7,538 results match your criteria Biopolymers[Journal]


A facile on-bead method for fully symmetric tetra-substituted DOTA derivatizations using peptoid moieties.

Biopolymers 2018 Dec 14:e23249. Epub 2018 Dec 14.

Department of Pharmacological & Pharmaceutical Sciences, University of Houston, 4849 Calhoun Rd, Health Building 2, Room 7033, Houston, Texas 77204-5037.

The metal-chelated 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) has made a significant impact on the field of diagnostic imaging. This imaging mechanism is largely dependent on the four side arm functionalities around the DOTA scaffold. We previously demonstrated the effect of peptoid residue modification on these DOTA side arms, thereby conferring diverse physiochemical properties to the imaging mechanism. Read More

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December 2018

Silk fibroin hydrogels for potential applications in photodynamic therapy.

Biopolymers 2018 Dec 13:e23245. Epub 2018 Dec 13.

Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, Brazil.

In this study, we prepared translucid hydrogels with different concentrations of silk fibroin, extracted from raw silk fibers, and used them as a matrix to incorporate the photosensitizer 5-(4-aminophenyl)-10,15,20-tris-(4-sulphonatophenyl) porphyrin trisodium for application in photodynamic therapy (PDT). The hydrogels obtained were characterized by rheology, spectrophotometry, and scattering techniques to elucidate the factors involved in the formation of the hydrogel, and to characterize the behavior of silk fibroin (SF) after incorporating of the porphyrin to the matrix. The rheology results demonstrated that the SF hydrogels had a shear thinning behavior. Read More

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December 2018
1 Read

Macrocyclization enhances affinity of chemokine-binding peptoids.

Biopolymers 2018 Dec 13:e23244. Epub 2018 Dec 13.

Clemens-Schöpf-Institute of Organic Chemistry and Biochemistry, TU Darmstadt, Darmstadt, Germany.

Peptoids that bind to protein targets can be selected from one-bead-one-compound libraries. Macrocyclization has been often used to increase conformational rigidity and binding affinity in both peptides and peptoids. Here we describe a combined strategy to label and cyclize hexameric peptoid sequences previously identified in a screen against the inflammatory chemokine interleukin-8/CXCL8 that is involved in a number of inflammatory diseases. Read More

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December 2018

Dual-responsive pegylated polypeptoids with tunable cloud point temperatures.

Biopolymers 2018 Dec 8:e23243. Epub 2018 Dec 8.

Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department, College of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, China.

A series of pegylated polypeptoids have been readily synthesized by a strategy combining ring-opening polymerization (ROP) and thiol-yne photoaddition. The polypeptoids simultaneously incorporated branched oligo(ethylene glycol) (OEG) units and thioether bonds in the side-chains. All the polypeptoids are readily soluble in aqueous solution and show reversible thermo-responsive properties. Read More

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December 2018

Characterization of thin gelatin hydrogel membranes with balloon properties for dynamic tissue engineering.

Biopolymers 2018 Dec 8:e23241. Epub 2018 Dec 8.

Department of Micro- and Nanotechnology, The Danish National Research Foundation and Villum Foundation's Center for Intelligent Drug Delivery and Sensing Using Microcontainers and Nanomechanics (IDUN), Technical University of Denmark, Kongens Lyngby, Denmark.

Cell or tissue stretching and strain are present in any in vivo environment, but is difficult to reproduce in vitro. Here, we describe a simple method for casting a thin (about 500 μm) and soft (about 0.3 kPa) hydrogel of gelatin and a method for characterizing the mechanical properties of the hydrogel simply by changing pressure with a water column. Read More

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December 2018
2 Reads

Silk nano-discs: A natural material for cancer therapy.

Biopolymers 2018 Nov;109(11):e23231

Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.

The article demonstrates the crystalline silk nano-discs (CSNs), with well-controlled morphology, which upon magnetization, yields magnetic crystalline silk nano-discs, making both prominent alternatives for replacing metal templates such as gold, silver, and so on in therapeutics and implants. The isolated β-sheet-rich discotic CSNs have ~50 nm diameter, high crystallinity (> 90%), and are insoluble but provide good dispersibility and stability in aqueous solutions. The melt blending-cum-electrospinning of functionalized CSN with poly(lactic acid) results in biocompatible nanofiber-based scaffolds having in vitro cell cytocompatibility with improved cell adhesion and proliferation. Read More

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November 2018
3 Reads

Parametric optimization of polycaprolactone synthesis catalysed by Candida antarctica lipase B using response surface methodology.

Biopolymers 2018 Dec 29;109(12):e23240. Epub 2018 Nov 29.

Graphene & Advanced 2D Materials Group (GAMRG), School of Science & Technology, Sunway University, Subang Jaya, Selangor, Malaysia.

A statistical approach with D-optimal design was used to optimize the process parameters for polycaprolactone (PCL) synthesis. The variables selected were temperature (50°C-110°C), time (1-7 h), mixing speed (50-500 rpm) and monomer/solvent ratio (1:1-1:6). Molecular weight was chosen as response and was determined using matrix-assisted laser desorption/ionization time of flight (MALDI TOF). Read More

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December 2018

Bacterial expression, purification and biophysical characterization of wheat germ agglutinin and its four hevein-like domains.

Biopolymers 2018 Nov 28:e23242. Epub 2018 Nov 28.

Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México, Mexico.

Wheat germ agglutinin (WGA), a chitin binding lectin, has attracted increasing interest because of its unique characteristics such as conformational stability, binding specificity and transcytosis capacity. To pave the way for the study of the molecular basis of WGA's structural stability and binding capacity, as well as to facilitate its use in biomedical and biotechnological developments, we produced recombinant WGA and its 4 isolated hevein-like domains in a bacterial system. All the proteins were expressed as fusion constructs linked to a thioredoxin domain, which was enzymatically or chemically released. Read More

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November 2018

Price of disorder in the lac repressor hinge helix.

Biopolymers 2018 Nov 28:e23239. Epub 2018 Nov 28.

Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, Texas.

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Read More

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November 2018

Effects of Tyr555 and Trp678 on the processivity of cellobiohydrolase A from Ruminiclostridium thermocellum: A simulation study.

Biopolymers 2018 Dec 28;109(12):e23238. Epub 2018 Nov 28.

Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China.

Cellobiohydrolase A from Ruminiclostridium thermocellum (Cbh9A) is a processive exoglucanase from family 9 and is an important cellobiohydrolase that hydrolyzes cello-oligosaccharide into cellobiose. Residues Tyr555 and Trp678 considerably affect catalytic activity, but their mechanisms are still unknown. To investigate how the Tyr555 and Trp678 affect the processivity of Cbh9A, conventional molecular dynamics, steered molecular dynamics, and free energy calculation were performed to simulate the processive process of wild type (WT)-Cbh9A, Y555S mutant, and W678G mutant. Read More

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December 2018
1 Read

Vincenzo Pavone: Friend, mentor and inspiring scientist.

Biopolymers 2018 Aug;109(10):e23234

Department of Chemical Sciences, University of Napoli Federico II, Naples, Italy.

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Amino acid modifications for conformationally constraining naturally occurring and engineered peptide backbones: Insights from the Protein Data Bank.

Biopolymers 2018 Aug 25;109(10):e23230. Epub 2018 Oct 25.

RCSB Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, U.S.A.

Extensive efforts invested in understanding the rules of protein folding are now being applied, with good effect, in de novo design of proteins/peptides. For proteins containing standard α-amino acids alone, knowledge derived from experimentally determined three-dimensional (3D) structures of proteins and biologically active peptides are available from the Protein Data Bank (PDB), and the Cambridge Structural Database (CSD). These help predict and design protein structures, with reasonable confidence. Read More

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August 2018
2 Reads

The effects of fluorescent labels on Aβ aggregation detected by fluorescence correlation spectroscopy.

Biopolymers 2018 Nov 11;109(11):e23237. Epub 2018 Oct 11.

School of Sciences, Beijing Jiaotong University, Beijing, China.

Fluorescence-based methods are promising for measuring amyloid beta (Aβ) oligomers, given their capacity to analyse a sample at the single-molecule level. As the attachment of fluorescent labels may influence the biochemical properties of the Aβ oligomers, the effects of fluorescent labels on Aβ oligomers must be evaluated. In this paper, we compared the impacts of five different fluorescent dyes on the aggregation of Aβ oligomers using fluorescence correlation spectroscopy (FCS). Read More

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November 2018
3 Reads

Jack Aviv: An incredible, generous and humble human being.

Authors:
Shuguang Zhang

Biopolymers 2018 08;109(8)

Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA, U.S.A.

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Discovery of the first self-assembling peptide, study of peptide dynamic behaviors, and G protein-coupled receptors using an Aviv circular dichroism spectropolarimeter.

Authors:
Shuguang Zhang

Biopolymers 2018 Aug;109(8):e23235

Center for Bits and Atoms E15-401, Massachusetts Institute of Technology, Cambridge, Massachusetts.

Circular dichroism (CD) spectroscopy is a useful technique to study the structure and dynamics of peptides, proteins and nucleic acids. CD is particularly useful because sample volumes may be as low as 50 μL, it provides high precision and sensitivity, and it achieves a good signal to noise ratio. CD characterizes molecular conformational changes in real time by finely controlling temperature, pH, and titrating urea and guanidine·HCl which is necessary for studying protein folding. Read More

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August 2018
5 Reads

Association of κ-carrageenan subjected to deep alkaline hydrolysis.

Biopolymers 2018 Sep 30;109(9):e23236. Epub 2018 Sep 30.

St. Petersburg State University, St. Petersburg, Russia.

κ-carrageenan is a linear sulfated anionic gelling polysaccharide obtained from red seaweed algae by an alkaline hydrolysis. We applied static and dynamic light scattering (DLS), capillary viscometry, FT-IR, and electrophoretic DLS to gain insight into the effect of deep alkaline hydrolysis (95 °C, pH = 10 during T = 60, 75, and 90 min) on κ-carrageenan macromolecules in a coil conformation. As DLS of coil-like κ-carrageenans is usually complicated by spurious permanent aggregates, the alkaline hydrolysis of κ-carrageenans has not been studied by DLS. Read More

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September 2018
6 Reads

Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster.

Biopolymers 2018 Aug 11;109(10):e23339. Epub 2018 Sep 11.

Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, California.

De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn clusters. Read More

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Storage stability of electrospun pure gelatin stabilized with EDC/Sulfo-NHS.

Biopolymers 2018 Sep 6;109(9):e23232. Epub 2018 Sep 6.

Department of Chemical, Biochemical and Environmental Engineering, Bioelectronics Laboratory, University of Maryland Baltimore County, Baltimore, Maryland.

With the rapid development of biomimetic polymers for cell-based assays and tissue engineering, crosslinking electrospun nanofibrous biopolymer constructs is of great importance for achieving sustainable and efficient three-dimensional scaffold constructs. Uncrosslinked electrospun gelatin nanofibrous constructs immediately and completely dissolved in aqueous solutions due to their aqueous solubility and poor storage stability. Here, a novel and versatile approach for the fabrication and crosslinking of electrospun gelatin construct with tunable porosity and high aspect ratio nanofibers is presented. Read More

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September 2018

Rational design of a hexameric protein assembly stabilized by metal chelation.

Biopolymers 2018 Aug 6;109(10):e23233. Epub 2018 Sep 6.

School of Molecular Sciences, Arizona State University, Tempe, Arizona.

Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. Read More

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To achieve self-assembled collagen mimetic fibrils using designed peptides.

Biopolymers 2018 Jul;109(7):e23226

Department of Chemistry, Hunter College, Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10065, U.S.A.

It has proven challenging to obtain collagen-mimetic fibrils by protein design. We recently reported the self-assembly of a mini-fibril showing a 35 nm, D-period like, axially repeating structure using the designed triple helix Col108. Peptide Col108 was made by bacterial expression using a synthetic gene; its triple helix domain consists of three pseudo-identical units of amino acid sequence arranged in tandem. Read More

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July 2018
4 Reads

Unveiling the structure of a novel artificial heme-enzyme with peroxidase-like activity: A theoretical investigation.

Biopolymers 2018 Aug 9;109(10):e23225. Epub 2018 Aug 9.

Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Complesso Universitario di M.S.Angelo, via Cintia, Napoli, 80126, Italy.

Fe(III)-Mimochrome VI (MC6) is a recently reported artificial heme-peptide conjugate system with a high peroxidase-like activity. By design, its structure features a five-coordinated Fe(III)-deuteroporphyrin active site, embedded in a compact α-helix-heme-α-helix "sandwich" motif. Up to now, no detailed MC6 structural characterization is available. Read More

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August 2018
1 Read

Jack Aviv: Scientist, instrument wizard, humanist and philanthropist.

Biopolymers 2018 08 9;109(8). Epub 2018 Aug 9.

Linus C. Pauling Distinguished Professor, Dean of Life Sciences, Vice President for Health Science Partnerships, Department of Chemistry and Chemical Biology, The Cancer Institute of New Jersey, Rutgers University, Piscataway, NJ, U.S.A.

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August 2018
1 Read

Effect of ferric citrate on amyloid-beta peptides behavior.

Biopolymers 2018 Jun 13;109(6):e23224. Epub 2018 Jun 13.

Institute for Macromolecular Studies, National Research Council, Genova, 16149, Italy.

Amyloid beta (Aβ) aggregation and oxidative stress are two of the central events in Alzheimer's Disease (AD). Both these phenomena can be caused by the interaction of Aβ with metal ions. In the last years the interaction between Zn , Cu , and Aβ was much studied, but between iron and Aβ it is still little known. Read More

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June 2018
2 Reads

Protein purification by chemo-selective precipitation using thermoresponsive polymers.

Biopolymers 2018 Jun 6;109(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

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June 2018
3 Reads

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 Jul 6;109(7):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

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July 2018
2 Reads

Dissecting the conformational determinants of chitosan and chitlac oligomers.

Biopolymers 2018 Jun 3;109(6):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

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June 2018
22 Reads

PHBV-TiO mats prepared by electrospinning technique: Physico-chemical properties and cytocompatibility.

Biopolymers 2018 May 28;109(5):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

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May 2018
2 Reads

Synthetic polymers as substrates for a DNA-sliding clamp protein.

Biopolymers 2018 May 26;109(5):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

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May 2018
2 Reads

Formation of G-wires, bimolecular and tetramolecular quadruplex: Cation-induced structural polymorphs of G-rich DNA sequence of human SYTX gene.

Biopolymers 2018 May 19;109(5):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

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May 2018
13 Reads

Improvement of functional properties of a thermostable β-glycosidase for milk lactose hydrolysis.

Biopolymers 2018 Aug 2;109(10):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

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August 2018
4 Reads

Structural determinants of ligand binding in truncated hemoglobins: Resonance Raman spectroscopy of the native states and their carbon monoxide and hydroxide complexes.

Biopolymers 2018 Aug 30;109(10):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

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August 2018
5 Reads

Molecular determinants of the interaction of EGCG with ordered and disordered proteins.

Biopolymers 2018 Aug 30;109(10):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

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August 2018
3 Reads

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

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April 2018
4 Reads

Understanding and designing head-to-tail cyclic peptides.

Biopolymers 2018 Aug 12;109(10):e23113. 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

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August 2018
3 Reads

Bromotryptophans and their incorporation in cyclic and bicyclic privileged peptides.

Biopolymers 2018 Aug 12;109(10):e23112. 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

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August 2018
3 Reads

N-methylation in amino acids and peptides: Scope and limitations.

Biopolymers 2018 Aug 12;109(10):e23110. 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

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August 2018
4 Reads

Gold nanoparticles crosslinking by peptides and amino acids: A tool for the colorimetric identification of amino acids.

Biopolymers 2018 Aug 12;109(10):e23111. 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

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August 2018
3 Reads

Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches.

Biopolymers 2018 Aug 9;109(10):e23109. 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

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August 2018
3 Reads

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

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April 2018
3 Reads

Mechanisms of GTP hydrolysis and conformational transitions in the dynamin superfamily.

Biopolymers 2018 02 17;109(2). Epub 2017 Nov 17.

Abteilung Hämatologie/Transfusionsmedizin, Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, Langen, 63225, Germany.

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February 2018
3 Reads

Oxidation catalysis by iron and manganese porphyrins within enzyme-like cages.

Biopolymers 2018 Aug 22;109(10):e23107. 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

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August 2018
14 Reads

"Cooperative collapse" of the denatured state revealed through Clausius-Clapeyron analysis of protein denaturation phase diagrams.

Biopolymers 2018 Aug 19;109(8):e23106. 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 and the urea m-value interconvert through the slope of c versus T, . Read More

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August 2018
5 Reads

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

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March 2018
8 Reads

Counteraction ability of TMAO toward different denaturing agents.

Biopolymers 2018 Aug 7;109(10):e23104. 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

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August 2018
4 Reads

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

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January 2018
6 Reads

The effect of interleukin-8 truncations on its interactions with glycosaminoglycans.

Biopolymers 2018 Aug 27;109(10):e23103. 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

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August 2018
4 Reads

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

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March 2018
5 Reads
2.380 Impact Factor

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

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January 2018
8 Reads

Impact of bistrand abasic sites and proximate orientation on DNA global structure and duplex energetics.

Biopolymers 2018 Aug 11;109(8):e23098. 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

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August 2018
6 Reads
1 Citation
2.385 Impact Factor

A long-lived Aβ oligomer resistant to fibrillization.

Biopolymers 2018 Aug 10;109(8):e23096. 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

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August 2018
6 Reads