Hexylation Stabilises Twisted Backbone Configurations in the Prototypical Low-Bandgap Copolymer PCDTBT

Conjugated donor-acceptor copolymers hold great potential as materials for high-performance organic photovoltaics, organic transistors and organic thermoelectric devices. Their low optical bandgap is achieved by alternation of donor and acceptor moieties along the polymer chain, leading to a pronounced charge-transfer character of electronic excitations. However, the influence of appended side chains and of chemical defects of the backbone on their photophysical and conformational properties remains largely unexplored on the level of individual chains. Here, we employ room temperature single-molecule photoluminescence spectroscopy on four compounds based on the prototypical copolymer PCDTBT with systematically changed chemical structure. Our results show that an increasing density of statistically added hexyl chains to the TBT comonomer distorts the molecular conformation, likely through the increase of average dihedral angles along the backbone. We find that, although the conformation becomes more twisted with high hexyl density, the side chains appear to stabilize the backbone in this twisted conformation. In addition, we demonstrate that homocoupling defects along the backbone barely influence the PL spectra of single chains, and thus intra-chain electronic properties.

Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface

Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin–hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein–polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.

Thermoconformational Behavior of Cellulose Nanofiber Films as a Device Substrate and Their Superior Flexibility and Durability to Glass

The design and high-throughput manufacturing of thin renewable energy devices with high structural and atomic configurational stability are crucial for the fabrication of green electronics. Yet, this concept is still in its infancy. In this work, we report the extraordinary durability of thin molecular interlayered organic flexible energy devices based on chemically tuned cellulose nanofiber transparent films that outperform glass by decreasing the substrate weight by 50%. The nanofabricated flexible thin film has an exceptionally low thermal coefficient of expansion of 1.8 ppm/K and a stable atomic configuration under a harsh fabrication condition (over 190 °C for an extended period of 5 h). A flexible optoelectronic device using the same renewable cellulose nanofiber film substrate was found to be functionally operational over a life span of 5 years under an intermittent operating condition. The success of this device's stability opens up an entirely new frontier of applications of flexible electronics.

Geometrical constraints limiting the poly(ADP-ribose) conformation investigated by molecular dynamics simulation

Poly(ADP-ribosylation) is a post-transductional modification that regulates protein's function. Most of the proteins subjected to this control mechanism belong to machineries involved in DNA damage repair, or DNA interacting proteins. Poly(ADP-ribose) polymers are long chains of even 100 monomer length that can be branched at several positions but, not withstanding its importance, nothing is known concerning its structure. To understand, which are the geometrical parameters that confer to the polymer the structural constraints that determine its interaction with the target proteins, we have performed molecular dynamics of three chains of different length, made by 5, 25, and 30 units, the last one being branched. Analysis of the simulations allowed us to identify the main intra- and inter-monomer dihedral angles that govern the structure of the polymer that however, does not reach a unique definite conformation.

Artificial neural networks for dihedral angles prediction in enzyme loops: a novel approach

Structure prediction of proteins is considered a limiting step and determining factor in drug development and in the introduction of new therapies. Since the 3D structures of proteins determine their functionalities, prediction of dihedral angles remains an open and important problem in bioinformatics, as well as a major step in discovering tertiary structures. This work presents a method that predicts values of the dihedral angles φ and ψ for enzyme loops based on data derived from amino acid sequences. The prediction of dihedral angles is implemented through a neural network based mining mechanism. The amino acid sequence data represents 6342 enzyme loop chains with 18,882 residues. The initial neural network input was a selection of 115 features and the outputs were the predicted dihedral angles φ and ψ. The simulation results yielded a 0.64 Pearson's correlation coefficient. After feature selection through determining insignificant features, the input feature vector size was reduced to 45, while maintaining close to identical performance.

Structural and sequence features of two residue turns in beta-hairpins

Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.

Three-residue loop closure in proteins: a new kinematic method reveals a locus of connected loop conformations

The closure of a three-residue loop was studied using a developed kinematic method. It was shown that there are infinite number of three-residue loops (a locus of conformations), which can connect two segments of a polypeptide. This adds to the current understanding of a finite number of conformations for three-residue loop-closure. In the developed method, some of the equations can be solved analytically to reduce the computation cost. Benefiting from the reduced computation time, we determined all the relative positions of two polypeptide segments that can be connected by a three-residue loop.

Dihedral angle and secondary structure database of short amino acid fragments

Dihedral angles of amino acids are of considerable importance in protein tertiary structure prediction as they define the backbone of a protein and hence almost define the protein's entire conformation. Most ab initio protein structure prediction methods predict the secondary structure of a protein before predicting the tertiary structure because three-dimensional fold consists of repeating units of secondary structures. Hence, both dihedral angles and secondary structures are important in tertiary structure prediction of proteins. Here we describe a database called DASSD (Dihedral Angle and Secondary Structure Database of Short Amino acid Fragments) that contains dihedral angle values and secondary structure details of short amino acid fragments of lengths 1, 3 and 5. Information stored in this database was extracted from a set of 5,227 non-redundant high resolution (less than 2-angstroms) protein structures. In total, DASSD stores details for about 733,000 fragments. This database finds application in the development of ab initio protein structure prediction methods using fragment libraries and fragment assembly techniques. It is also useful in protein secondary structure prediction.

AVAILABILITY

DASSD can be accessed and downloaded from http://www.cs.rmit.edu.au/dassd/

Carbon-13 relaxation and proton nuclear magnetic resonance studies of prostaglandin F2alpha

Carbon magnetic resonance T(1) relaxation and chemical shift measurements at 22.63 MHz establish hydrophobic aggregation of prostaglandin F(2alpha) in phosphate buffer solutions between 0.05 and 0.2 M. Analysis of the proton magnetic resonance spectra of prostaglandin F(2alpha) at 270 MHz by double resonance techniques yield all the proton-proton coupling constants for the five-membered ring indicating a favored half-chair conformation for the ring in which the dihedral angle for the C-8 and C-12 protons is close to 180 degrees . Effective correlation times derived from carbon magnetic resonance T(1) values for all the carbon atoms show segmental motion for ring carbon C-10 and in the aliphatic portions of both side chains, while the double bonded portions of the side chains and the ring carbons act as a more rigidly interconnected network. Chemical shift changes in the carbon magnetic resonance and proton magnetic resonance spectra upon aggregation suggest that the 5-6 double bond, C-7, and C-9 participate in the aggregation process.