7,563 results match your criteria Biopolymers[Journal]


A novel numerical model for protein sequences analysis based on spherical coordinates and multiple physicochemical properties of amino acids.

Biopolymers 2019 Apr 12:e23282. Epub 2019 Apr 12.

Department of Biomedical Engineering, College of Engineering, and Centre for Quantitative Biology, Peking University, Beijing, China.

How to characterize short protein sequences to make an effective connection to their functions is an unsolved problem. Here we propose to map the physicochemical properties of each amino acid onto unit spheres so that each protein sequence can be represented quantitatively. We demonstrate the usefulness of this representation by applying it to the prediction of cell penetrating peptides. Read More

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http://dx.doi.org/10.1002/bip.23282DOI Listing

Helical side chain chemistry of a peptoid-based SP-C analogue: Balancing structural rigidity and biomimicry.

Biopolymers 2019 Apr 10:e23277. Epub 2019 Apr 10.

Department of Bioengineering, Stanford University, Stanford, California.

Surfactant protein C (SP-C) is an important constituent of lung surfactant (LS) and, along with SP-B, is included in exogenous surfactant replacement therapies for treating respiratory distress syndrome (RDS). SP-C's biophysical activity depends upon the presence of a rigid C-terminal helix, of which the secondary structure is more crucial to functionality than precise side-chain chemistry. SP-C is highly sequence-conserved, suggesting that the β-branched, aliphatic side chains of the helix are also important. Read More

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http://dx.doi.org/10.1002/bip.23277DOI Listing

Collagen type I and hyaluronic acid based hybrid scaffolds for heart valve tissue engineering.

Biopolymers 2019 Apr 8:e23278. Epub 2019 Apr 8.

Department of Materials, University of Oxford, Oxford, UK.

Tissue engineers have achieved limited success so far in designing an ideal scaffold for aortic valve; scaffolds lack in mechanical compatibility, appropriate degradation rate, and microstructural similarity. This paper, therefore, has demonstrated a carbodiimide-based sequential crosslinking technique to prepare aortic valve extracellular matrix mimicking (ECM) hybrid scaffolds from collagen type I and hyaluronic acid (HA), the building blocks of heart valve ECM, with tailorable crosslinking densities. Swelling studies revealed that crosslinking densities of parent networks increased with increasing the concentration of the crosslinking agents whereas crosslinking densities of hybrid scaffolds averaged from those of parent collagen and HA networks. Read More

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http://dx.doi.org/10.1002/bip.23278DOI Listing
April 2019
1 Read

Antibacterial mechanisms of GN-2 derived peptides and peptoids against Escherichia coli.

Biopolymers 2019 Apr 5:e23275. Epub 2019 Apr 5.

Department of Science and Environment, Roskilde University, Roskilde, Denmark.

Escherichia coli is the main etiological agent of urinary trait infections, able to form biofilms in indwelling devices, resulting in chronic infections which are refractory to antibiotics treatment. In this study, we investigated the antimicrobial and anti-biofilm properties exerted against E. coli ATCC 25922, by a set of peptoids and peptides modeled upon the peptide GN-2, previously reported as a valid antimicrobial agent. Read More

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http://dx.doi.org/10.1002/bip.23275DOI Listing

Toward a clinical antifungal peptoid: Investigations into the therapeutic potential of AEC5.

Biopolymers 2019 Apr 2:e23276. Epub 2019 Apr 2.

Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee.

Cryptococcus neoformans is a fungal pathogen that causes cryptococcal meningitis in immunocompromised individuals. Existing antifungal treatment plans have high mammalian toxicity and increasing drug resistance, demonstrating the dire need for new, nontoxic therapeutics. Antimicrobial peptoids are one alternative to combat this issue. Read More

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http://dx.doi.org/10.1002/bip.23276DOI Listing

PEGylated PAMAM dendrimers loading oxaliplatin with prolonged release and high payload without burst effect.

Biopolymers 2019 Mar 21:e23272. Epub 2019 Mar 21.

Biomaterials and Nanotechnology Research Group, Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.

Oxaliplatin (OXA) was coupled to PEGylated polyamidoamine dendrimers of fourth generation (G4-PEG@OXA) in the comparison to PEGylated ones of odd generation (G3.5-PEG@OXA). Proton nuclear magnetic resonance and Fourier-transform infrared spectroscopy were used to confirm the successful incorporation of OXA as well as the synthesis of carrier systems. Read More

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March 2019
5 Reads

NCα-gem-dimethylated peptoid side chains: A novel approach for structural control and peptide sequence mimetics.

Biopolymers 2019 Mar 21:e23273. Epub 2019 Mar 21.

Université Clermont Auvergne, CNRS, SIGMA Clermont, ICCF, F-63000 Clermont-Ferrand, France.

The design of linear peptoid oligomers adopting well-defined secondary structures while mimicking defined peptide primary sequences is a major challenge in the context of drug discovery. To this end, chemists have developed cis-inducing peptoid side chains to build robust polyproline type I helices. However, the number of efficient examples remains scarce and chemical diversity accessible through the use of these side chains is limited. Read More

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http://dx.doi.org/10.1002/bip.23273DOI Listing

Peptoid drug discovery and optimization via surface X-ray scattering.

Biopolymers 2019 Mar 20:e23274. Epub 2019 Mar 20.

Center for the Molecular Study of Condensed Soft Matter and Department of Physics, Illinois Institute of Technology, Chicago, Illinois.

Synthetic polymers mimicking antimicrobial peptides have drawn considerable interest as potential therapeutics. N-substituted glycines, or peptoids, are recognized by their in vivo stability and ease of synthesis. Peptoids are thought to act primarily on the negatively charged lipids that are abundant in bacterial cell membranes. Read More

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Local and long range potentials for heparin-protein systems for coarse-grained simulations.

Biopolymers 2019 Mar 13:e23269. Epub 2019 Mar 13.

Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.

Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Read More

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http://dx.doi.org/10.1002/bip.23269DOI Listing

Phosphoramitoids-A submonomer approach to sequence defined N-substituted phosphoramidate polymers.

Biopolymers 2019 Mar 13:e23268. Epub 2019 Mar 13.

The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California.

There is a growing interest in new methods to generate bio-inspired, chemically diverse, sequence-defined synthetic polymers. Solid-phase submonomer approaches offer facile access to these types of materials, since they take advantage of readily available synthons. Submonomer approaches to date have been applied to peptidomimetics with oligo-amide backbones. Read More

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http://doi.wiley.com/10.1002/bip.23268
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March 2019
8 Reads

Stereochemistry of polypeptoid chain configurations.

Biopolymers 2019 Mar 5:e23266. Epub 2019 Mar 5.

Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California.

Like polypeptides, peptoids, or N-substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N-substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. Read More

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http://doi.wiley.com/10.1002/bip.23266
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March 2019
4 Reads

Unconstrained peptoid tetramer exhibits a predominant conformation in aqueous solution.

Biopolymers 2019 Mar 5:e23267. Epub 2019 Mar 5.

The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California.

Conformational control in peptoids, N-substituted glycines, is crucial for the design and synthesis of biologically-active compounds and atomically-defined nanomaterials. While there are a growing number of structural studies in solution, most have been performed with conformationally-constrained short sequences (e.g. Read More

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Design and preparation of organic nanomaterials using self-assembled peptoids.

Biopolymers 2019 Feb 23:e23265. Epub 2019 Feb 23.

School of Engineering, Center for Biomedical Engineering, Institute for Molecular and Nanoscale Innovation, Brown University, Providence, Rhode Island.

The self-assembly and self-organization of peptoids, peptidomimetic polymers composed of N-substituted glycine monomers, can result in a plethora of well-defined organic nanostructures. Such classes of nanomaterials represent highly interesting functional platforms for many applications, for example, drug delivery, sensing, and catalysis. The main advantages of using self-assembling peptoids to engineer organic nanostructures include their chemical diversity, biocompatibility, enzymatic stability, and ease of synthesis. Read More

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http://dx.doi.org/10.1002/bip.23265DOI Listing
February 2019

Reversing the typical pH stability profile of the Trp-cage.

Biopolymers 2019 Mar 19;110(3):e23260. Epub 2019 Feb 19.

Department of Chemistry, University of Washington, Seattle, Washington.

The Trp-cage, an 18-20 residue miniprotein, has emerged as a primary test system for evaluating computational fold prediction and folding rate determination efforts. As it turns out, a number of stabilizing interactions in the Trp-cage folded state have a strong pH dependence; all prior Trp-cage mutants have been destabilized under carboxylate-protonating conditions. Notable among the pH dependent stabilizing interactions within the Trp-cage are: (1) an Asp as the helix N-cap, (2) an H-bonded Asp9/Arg16 salt bridge, (3) an interaction between the chain termini which are in close spatial proximity, and (4) additional side chain interactions with Asp9. Read More

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http://doi.wiley.com/10.1002/bip.23260
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March 2019
4 Reads

Polymerization rate difference of N-alkyl glycine NCAs: Steric hindrance or not?

Biopolymers 2019 Feb 12:e23261. Epub 2019 Feb 12.

MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, China.

Polypeptoids synthesized from N-substituted glycine N-carboxyanhydrides (NNCAs) are widely applied in biological fields. The effect of side groups in NNCA polymerizations is a key to develop novel polypeptoids with complex topologies and constituents. In this work, density functional theory (DFT) calculations are employed to investigate the propagation of a series of alkyl substituted NNCAs with solvation model. Read More

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http://dx.doi.org/10.1002/bip.23261DOI Listing
February 2019

Linking two worlds in polymer chemistry: The influence of block uniformity and dispersity in amphiphilic block copolypeptoids on their self-assembly.

Biopolymers 2019 Feb 7:e23259. Epub 2019 Feb 7.

Lehrstuhl für Chemische Technologie der Materialsynthese, Universität Würzburg, Würzburg, Germany.

The self-assembly of block copolymers has captured the interest of scientists for many decades because it can induce ordered structures and help to imitate complex structures found in nature. In contrast to proteins, nature's most functional hierarchical structures, conventional polymers are disperse in their length distribution. Here, we synthesized hydrophilic and hydrophobic polypeptoids via solid-phase synthesis (uniform) and ring-opening polymerization (disperse). Read More

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http://dx.doi.org/10.1002/bip.23259DOI Listing
February 2019
1 Read

Solid-phase synthesis of three-armed star-shaped peptoids and their hierarchical self-assembly.

Biopolymers 2019 Jan 24:e23258. Epub 2019 Jan 24.

Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Western Australia.

Due to the branched structure feature and unique properties, a variety of star-shaped polymers have been designed and synthesized. Despite those advances, solid-phase synthesis of star-shaped sequence-defined synthetic polymers that exhibit hierarchical self-assembly remains a significant challenge. Hence, we present an effective strategy for the solid-phase synthesis of three-armed star-shaped peptoids, in which ethylenediamine was used as the centric star pivot. Read More

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http://dx.doi.org/10.1002/bip.23258DOI Listing
January 2019
1 Read

Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs.

Biopolymers 2019 Mar 24;110(3):e23247. Epub 2019 Jan 24.

Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain.

The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Read More

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http://dx.doi.org/10.1002/bip.23247DOI Listing

Molecular dynamics insights into protein-glycosaminoglycan systems from microsecond-scale simulations.

Biopolymers 2019 Jan 22:e23252. Epub 2019 Jan 22.

Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.

Heparin is a key player in cell signaling via its physical interactions with protein targets in the extracellular matrix. However, basic molecular level understanding of these highly biologically relevant intermolecular interactions is still incomplete. In this study, for the first time, microsecond-scale MD simulations are reported for a complex between fibroblast growth factor 1 and heparin. Read More

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http://dx.doi.org/10.1002/bip.23252DOI Listing
January 2019
1 Read

Insight on mutation-induced resistance to anaplastic lymphoma kinase inhibitor ceritinib from molecular dynamics simulations.

Biopolymers 2019 Feb 21;110(2):e23257. Epub 2019 Jan 21.

Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, People's Republic of China.

Ceritinib, an advanced anaplastic lymphoma kinase (ALK) next-generation inhibitor, has been proved excellent antitumor activity in the treatment of ALK-associated cancers. However, the accumulation of acquired resistance mutations compromise the therapeutic efficacy of ceritinib. Despite abundant mutagenesis data, the structural determinants for reduced ceritinib binding in mutants remains elusive. Read More

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http://dx.doi.org/10.1002/bip.23257DOI Listing
February 2019
4 Reads

Peptoids advance multidisciplinary research and undergraduate education in parallel: Sequence effects on conformation and lipid interactions.

Biopolymers 2019 Jan 11:e23256. Epub 2019 Jan 11.

Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, California, U.S.A.

Peptoids are versatile peptidomimetic molecules with wide-ranging applications from drug discovery to materials science. An understanding of peptoid sequence features that contribute to both their three-dimensional structures and their interactions with lipids will expand functions of peptoids in varied fields. Furthermore, these topics capture the enthusiasm of undergraduate students who prepare and study diverse peptoids in laboratory coursework and/or in faculty led research. Read More

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http://doi.wiley.com/10.1002/bip.23256
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January 2019
15 Reads

Complete observation of all structural, conformational, and fibrillation transitions of monomeric globular proteins at submicellar sodium dodecyl sulfate concentrations.

Biopolymers 2019 Jan 11:e23255. Epub 2019 Jan 11.

School of Chemistry, University of Hyderabad, Hyderabad, India.

Although considerable information is available regarding protein-sodium dodecyl sulfate (SDS) interactions, it is still unclear as to how much SDS is needed to denature proteins. The role of protein charge and micellar surfactant concentration on amyloid fibrillation is also unclear. This study reports on equilibrium measurements of SDS interaction with six model proteins and analyzes the results to obtain a general understanding of conformational breakdown, reorganization and restructuring of secondary structure, and entry into the amyloid fibrillar state. Read More

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http://dx.doi.org/10.1002/bip.23255DOI Listing
January 2019
1 Read

Rational design and characterization of bioplastics from Hermetia illucens prepupae proteins.

Biopolymers 2018 Dec 27:e23250. Epub 2018 Dec 27.

Department of Science and Methods for Engineering, University of Modena and Reggio Emilia, Reggio Emilia, Italy.

In this study proteins extracted from prepupae of Hermetia illucens, also known as black soldier fly, are investigated as promising base for a new type of bioplastics for agricultural purposes. Design of experiments techniques are employed to perform a rational study on the effects of different combination of glycerol as plasticizer, citric acid as cross-linking agent and distilled water as solvent on the capability of proteins to form a free-standing film through casting technique, keeping as fixed the quantity of proteins. Glycerol shows interesting properties as plasticizer contributing to the formation of homogenous and free-standing film. Read More

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http://dx.doi.org/10.1002/bip.23250DOI Listing
December 2018
1 Read

Impact of tetramerization on the ligand recognition of N1 influenza neuraminidase via MMGBSA approach.

Authors:
Martiniano Bello

Biopolymers 2018 Dec 27:e23251. Epub 2018 Dec 27.

Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, Mexico.

Influenza virus neuraminidase (NA) is a homotetrameric surface protein that, in contrast to other non-influenza NAs, requires a quaternary assembly to exhibit enzymatic activity, suggesting that the oligomeric state significantly impacts the active site of influenza NA. Nevertheless, most structure-based drug design studies have been reported by employing the monomeric state in the closed or open-loop due to the computational cost of employing the tetrameric NA. In this work, we present MD simulations coupled to the MMGBSA approach of avian N1 type NA in its monomeric and tetrameric closed and open-loop state both with and without the inhibitor oseltamivir and its natural substrate, sialic acid. Read More

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http://dx.doi.org/10.1002/bip.23251DOI Listing
December 2018
2 Reads

Solution effects on the self-association of a water-soluble peptoid.

Biopolymers 2018 Dec 22:e23248. Epub 2018 Dec 22.

Department of Bioengineering, Santa Clara University, Santa Clara, California, USA.

A desire to replicate the structural and functional complexity of proteins with structured, sequence-specific oligomers motivates study of the structural features of water-soluble peptoids (N-substituted glycine oligomers). Understanding the molecular-level details of peptoid self-assembly in water is essential to advance peptoids' application as novel materials. Peptoid 1, an amphiphilic, putatively helical peptoid previously studied in our laboratory, shows evidence of self-association in aqueous solution. Read More

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http://doi.wiley.com/10.1002/bip.23248
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December 2018
2 Reads

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
1 Read

Silk fibroin hydrogels for potential applications in photodynamic therapy.

Biopolymers 2019 Feb 13;110(2):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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http://dx.doi.org/10.1002/bip.23245DOI Listing
February 2019
3 Reads

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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https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.23244
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December 2018
2 Reads

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
1 Read

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

Biopolymers 2019 Jan 8;110(1):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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January 2019
11 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
25 Reads
2.385 Impact Factor

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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http://dx.doi.org/10.1002/bip.23240DOI Listing
December 2018
4 Reads

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

Biopolymers 2019 Jan 28;110(1):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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http://dx.doi.org/10.1002/bip.23242DOI Listing
January 2019
2 Reads

Price of disorder in the lac repressor hinge helix.

Biopolymers 2019 Jan 28;110(1):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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http://dx.doi.org/10.1002/bip.23239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335174PMC
January 2019
1 Read

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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http://doi.wiley.com/10.1002/bip.23238
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December 2018
3 Reads

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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http://dx.doi.org/10.1002/bip.23234DOI Listing
August 2018
1 Read

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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http://doi.wiley.com/10.1002/bip.23230
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August 2018
3 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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http://doi.wiley.com/10.1002/bip.23237
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http://dx.doi.org/10.1002/bip.23237DOI Listing
November 2018
6 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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http://dx.doi.org/10.1002/bip.23228DOI Listing
August 2018
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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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http://dx.doi.org/10.1002/bip.23235DOI Listing
August 2018
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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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http://doi.wiley.com/10.1002/bip.23236
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http://dx.doi.org/10.1002/bip.23236DOI Listing
September 2018
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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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http://dx.doi.org/10.1002/bip.23229DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6218314PMC
August 2018
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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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http://dx.doi.org/10.1002/bip.23232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6378955PMC
September 2018
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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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http://dx.doi.org/10.1002/bip.23233DOI Listing
August 2018
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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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http://dx.doi.org/10.1002/bip.23226DOI Listing
July 2018
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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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http://dx.doi.org/10.1002/bip.23225DOI Listing
August 2018
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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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http://dx.doi.org/10.1002/bip.23227DOI Listing
August 2018
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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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http://dx.doi.org/10.1002/bip.23224DOI Listing
June 2018
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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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http://dx.doi.org/10.1002/bip.23222DOI Listing
June 2018
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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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http://dx.doi.org/10.1002/bip.23223DOI Listing
July 2018
5 Reads