine with various enzyme substrates. Enzymatic cleavage of these sequences unmasked the ɛ-amine, allowing for further digestion by a second enzyme, which was monitored colorimetrically. This modular peptide design should provide substrates for a large combination of clinically relevant enzymes. Read More

    Homo- and heteropolymer self-assembly of recombinant trichocytic keratins.
    Biopolymers 2017 Oct 24;107(10). Epub 2017 Jul 24.
    Department of Chemistry and Macromolecules Innovation Institute, Virginia Tech, Blacksburg, Virginia, 24060.
    In the past two decades, keratin biomaterials have shown impressive results as scaffolds for tissue engineering, wound healing, and nerve regeneration. In addition to its intrinsic biocompatibility, keratin interacts with specific cell receptors eliciting beneficial biochemical cues. However, during extraction from natural sources, such as hair and wool fibers, natural keratins are subject to extensive processing conditions that lead to formation of unwanted by-products. Read More

    Ensemble characterization of an intrinsically disordered FG-Nup peptide and its F>A mutant in DMSO-d6.
    Biopolymers 2017 Jul 22. Epub 2017 Jul 22.
    Department of Chemistry, California State University, Fresno, California, 93740.
    Intrinsically disordered proteins (IDP) lack a well-defined 3D-structure under physiological conditions, yet, the inherent disorder represented by an ensemble of conformation plays a critical role in many cellular and regulatory processes. Nucleoporins, or Nups, are the proteins found in the nuclear pore complex (NPC). The central pore of the NPC is occupied by Nups, which have phenylalanine-glycine domain repeats and are intrinsically disordered, and therefore are termed FG-Nups. Read More

    Fusion of plectasin derivative NZ2114 with hydrophilic random coil polypeptide: Recombinant production in Pichia pastoris and antimicrobial activity against clinical strain MRSA.
    Biopolymers 2017 Jun 12. Epub 2017 Jun 12.
    Centro de Análises, Proteômicas e Bioquímicas, Programa de Pós Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, Brazil.
    One of the roadblocks towards the practical use of antimicrobial peptides for medical use is their relatively high cost when synthesized chemically. Effective recombinant production has only been successful in some cases, such as the previously reported production in Pichia pastoris of the antimicrobial plectasin derivative peptide NZ2114. The same production host has also been used extensively to produce so-called protein-polymers: sequences that consist of repetitions of simple amino acid motifs found in structural proteins such as collagen and elastin, and that can be designed to self-assemble in micelles, fibers and hydrogels. Read More

    Self-Assembly of t-Butyloxycarbonyl Protected Dipeptide Methyl Esters Composed of Leucine, Isoleucine and Valine into Highly Organized Structures from Alcohol and Aqueous Alcohol Mixtures.
    Biopolymers 2017 Jun 7. Epub 2017 Jun 7.
    CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500007, India.
    Short peptides composed of phenylalanine and sequences derived from amyloidogenic peptides have the ability to self-assemble to form nanostructures including hydrogels. The self-assembly of peptides composed of only hydrophobic amino acids and aliphatic protecting groups have not been investigated in detail. We have examined various aspects of nanostructures formed by N-terminal t-butyloxycarbonyl-protected aliphatic dipeptide methyl esters dissolved in various solvents. Read More

    Activity of synthetic peptides against Chlamydia.
    Biopolymers 2017 May 27. Epub 2017 May 27.
    Centre of Proteomics and Biochemistry, Catholic University of Brasilia, Brasilia, DF, Brazil.
    The in vitro activity of six synthetic peptides against 36 strains of Chlamydia from different origins was investigated. Clavanin MO proved to be the most active peptide, reducing the inclusion number of all Chlamydia strains from 8 different species tested by ≥50% at 10 µ . Read More

    Fabrication of elastomeric silk fibers.
    Biopolymers 2017 Sep;107(9)
    Department of Biomedical Engineering, Tufts University, Medford, Massachusetts.
    Methods to generate fibers from hydrogels, with control over mechanical properties, fiber diameter, and crystallinity, while retaining cytocompatibility and degradability, would expand options for biomaterials. Here, we exploited features of silk fibroin protein for the formation of tunable silk hydrogel fibers. The biological, chemical, and morphological features inherent to silk were combined with elastomeric properties gained through enzymatic crosslinking of the protein. Read More

    Design and chemical syntheses of potent matriptase-2 inhibitors based on trypsin inhibitor SFTI-1 isolated from sunflower seeds.
    Biopolymers 2017 May 27. Epub 2017 May 27.
    Department of Molecular Biochemistry, Faculty of Chemistry University of Gdansk, ul. Wita Stwosza 63, 80-308, Gdansk, Poland.
    Matriptase-2 plays a pivotal role in keeping iron concentrations within a narrow physiological range in humans. The opportunity to reduce matriptase-2 proteolytic activity may open a novel possibility to treat iron overload diseases, such as hereditary hemochromatosis and thalassemia. Here, we present 23 new analogues of trypsin inhibitor SFTI-1 designed to inhibit human matriptase-2. Read More

    Inhibition of melanoma metastasis by dual-peptide PLGA NPS.
    Biopolymers 2017 Sep;108(5)
    Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, SP, Brazil.
    Despite the positive results observed in vitro and in vivo, clinical trials with bioactive peptides are generally hampered by their fast degradation in the biological system. Two bioactive peptides, P20 (CSSRTMHHC) and the combined peptide C (CVNHPAFACGYGHTMYYHHYQHHL) have been identified as anticancer therapeutics. Combined peptide C consists of peptide C (CVNHPAFAC), a tumor-homing peptide, conjugated to the antiangiogenic peptide HTMYYHHYQHHL with a GYG. Read More

    Structural and functional study of a simple, rapid, and label-free DNAzyme-based DNA biosensor for optimization activity.
    Biopolymers 2017 Oct;107(10)
    Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
    Peroxidase-mimicking DNAzyme has a potential to self-assemble into a G-quadruplex and shows peroxidase activity. In comparison to proteins, peroxidase-mimicking DNAzyme is less expensive and more stable. Herein, it is used in fabricating non-labeling biosensors. Read More

    Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants.
    Biopolymers 2017 Aug;107(8)
    Centro de Investigación en Dinámica Celular-IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México.
    Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Read More

    Alanine scan of the opioid peptide dynorphin B amide.
    Biopolymers 2017 Sep;108(5)
    Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas, 66045.
    To date structure-activity relationship (SAR) studies of the dynorphins (Dyn), endogenous peptides for kappa opioid receptors (KOR), have focused almost exclusively on Dyn A with minimal studies on Dyn B. While both Dyn A and Dyn B have identical N-terminal sequences, their C-terminal sequences differ, which could result in differences in pharmacological activity. We performed an alanine scan of the non-glycine residues up through residue 11 of Dyn B amide to explore the roles of these side chains in the activity of Dyn B. Read More

    Lysine to arginine mutagenesis of chlorotoxin enhances its cellular uptake.
    Biopolymers 2017 Sep;108(5)
    Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
    Chlorotoxin (CTX), a disulfide-rich peptide from the scorpion Leiurus quinquestriatus, has several promising biopharmaceutical properties, including preferential affinity for certain cancer cells, high serum stability, and cell penetration. These properties underpin its potential for use as a drug design scaffold, especially for the treatment of cancer; indeed, several analogs of CTX have reached clinical trials. Here, we focus on its ability to internalize into cells-a trait associated with a privileged subclass of peptides called cell-penetrating peptides-and whether it can be improved through conservative substitutions. Read More

    Identification and characterization of multifunctional cationic and amphipathic peptides from soybean proteins.
    Biopolymers 2017 Jul;108(4)
    Department of Materials Science and Technology, Graduate School of Science and Technology, Niigata University, Niigata, 950-2181, Japan.
    In this study, we identified and chemically synthesized three cationic and amphipathic peptides (Glycinin-17, BCAS-16, and BCBS-11) from soybean proteins. These peptides had high isoelectric points, high positive net charges, and included multiple hydrophobic amino acids. Subsequently, we identified multiple functions of these peptides, including antimicrobial, lipopolysaccharide-neutralizing, and angiogenic activities, and examined their cytotoxic activities against mammalian red blood cells. Read More

    Tau peptides and tau mutant protein aggregation inhibition by cationic polyethyleneimine and polyarginine.
    Biopolymers 2017 Sep;107(9)
    Department of Mechanical Engineering (Bioengineering program), University of Michigan-Dearborn, Dearborn, Michigan, 48128.
    Tau protein plays a major role in Alzheimer's disease. The tau protein loses its functionality by self-aggregation due to the two six-amino acid sequences VQIVYK and VQIINK of the protein. Hence it is imperative to find therapeutics that could inhibit the self-aggregation of this tau peptide fragments. Read More

    Modeling interactions between a β-O-4 type lignin model compound and 1-allyl-3-methylimidazolium chloride ionic liquid.
    Biopolymers 2017 Aug;107(8)
    Key Lab of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, People's Republic of China.
    Aiming at understanding the molecular mechanism of the lignin dissolution in imidazolium-based ionic liquids (ILs), this work presents a combined quantum chemistry (QC) calculation and molecular dynamics (MD) simulation study on the interaction of the lignin model compound, veratrylglycerol-β-guaiacyl ether (VG) with 1-allyl-3-methylimidazolium chloride ([Amim]Cl). The monomer of VG is shown to feature a strong intramolecular hydrogen bond, and its dimer is indicated to present important π-π stacking and intermolecular hydrogen bonding interactions. The interactions of both the cation and anion of [Amim]Cl with VG are shown to be stronger than that between the two monomers, indicating that [Amim]Cl is capable of dissolving lignin. Read More

    Inhibition of polyglutamine aggregation by SIMILAR huntingtin N-terminal sequences: Prospective molecules for preclinical evaluation in Huntington's disease.
    Biopolymers 2017 Jul;108(4)
    Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
    The mutant huntingtin protein (mHtt) fragments with expanded polyglutamine sequence forms microscopically visible aggregates in neurons, a hallmark of Huntington's disease (HD). The aggregation process and aggregates are possible targets of therapeutic intervention in HD. Owing to the lack of treatment and cure, the patients die within 15-20 years after the disease onset. Read More

    Hydrophobic-hydrophilic forces in protein folding.
    Biopolymers 2017 Aug;107(8)
    Department of Physical Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
    The process of protein folding is obviously driven by forces exerted on the atoms of the amino-acid chain. These forces arise from interactions with other parts of the protein itself (direct forces), as well as from interactions with the solvent (solvent-induced forces). We present a statistical-mechanical formalism that describes both these direct and indirect, solvent-induced thermodynamic forces on groups of the protein. Read More

    On-demand tuned hazard free elastomeric composites: A green approach.
    Biopolymers 2017 Jul;107(7)
    Indian Institute of Technology, Rubber Technology Centre, Kharagpur, 721302, India.
    Rising ecological concerns and depletion of the potentially harmful environmental impacts caused by rubber products, are of prime importance in the industry. Therefore, implementation of sustainable greener materials is required to minimize the detrimental influences. In this research, we investigated the beneficial influence of naturally derived bio-resin toward the effects of association with Zinc Oxide Nanoparticles in highly dispersible silica (HDS) reinforced Natural rubber (NR)/Epoxidized Natural Rubber (ENR)-based composites. Read More

    Magnesium and molecular crowding of the cosolutes stabilize the i-motif structure at physiological pH.
    Biopolymers 2017 Jul;107(7)
    Department of Chemistry, Nucleic Acids Research laboratory, University of Delhi (North Campus), Delhi, 110007, India.
    Most of the important genomic regions, especially the G,C rich gene promoters, consist of sequences with potential to form G,C-tetraplexes on both the DNA strands. In this study, we used three C-rich oligonucleotides (11Py, 21Py, and HTPy), of which 11Py and 21Py are located at various transcriptional regulatory elements of the human genome while HTPy sequence is a C-rich strand of human telomere sequence. These C-rich oligonucleotides formed i-motif structures, verified by Circular Dichroism (CD), UV absorption melting experiments, and native gel electrophoresis. Read More

    Structural changes in cartilage and collagen studied by high temperature Raman spectroscopy.
    Biopolymers 2017 Jun;107(6)
    Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, United Kingdom.
    Understanding the high temperature behavior of collagen and collagenous tissue is important for surgical procedures and biomaterials processing for the food, pharmaceutical, and cosmetics industries. One primary event for proteins is thermal denaturation that involves unfolding the polypeptide chains while maintaining the primary structure intact. Collagen in the extracellular matrix of cartilage and other connective tissue is a hierarchical material containing bundles of triple-helical fibers associated with water and proteoglycan components. Read More

    Mesoscopic structure of pectin in solution.
    Biopolymers 2017 Jun;107(6)
    Department of Biological Sciences, University of Huddersfield, HD1 3DH, United Kingdom.
    Mesoscopic structure of pectin with different molecular characteristics was investigated by means of small angle X-ray scattering (SAXS), electrokinetic measurements and data modelling. The influence of a broad range of pH (2-7) on chain conformation in the dilute and semi-diluted regime was investigated. Scattering data and concomitant analysis revealed two length scales at all environmental conditions studied. Read More

    DNA interaction with DAPI fluorescent dye: Force spectroscopy decouples two different binding modes.
    Biopolymers 2017 May;107(5)
    Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Minas Gerais, Brazil.
    In this work, we use force spectroscopy to investigate the interaction between the DAPI fluorescent dye and the λ-DNA molecule under high (174 mM) and low (34 mM) ionic strengths. Firstly, we have measured the changes on the mechanical properties (persistence and contour lengths) of the DNA-DAPI complexes as a function of the dye concentration in the sample. Then, we use recently developed models in order to connect the behavior of both mechanical properties to the physical chemistry of the interaction. Read More

    Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids.
    Biopolymers 2017 Jul;108(4)
    Department of Physics, Durham University, South Road, Durham, DH1 3LE, United Kingdom.
    Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP-HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. Read More

    Hydrocarbon-stapled lipopeptides exhibit selective antimicrobial activity.
    Biopolymers 2017 May;108(3)
    Department of Chemistry and Biochemistry, Southwestern University, Georgetown, Texas, 78626.
    Antimicrobial peptides (AMPs) occur widely in nature and have been studied for their therapeutic potential. AMPs are of interest due to the large number of possible chemical structural combinations using natural and unnatural amino acids, with varying effects on their biological activities. Using physicochemical properties from known naturally occurring amphipathic cationic AMPs, several hydrocarbon-stapled lipopeptides (HSLPs) were designed, synthesized, and tested for antimicrobial properties. Read More

    Antimicrobial activity and mechanism of action of a thionin-like peptide from Capsicum annuum fruits and combinatorial treatment with fluconazole against Fusarium solani.
    Biopolymers 2017 May;108(3)
    Laboratório de Fisiologia e Bioquímica de Microrganismos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio De Janeiro, 28013-602, Brazil.
    Many Fusarium species are able to cause severe infections in plants as well as in animals and humans. Therefore, the discovery of new antifungal agents is of paramount importance. CaThi belongs to the thionins, which are cationic peptides with low molecular weights (∼5 kDa) that have toxic effects against various microorganisms. Read More

    Acceleration of protein backbone NMR assignment by combinatorial labeling: Application to a small molecule binding study.
    Biopolymers 2017 May;107(5)
    Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt, 60438, Germany.
    Selective labeling with stable isotopes has long been recognized as a valuable tool in protein NMR to alleviate signal overlap and sensitivity limitations. In this study, combinatorial (15) N-, (13) C(α) -, and (13) C'-selective labeling has been used during the backbone assignment of human cyclophilin D to explore binding of an inhibitor molecule. Using a cell-free expression system, a scheme that involves (15) N, 1-(13) C, 2-(13) C, fully (15) N/(13) C, and unlabeled amino acids was optimized to gain a maximum of assignment information from three samples. Read More

    Design, synthesis, and biological evaluation of cyclic peptidotriazoles derived from BPC194 as novel agents for plant protection.
    Biopolymers 2017 May;108(3)
    LIPPSO, Department of Chemistry, University of Girona, Campus Montilivi, 17003, Girona, Spain.
    The search for novel antimicrobial agents to be used for plant protection has prompted us to design analogues incorporating non-natural amino acids. Herein, we designed and synthesized cyclic peptidotriazoles derived from the lead antimicrobial cyclic peptide c(Lys-Lys-Leu(3) -Lys-Lys(5) -Phe-Lys-Lys-Leu-Gln) (BPC194). In particular, Leu(3) and Lys(5) were replaced by a triazolyl alanine, a triazolyl norleucine or a triazolyl lysine. Read More

    Conformational properties and aggregation of homo-oligomeric β(3) (R)-valine peptides in organic solvents.
    Biopolymers 2017 May;108(3)
    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India.
    The conformational characteristics of protected homo-oligomeric Boc-[β(3) (R)Val]n -OMe, n = 1, 2, 3, 4, 6, 9, and 12 have been investigated in organic solvents using nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) absorption spectroscopy and circular dichroism (CD) methods. The detailed (1) H NMR analysis of Boc-[β(3) (R)Val]12 -OMe reveals that the peptide aggregates extensively in CDCl3 , but is disaggregated in 20%, (v/v) dimethyl sulfoxide (DMSO) in CDCl3 and in CD3 OH. Limited assignment of the N-terminus NH groups, together with solvent dependence of NH chemical shifts and temperature coefficients provides evidence for 14-helix conformation in the 12-residue peptide. Read More

    Single-step purification of cyclotides using affinity chromatography.
    Biopolymers 2017 May;108(3)
    Division of Pharmacognosy, Uppsala University, Biomedical Center, Uppsala, SE, 75123, Sweden.
    Cyclotides are considered promising scaffolds for drug development owing to their inherent host defence activities and highly stable structure, defined by the cyclic cystine knot. These proteins are expressed as complex mixtures in plants. Although several methods have been developed for their isolation and analysis, purification of cyclotides is still a lengthy process. Read More

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