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Harshini Pakalapati, Senthil Kumar Arumugasamy, Jegalakshimi Jewaratnam, Yong Jie Wong, Mohammad Khalid
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). Using the D-optimal method in design of experiments, the interactions between parameters and responses were analysed and validated...
November 29, 2018: Biopolymers
Eduardo Leyva, Jorge L Medrano-Cerano, Patricia Cano-Sánchez, Itzel López-González, Homero Gómez-Velasco, Federico Del Río-Portilla, Enrique García-Hernández
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...
November 28, 2018: Biopolymers
Danielle Seckfort, B Montgomery Pettitt
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. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix...
November 28, 2018: Biopolymers
Fei Han, Ye Liu, Jingwen E, Shanshan Guan, Weiwei Han, Yaming Shan, Song Wang, Hao Zhang
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...
November 28, 2018: Biopolymers
Yanpeng Zheng, Lingwan Xu, Jingfa Yang, Xianglei Peng, He Wang, Na Yu, Ying Hua, Jiang Zhao, Jinsheng He, Tao Hong
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 Aβ42 oligomers using fluorescence correlation spectroscopy (FCS). We found that fluorescent labels of BODIPY® FL-C5 (BP), N-hydroxysuccinimide rhodamine B ester (RB) and rhodamine B isothiocyanate (RITC) increased the propensity of labelled Aβ42 oligomers to aggregate, whereas 6-(fluorescein-5-carboxamido) hexanoic acid succinimidyl ester (5-SFX) and fluorescein 5(6)-isothiocyanate (5(6)-FITC) decreased the propensity of labelled Aβ42 oligomers to aggregate...
October 11, 2018: Biopolymers
Ekaterina R Gasilova, Galina P Aleksandrova, Elena N Vlasova, Vadim A Baigildin
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 Th = 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...
September 30, 2018: Biopolymers
Rahul Patwa, Narendren Soundararajan, Neha Mulchandani, Siddharth M Bhasney, Manisha Shah, Sachin Kumar, Amit Kumar, Vimal Katiyar
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...
November 2018: Biopolymers
Rafael Alcala-Torano, Mathieu Walther, Dayn J Sommer, Chad K Park, Giovanna Ghirlanda
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. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes...
September 6, 2018: Biopolymers
Zahra Ghassemi, Gymama Slaughter
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...
September 2018: Biopolymers
Fulvio Perrella, Umberto Raucci, Maria Gabriella Chiariello, Marco Chino, Ornella Maglio, Angela Lombardi, Nadia Rega
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. In this work we propose a theoretical investigation based on molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) optimizations, aimed to shed light on several Fe(III)-MC6 structural features and to validate the de novo designed fold...
August 9, 2018: Biopolymers
Flavia Nastri, Ornella Maglio, Angela Lombardi
No abstract text is available yet for this article.
August 2018: Biopolymers
Luigi Di Costanzo, Shuchismita Dutta, Stephen K Burley
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. However, our knowledge of 3D structures of biomolecules containing backbone modified amino acids is still evolving...
August 2018: Biopolymers
Shuguang Zhang
No abstract text is available yet for this article.
August 2018: Biopolymers
Shuguang Zhang
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. Although CD does not provide detailed structure at the atomic level, it provides a global structural framework...
August 2018: Biopolymers
Marco Chino, Shao-Qing Zhang, Fabio Pirro, Linda Leone, Ornella Maglio, Angela Lombardi, William F DeGrado
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-Zn2+ clusters...
August 2018: Biopolymers
Kenneth J Breslauer
No abstract text is available yet for this article.
August 2018: Biopolymers
Diana P Slough, Sean M McHugh, Yu-Shan Lin
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. Herein, we describe the current experimental and computational efforts in understanding and designing head-to-tail CPs along with their respective challenges...
August 2018: Biopolymers
Alexander Tischer, Venkata R Machha, Jörg Rösgen, Matthew Auton
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)...
August 2018: Biopolymers
Conceição A Minetti, Jeffrey Y Sun, Daniel P Jacobs, Inkoo Kang, David P Remeta, Kenneth J Breslauer
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...
August 2018: Biopolymers
Mimi Nick, Yibing Wu, Nathan W Schmidt, Stanley B Prusiner, Jan Stöhr, William F DeGrado
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. The suppression of fibril formation was observed by amyloid-binding dye Thioflavin T and solution nuclear magnetic resonance (NMR)...
August 2018: Biopolymers
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