Identifying the coiled-coil triple helix structure of β-peptide nanofibers at atomic resolution

Peptide self-assembly represents a powerful bottom-up approach to the fabrication of new nanomaterials. β3-peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone and we reported the first fibers derived from the self-assembly of β3-peptides that adopt unique 14-helical structures. β3-peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. In order to develop structure-based criteria for the design of new β3-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β3-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β3[LIA] in water and used to inform and validate the model structure. Models with threefold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macro-scale fibers derived from β3-peptide-based materials provide valuable insight into the effects of the geometric placement of the side-chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology

The structures of E. coli NfsA bound to the antibiotic nitrofurantoin; to 1,4-benzoquinone and to FMN

NfsA is a dimeric flavoprotein that catalyses the reduction in nitroaromatics and quinones by NADPH. This reduction is required for the activity of nitrofuran antibiotics. The crystal structure of free Escherichia coli NfsA and several homologues have been determined previously, but there is no structure of the enzyme with ligands. We present here crystal structures of oxidised E. coli NfsA in the presence of several ligands, including the antibiotic nitrofurantoin. Nitrofurantoin binds with the furan ring, rather than the nitro group that is reduced, near the N5 of the FMN. Molecular dynamics simulations show that this orientation is only favourable in the oxidised enzyme, while potentiometry suggests that little semiquinone is formed in the free protein. This suggests that the reduction occurs by direct hydride transfer from FMNH(−) to nitrofurantoin bound in the reverse orientation to that in the crystal structure. We present a model of nitrofurantoin bound to reduced NfsA in a viable hydride transfer orientation. The substrate 1,4-benzoquinone and the product hydroquinone are positioned close to the FMN N5 in the respective crystal structures with NfsA, suitable for reaction, but are mobile within the active site. The structure with a second FMN, bound as a ligand, shows that a mobile loop in the free protein forms a phosphate-binding pocket. NfsA is specific for NADPH and a similar conformational change, forming a phosphate-binding pocket, is likely to also occur with the natural cofactor

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

A Computational Investigation of the Mechanism of CB1954 Reduction by E.coli Nitroreductase

The flavoenzyme NTR (nitroreductase nfsB from Escherichia coli) and the prodrug CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide) have been found to be a good potential combination for virus-directed enzyme prodrug therapy (VDEPT). However, wild-type NTR has poor kinetics and binding with CB1954, and the mechanism for the reduction of CB1954 by NTR is poorly understood. The aim of this work has been to investigate, using quantum mechanical computational methods, the potential underlying reaction mechanisms so as to identify the order of electron and proton transfers, and source of the protons, that make up the initial reduction step. Additionally, molecular mechanics and molecular dynamics have been used to examine the nature of the active site of the wild-type enzyme, as well as several mutants, and determine possible binding modes of the substrate. Finally, ONIOM calculations were utilised to examine substrate orientations and electronic states at a quantum mechanical level with key active site amino acids present at a molecular mechanics level. Calculations with the MPW1PW91 density functional and 6-31G** basis set yielded a single gas phase transition state geometry for the hydride transfer from the FMN (flavin mononucleotide) cofactor of NTR to a nitro group of CB1954. Additionally, three reaction profiles were generated which suggest that in the gas phase, the reduction proceeds by electron transfer from FMN, proton transfer , then second proton transfer and electron transfer concerted with N-O bond breaking, regardless of the source (FMN or solution) or order of the protons. Molecular mechanics calculations with the FF03 force field found a binding mode with the amide group of CB1954 bound in the active site of NTR—an orientation ideally suited for an electron transfer mechanism

Surface-water interface induces conformational changes critical for protein adsorption:Implications for monolayer formation of EAS hydrophobin

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Exploring Solvation Properties of Protic Ionic Liquids by Employing Solvatochromic Dyes and Molecular Dynamics Simulation Analysis

Solvation properties are key for understanding the interactions between solvents and solutes, making them critical for optimizing chemical synthesis and biochemical applications. Designable solvents for targeted optimization of these end-uses could, therefore, play a big role in the future of the relevant industries. The tailorable nature of protic ionic liquids (PILs) as designable solvents makes them ideal candidates. By alteration of their constituent structural groups, their solvation properties can be tuned as required. The solvation properties are determined by the polar and non-polar interactions of the PIL, but they remain relatively unknown for PILs as compared to aprotic ILs and their characterization is non-trivial. Here, we use solvatochromic dyes as probe molecules to investigate the solvation properties of nine previously uncharacterized alkyl- and dialkylammonium PILs. These properties include the Kamlet–Aboud–Taft (KAT) parameters: π* (dipolarity/polarizability), α (H-bond acidity) and β (H-bond basicity), along with the ET(30) scale (electrophilicity/polarizability). We then used molecular dynamics simulations to calculate the radial distribution functions (RDF) of 21 PILs, which were correlated to their solvation properties and liquid nanostructure. It was identified that the hydroxyl groups on the PIL cation increase α, π* and ET(30), and correspondingly increase the cation–anion distance in their RDF plots. The hydroxyl group, therefore, reduces the strength of the ionic interaction but increases the polarizability of the ions. An increase in the alkyl chain length on the cation led to a decrease in the distances between cations, while also increasing the β value. The effect of the anion on the PIL solvation properties was found to be variable, with the nitrate anion greatly increasing π*, α and anion–anion distances. The research presented herein advances the understanding of PIL structure–property relationships while also showcasing the complimentary use of molecular dynamics simulations and solvatochromic analysis together