Sequence-Tunable Phase Behavior and Intrinsic Fluorescence in Dynamically Interacting Peptides

A conceptual framework towards understanding biological condensed phases is emerging, derived from biological, biomimetic, and synthetic sequences. However, de novo peptide condensate design remains a challenge due to an incomplete understanding of the structural and interactive complexity. We designed peptide modules based on a simple repeat motif composed of tripeptide spacers (GSG, SGS, GLG) interspersed with adhesive amino acids (R/H and Y). We show, using sequence editing and a combination of computation and experiment, that n→π* interactions in GLG backbones are a dominant factor in providing sufficient backbone structure, which in turn regulates the water interface, collectively promoting liquid droplet formation. Moreover, these R(GLG)Y and H(GLG)Y condensates unexpectedly display sequence-dependent emission that is a consequence of their non-covalent network interactions, and readily observable by confocal microscopy.     

Effect of sodium diclofenac loads on mesophase components and structure

We studied the effect of a model electrolytic drug on intermolecular interactions, conformational changes, and phase transitions in structured discontinuous cubic QL lyotropic liquid crystals. These changes were due to competition with hydration of the lipid headgroups. Structural changes of the phase induced by solubilization loads of sodium diclofenac (Na-DFC) were investigated by directly observing the water, ethanol, and Na-DFC components of the resulting phases using 2H and 23Na NMR. Na-DFC interacted with the surfactant glycerol monoolein (GMO) at the interface while interfering with the mesophase curvature and also competed with hydration of the surfactant headgroups. Increasing quantities of solubilized Na-DFC promoted phase transitions from cubic phase (discontinuous (QL) and bicontinuous (Q)) into lamellar structures and subsequently into a disordered lamellar phase. Quadrupolar coupling of deuterated ethanol by 2H NMR showed that it is located near the headgroups of the lipid and apparently is hydrogen bonded to the GMO headgroups. A phase transition between two lamellar phases (L alpha to L alpha*) was seen by 23Na NMR of Na-DFC at a concentration where the characteristics of the drug change from kosmotropic to chaotropic. These findings show that loads of solubilized drug may affect the structure of its vehicle and, as a result, its transport across skin-blood barriers. The structural changes of the mesophase may also aid controlled drug delivery.     

Ultrafast electronic and vibrational dynamics of stabilized A state mutants of the green fluorescent protein (GFP): Snipping the proton wire

Two blue absorbing and emitting mutants (S65G/T203V/E222Q and S65T at pH 5.5) of the green fluorescent protein (GFP) have been investigated through ultrafast time resolved infra-red (TRIR) and fluorescence spectroscopy. In these mutants, in which the excited state proton transfer reaction observed in wild-type GFP has been blocked, the photophysics are dominated by the neutral A state. It was found that the A* excited state lifetime is short, indicating that it is relatively less stabilised in the protein matrix than the anionic form. However, the lifetime of the A state can be increased through modifications to the protein structure. The TRIR spectra show that a large shifts in protein vibrational modes on excitation of the A state occurs in both these GFP mutants. This is ascribed to a change in H-bonding interactions between the protein matrix and the excited state.     

Intracule functional models. Part III. The dot intracule and its Fourier transform

The dot intracule D(x) of a system gives the Wigner quasi-probability of finding two of its electrons with u.v = x, where u and v are the interelectronic distance vectors in position and momentum space, respectively. In this paper, we discuss D(x) and show that its Fourier transform d(k) can be obtained in closed form for any system whose wavefunction is expanded in a Gaussian basis set. We then invoke Parseval's theorem to transform our intracule-based correlation energy method into a d(k)-based model that requires, at most, a one-dimensional quadrature.     

Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase

Herein, the structure resulting from in situ turnover in a chemically challenging quaternary ammonium oxidative demethylation reaction was captured via crystallographic analysis and analyzed via single-crystal spectroscopy. Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 ? resolution) and in the product complex (at 2.2 ? resolution). The ligand complex was obtained from enzyme aerobically cocrystallized with the substrate stachydrine (N,N-dimethylproline). The ligand electron density in the complex was interpreted as proline, generated within the active site at 100 K by the absorption of X-ray photon energy and two consecutive demethylation cycles. The oxidation state of the Rieske iron-sulfur cluster was characterized by UV-visible spectroscopy throughout X-ray data collection in conjunction with resonance Raman spectra collected before and after diffraction data. Shifts in the absorption band wavelength and intensity as a function of absorbed X-ray dose demonstrated that the Rieske center was reduced by solvated electrons generated by X-ray photons; the kinetics of the reduction process differed dramatically for the liganded complex compared to unliganded demethylase, which may correspond to the observed turnover in the crystal.     

Integrated project views: decision support platform for drug discovery project teams

Drug discovery teams continuously have to decide which compounds to progress and which experiments to perform next, but the data required to make informed decisions is often scattered, inaccessible, or inconsistent. In particular, data tend to be stored and represented in a compound-centric or assay-centric manner rather than project-centric as often needed for effective use in drug discovery teams. The Integrated Project Views (IPV) system has been created to fill this gap; it integrates and consolidates data from various sources in a project-oriented manner. Its automatic gathering and updating of project data not only ensures that the information is comprehensive and available on a timely basis, but also improves the data consistency. Due to the lack of suitable off-the-shelf solutions, we were prompted to develop custom functionality and algorithms geared specifically to our drug discovery decision making process. In 10 years of usage, the resulting IPV application has become very well-accepted and appreciated, which is perhaps best evidenced by the observation that standalone Excel spreadsheets are largely eliminated from project team meetings.     

QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification

Systems biology requires knowledge of the absolute amounts of proteins in order to model biological processes and simulate the effects of changes in specific model parameters. Quantification concatamers (QconCATs) are established as a method to provide multiplexed absolute peptide standards for a set of target proteins in isotope dilution standard experiments. Two or more quantotypic peptides representing each of the target proteins are concatenated into a designer gene that is metabolically labelled with stable isotopes in Escherichia coli or other cellular or cell-free systems. Co-digestion of a known amount of QconCAT with the target proteins generates a set of labelled reference peptide standards for the unlabelled analyte counterparts, and by using an appropriate mass spectrometry platform, comparison of the intensities of the peptide ratios delivers absolute quantification of the encoded peptides and in turn the target proteins for which they are surrogates. In this review, we discuss the criteria and difficulties associated with surrogate peptide selection and provide examples in the design of QconCATs for quantification of the proteins of the nuclear factor κB pathway.     

Design and characterization of 1D nanotubes and 2D periodic arrays self-assembled from DNA multi-helix bundles

Among the key goals of structural DNA nanotechnology are to build highly ordered structures self-assembled from individual DNA motifs in 1D, 2D, and finally 3D. All three of these goals have been achieved with a variety of motifs. Here, we report the design and characterization of 1D nanotubes and 2D arrays assembled from three novel DNA motifs, the 6-helix bundle (6HB), the 6-helix bundle flanked by two helices in the same plane (6HB+2), and the 6-helix bundle flanked by three helices in a trigonal arrangement (6HB+3). Long DNA nanotubes have been assembled from all three motifs. Such nanotubes are likely to have applications in structural DNA nanotechnology, so it is important to characterize their physical properties. Prominent among these are their rigidities, described by their persistence lengths, which we report here. We find large persistence lengths in all species, around 1-5 μm. The magnitudes of the persistence lengths are clearly related to the designs of the linkages between the unit motifs. Both the 6HB+2 and the 6HB+3 motifs have been successfully used to produce well-ordered 2D periodic arrays via sticky-ended cohesion.     

Tuning Coordination in s‐Block Carbazol‐9‐yl Complexes

1,3,6,8‐Tetra‐tert‐butylcarbazol‐9‐yl and 1,8‐diaryl‐3,6‐di(tert‐butyl)carbazol‐9‐yl ligands have been utilized in the synthesis of potassium and magnesium complexes. The potassium complexes (1,3,6,8‐tBu₄carb)K(THF)₄ ( 1 ; carb=C₁₂H₄N), [(1,8‐Xyl₂‐3,6‐tBu₂carb)K(THF)]₂ ( 2 ; Xyl=3,5‐Me₂C₆H₃) and (1,8‐Mes₂‐3,6‐tBu₂carb)K(THF)₂ ( 3 ; Mes=2,4,6‐Me₃C₆H₂) were reacted with MgI₂ to give the Hauser bases 1,3,6,8‐tBu₄carbMgI(THF)₂ ( 4 ) and 1,8‐Ar₂‐3,6‐tBu₂carbMgI(THF) (Ar=Xyl 5 , Ar=Mes 6 ). Structural investigations of the potassium and magnesium derivatives highlight significant differences in the coordination motifs, which depend on the nature of the 1‐ and 8‐substituents: 1,8‐di(tert‐butyl)‐substituted ligands gave π‐type compounds ( 1 and 4 ), in which the carbazolyl ligand acts as a multi‐hapto donor, with the metal cations positioned below the coordination plane in a half‐sandwich conformation, whereas the use of 1,8‐diaryl substituted ligands gave σ‐type complexes ( 2 and 6 ). Space‐filling diagrams and percent buried volume calculations indicated that aryl‐substituted carbazolyl ligands offer a steric cleft better suited to stabilization of low‐coordinate magnesium complexes.     

A family of intracules, a conjecture and the electron correlation problem

We present a radical approach to the calculation of electron correlation energies. Unlike conventional methods based on Hartree-Fock or density functional theory, it is based on the two-electron phase-space information in the Omega intracule, a three-dimensional function derived from the Wigner distribution. Our formula for the correlation energy is isomorphic to the Hartree-Fock energy expression but requires a new type of four-index integral. Preliminary results, obtained using a model that is based on the known correlation energies of small atoms, are encouraging.