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    Highly efficiency antibacterial diblock copolypeptides based on lysine and phenylalanine.
    Biopolymers 2017 Sep 19. 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 Sep 18. 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 µg.ml(-1) . 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

    Temperature-dependent molecular dynamics study reveals an ionic liquid induced 310 - to α-helical switch in a neurotoxin.
    Biopolymers 2017 May;108(3)
    Department of Chemistry, Birla Institute of Technology and Science-Pilani, Hyderabad, Campus, Jawahar Nagar, Shameerpet Mandal, Hyderabad, Telangana, 500078, India.
    Thermal melting and recooling of AuIB, a neurotoxic conopeptide and a highly potent nonaddictive pain reliever is investigated thoroughly in water and an ionic liquid (IL) 1-butyl-3-methylimidazolium Chloride, [Im41 ][Cl] by classical molecular dynamics simulations. Structural evolution of AuIB in water and the IL is observed at different temperatures between 305 and 400 K, to explore how highly viscous ionic solvents affect the peptide structure as compared to conventional solvent water. At 305 K, unlike water, the coercive effect of IL frustrates AuIB secondary structural motifs significantly. Read More

    Single nucleotide polymorphisms and domain/splice variants modulate assembly and elastomeric properties of human elastin. Implications for tissue specificity and durability of elastic tissue.
    Biopolymers 2017 May;107(5)
    Molecular Structure and Function Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada.
    Polymeric elastin provides the physiologically essential properties of extensibility and elastic recoil to large arteries, heart valves, lungs, skin and other tissues. Although the detailed relationship between sequence, structure and mechanical properties of elastin remains a matter of investigation, data from both the full-length monomer, tropoelastin, and smaller elastin-like polypeptides have demonstrated that variations in protein sequence can affect both polymeric assembly and tensile mechanical properties. Here we model known splice variants of human tropoelastin (hTE), assessing effects on shape, polymeric assembly and mechanical properties. Read More

    Biophysical characterization of quaternary pyridinium functionalized polynorbornenes for DNA complexation and their cellular interactions.
    Biopolymers 2017 Apr;107(4)
    TUBITAK Marmara Research Center Genetic Engineering and Biotechnology Institute, Gebze 21, Kocaeli, 41470, Turkey.
    Cationic polymers with hydrophobic side chains have gained great interest as DNA carriers since they form a compact complex with negatively charged DNA phosphate groups and interact with the cell membrane. Amphiphilic polyoxanorbornenes with different quaternary alkyl pyridinium side chains with ethyl-p(OPy2) and hexyl units-p(OPy6) bearing 10 kDa MWT were synthesized by living Ring-Opening Metathesis Polymerization method. The physicochemical characteristics: critical micellar concentration, size distribution, surface charge, and condensation of polymer/DNA complex were investigated. Read More

    Design and characterization of symmetric nucleic acids via molecular dynamics simulations.
    Biopolymers 2017 Apr;107(4)
    Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
    Asymmetry (5'→3') associated with each strand of the deoxyribonucleic acid (DNA) is inherent in the sugar-phosphate backbone connectivity and is essential for replication and transcription. We note that this asymmetry is due to one single chemical bond (C3' to C2' ) in each nucleotide unit, and the absence of this bond results in directionally symmetric nucleic acids. We also discovered that creation of an extra chemical bond (C5' to C2' ) can lead to a symmetric backbone. Read More

    Analysis of ribosomal inter-subunit sites as targets for complementary oligonucleotides.
    Biopolymers 2017 Apr;107(4)
    Centre of New Technologies, University of Warsaw, Warsaw, 02-097, Poland.
    The bacterial ribosome has many functional ribosomal RNA (rRNA) sites. We have computationally analyzed the rRNA regions involved in the interactions between the 30S and 50S subunits. Various properties of rRNA such as solvent accessibility, opening energy, hydrogen bonding pattern, van der Waals energy, thermodynamic stability were determined. Read More

    Substrate specificity of an actively assembling amyloid catalyst.
    Biopolymers 2017 Jan;108(1)
    Freie Universität Berlin Department of Biology, Chemistry, Pharmacy Institute of Chemistry and Biochemistry Berlin, Germany.
    In the presence of Zn(2+) , the catalytic, amyloid-forming peptide Ac-IHIHIQI-NH2 , was found to exhibit enhanced selectivity for hydrophobic p-nitrophenyl ester substrates while in the process of self-assembly. As opposed to the substrate p-nitrophenyl acetate, which was more effectively hydrolyzed with Ac-IHIHIQI-NH2 in its fully fibrillar state, the hydrophobic substrate Z-L-Phe-ONp was converted with a second-order rate constant more than 11-times greater when the catalyst was actively assembling. Under such conditions, Z-L-Phe-ONp hydrolysis proceeded at a greater velocity than the more hydrophilic and otherwise more labile ester Boc-L-Asn-ONp. Read More

    DbpA is a region-specific RNA helicase.
    Biopolymers 2017 Mar;107(3)
    Department of Chemistry, University of Central Florida, 4111 Libra Dr, Physical Sciences Bldg. Room 255, Orlando, FL, 32816-2366, USA.
    DbpA is a DEAD-box RNA helicase implicated in RNA structural rearrangements in the peptidyl transferase center. DbpA contains an RNA binding domain, responsible for tight binding of DbpA to hairpin 92 of 23S ribosomal RNA, and a RecA-like catalytic core responsible for double-helix unwinding. It is not known if DbpA unwinds only the RNA helices that are part of a specific RNA structure, or if DbpA unwinds any RNA helices within the catalytic core's grasp. Read More

    Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides.
    Biopolymers 2017 Jan;107(1):28-34
    Fakultät für Chemie und Biochemie, Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, Bochum, 44801, Germany.
    A set of cyclic tetrapeptides of the general form cyclo (Boc-Cys-Pro-X-Cys-OMe) with X being L-/D-Ala, L-/D-Val, and L-/D-Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs - namely a β-turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β-turn conformational preferences using NMR, VCD, and Raman spectroscopy. Read More

    Effect of polyamines on mechanical and structural properties of Bombyx mori silk.
    Biopolymers 2017 Jan;107(1):20-27
    Department of Biotechnology, GITAM Institute of Science, GITAM University, Visakhapatnam, Andhra Pradesh, India.
    Silkworm, Bombyx mori (B. mori) belongs to the Lepidoptera family. The silk produced from this insect, mulberry silk, gained lot of importance as a fabric. Read More

    Morphological and transport characteristics of swollen chitosan-based proton exchange membranes studied by molecular modeling.
    Biopolymers 2017 Jan;107(1):5-19
    Parker H, Petit Institute for Bioengineering and Bioscience, G.W. Woodruff School of Mechanical, Engineering, Georgia Institute of Technology, Atlanta, 30332, GA.
    Chitosan biopolymer has been extensively applied in direct methanol fuel cells (DMFCs) as a potential replacement to conventional Nafion membrane for its considerably reduced methanol crossover. Here, we computationally explored the influences of methanol concentration, temperature, and pH parameters upon the nanostructure and dynamics, particularly the methanol crossover, in chitosan proton-exchange membrane (PEM) through molecular dynamics simulations. Theoretical results demonstrated the increased swelling and radius of gyration of chitosan chains at higher concentrations. Read More

    A parallel stranded G-quadruplex composed of threose nucleic acid (TNA).
    Biopolymers 2017 Mar;107(3)
    Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697.
    G-rich sequences can adopt four-stranded helical structures, called G-quadruplexes, that self-assemble around monovalent cations like sodium (Na(+) ) and potassium (K(+) ). Whether similar structures can be formed from xeno-nucleic acid (XNA) polymers with a shorter backbone repeat unit is an unanswered question with significant implications on the fold space of functional XNA polymers. Here, we examine the potential for TNA (α-l-threofuranosyl nucleic acid) to adopt a four-stranded helical structure based on a planar G-quartet motif. Read More

    DNA-doxorubicin interaction: New insights and peculiarities.
    Biopolymers 2017 Mar;107(3)
    Laboratório de Física Biológica, Departamento de Física, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil.
    We have investigated the interaction of the DNA molecule with the anticancer drug doxorubicin (doxo) by using three different experimental techniques: single molecule stretching, single molecule imaging, and dynamic light scattering. Such techniques allowed us to get new insights on the mechanical behavior of the DNA-doxo complexes as well as on the physical chemistry of the interaction. First, the contour length data obtained from single molecule stretching were used to extract the physicochemical parameters of the DNA-doxo interaction under different buffer conditions. Read More

    Identification of peptide sequences that selectively bind to pentaerythritol trinitrate hemisuccinate-a surrogate of PETN, via phage display technology.
    Biopolymers 2017 Mar;108(2)
    Department of Civil & Chemical Engineering Materials Science & Engineering Program, Youngstown State University, Youngstown, Ohio.
    The present research investigates the identification of amino acid sequences that selectively bind to a pentaerythritol tetranitrate (PETN) explosive surrogate. Through the use of a phage display technique and enzyme-linked immunosorbent assays (ELISA), a peptide library was tested against pentaerythritol trinitrate hemisuccinate (PETNH), a surrogate of PETN, to screen for those with amino acids having affinity toward the explosive. The results suggest that the library contains peptides selective to PETNH. Read More

    Collision-induced thermochemistry of reactions of dissociation of glycyl-homopeptides-An experimental and theoretical analysis.
    Biopolymers 2017 Feb;107(2):80-89
    Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221, Dortmund, Nordrhein-Westfalen, Deutschland.
    The research draws on experimental and theoretical data about energetics and kinetics of mass spectrometric (MS) reactions of glycyl homopenta- (G5) and glycyl homohexapeptides (G6). It shows the great applicability of the methods of quantum chemistry to predict MS profile of peptides using energetics of collision induced dissociation (CID) fragment species. Mass spectrometry is among irreplaceable methods, providing unambiguous qualitative, quantitative and structural information about analytes, applicable to many scientific areas like environmental chemistry; food chemistry; medicinal chemistry; and more. Read More

    Optimization of a β-sheet-cap for long loop closure.
    Biopolymers 2017 Mar;107(3)
    Department of Chemistry, University of Washington, Seattle, Washington.
    Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable β-sheet structures, including features that allow us to probe these questions. Read More

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