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Katherine A Graham, Aimee Byrne, Ruth Son, Niels H Andersen
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...
February 19, 2019: Biopolymers
Tianwen Bai, Jun Ling
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. According to both computational and experimental results, carbonyl addition is confirmed as rate determining step and steric hindrance is recognized as the major factor of low reactivity in β-C branched NNCAs...
February 12, 2019: Biopolymers
Niklas Gangloff, Marcel Höferth, Vladimir Stepanenko, Benedikt Sochor, Bernhard Schummer, Joachim Nickel, Heike Walles, Randolf Hanke, Frank Würthner, Ronald N Zuckermann, Robert Luxenhofer
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). Differential scanning calorimetry measurements showed that the uniform hydrophobic peptoids converge to a maximum of the melting temperature at a much lower chain length than their disperse analogs, showing that not only the chain length but also the dispersity has a considerable impact on the thermal properties of those homopolymers...
February 7, 2019: Biopolymers
Haibao Jin, Tengyue Jian, Yan-Huai Ding, Yulin Chen, Peng Mu, Lei Wang, Chun-Long Chen
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. Based on the sequence of monomer addition, a series of AA'A''-type and ABB'-type peptoids were synthesized and characterized by UPLC-MS (ultrahigh performance liquid chromatography-mass spectrometry)...
January 24, 2019: Biopolymers
Mauricio Alcolea Palafox
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. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo...
January 24, 2019: Biopolymers
Krzysztof K Bojarski, Adam K Sieradzan, Sergey A Samsonov
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. We rigorously analyze this molecular system in terms of the conformational space, structural, energetic, and dynamic characteristics...
January 22, 2019: Biopolymers
Mu-Yang He, Wei-Kang Li, Jens Meiler, Qing-Chuan Zheng, Hong-Xing Zhang
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. Focusing on the G1123S and F1174C mutations, we applied molecular dynamics (MD) simulations to study possible reasons for drug resistance caused by these mutations...
January 21, 2019: Biopolymers
Christian J Jimenez, Jiacheng Tan, Kalli M Dowell, Gillian E Gadbois, Cameron A Read, Nicole Burgess, Jesus E Cervantes, Shannon Chan, Anmol Jandaur, Tara Karanik, Jaenic J Lee, Mikaela C Ley, Molly McGeehan, Ann McMonigal, Kira L Palazzo, Samantha A Parker, Andre Payman, Maritza Soria, Lauren Verheyden, Vivian T Vo, Jennifer Yin, Anna L Calkins, Amelia A Fuller, Grace Y Stokes
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. Here, we present the synthesis and study of 21 peptoids with varied functionality, including 19 tripeptoids and 2 longer oligomers...
January 11, 2019: Biopolymers
Noorul Huda, Mujahid Hossain, Abani K Bhuyan
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...
January 11, 2019: Biopolymers
Silvia Barbi, Massimo Messori, Tiziano Manfredini, Martina Pini, Monia Montorsi
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...
December 27, 2018: Biopolymers
Martiniano Bello
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...
December 27, 2018: Biopolymers
Amelia A Fuller, Jonathan Huber, Christian J Jimenez, Kalli M Dowell, Samuel Hough, Alberto Ortega, Kyra N McComas, Jeffrey Kunkel, Prashanth Asuri
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...
December 22, 2018: Biopolymers
Vineeta Rustagi, D Gomika Udugamasooriya
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. We generated two on-bead Eu(III)-DOTA libraries with three side arm modifications, where the remaining arm was used to attach DOTA onto the resin...
December 14, 2018: Biopolymers
Jose Eduardo U Rojas, Barbara B Gerbelli, Anderson O Ribeiro, Iseli L Nantes-Cardoso, Francesca Giuntini, Wendel A Alves
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...
December 13, 2018: Biopolymers
Kevin Brahm, Julia S Wack, Stefanie Eckes, Victoria Engemann, Katja Schmitz
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. Cyclization can be performed on-bead in the presence of side-chain protecting groups so that this strategy can be applied to a large variety of sequences...
December 13, 2018: Biopolymers
Xiaohui Fu, Jiliang Tian, Zheng Li, Jing Sun, Zhibo Li
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. The cloud points (CPs) were demonstrated to be readily tunable in the range of ~25°C-60°C by varying the chemical composition, OEG chain length and the degree of polymerization...
December 8, 2018: Biopolymers
Morten Leth Jepsen, Line Hagner Nielsen, Anja Boisen, Kristoffer Almdal, Martin Dufva
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. The gelatin is crosslinked with mTransglutaminase and the area of the resulting hydrogel can be increased up 13-fold by increasing the radial water pressure...
December 8, 2018: Biopolymers
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
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
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