A flexible docking procedure for the exploration of peptide binding selectivity to known structures and homology models of PDZ domains

PDZ domains are important scaffolding modules that typically bind to the C-termini of their interaction partners. Several structures of such complexes have been solved, revealing a conserved binding site in the PDZ domain and an extended conformation of the bound peptide. A compendium of information regarding PDZ complexes demonstrates that dissimilar C-terminal peptides bind to the same PDZ domain, and different PDZ domains can bind the same peptides. A detailed understanding of the PDZ-peptide recognition is needed to elucidate this complexity. To this end, we have designed a family of docking protocols for PDZ domains (termed PDZ-DocScheme) that is based on simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking of long peptides (20-40 rotatable bonds) to both known PDZ structures and to the more complicated problem of homology models of these domains. The resulting protocol reproduces the structures of PDZ complexes with peptides 4-8 amino acids long within 1-2 A from the experimental structure when the docking is performed to the original structure. If the structure of the target PDZ domain is an apo structure or a homology model, the docking protocol yields structures within 3 A in 9 out of 12 test cases. The automated docking procedure PDZ-DocScheme can serve in the generation of a structural context for validation of PDZ domain specificity from mutagenesis and ligand binding data.     

Heterogeneous thermal excitation and relaxation in supercooled liquids

We investigate a phenomenological model which rationalizes the effects of dielectric hole burning on the basis of heterogeneous dielectric and specific heat relaxation in supercooled liquids. The quantitative agreement between model predictions and dielectric hole-burning observations is lost if the assumption of correlated dielectric and thermal relaxation times is removed from the model. This suggests that dynamically distinct domains in real liquids are associated with a time constant which characterizes both the structural and thermal relaxation behaviors. The calculations demonstrate that the observed burn-induced modifications reflect the spectral selectivity and persistence time of the fictive temperatures within these domains, and that 100 or more cycles of the sinusoidal burn field can be required to saturate the heat accumulated in the slow degrees of freedom. It is also shown that the recovery of dielectric holes is entirely accounted for by the model, and that the persistence times do not provide direct insight into rate exchange processes. Additionally, the model predicts that the heating effects considered here are a significant source of nonlinear dielectric behavior, even in the absence of deliberate frequency selective hole burning.     

Membrane lipids are both the substrates and a mechanistically responsive environment of TMEM16 scramblase proteins

Recent discoveries about functional mechanisms of proteins in the TMEM16 family of phospholipid scramblases have illuminated the dual role of the membrane as both the substrate and a mechanistically responsive environment in the wide range of physiological processes and genetic disorders in which they are implicated. This is highlighted in the review of recent findings from our collaborative investigations of molecular mechanisms of TMEM16 scramblases that emerged from iterative functional, structural, and computational experimentation. In the context of this review, we present new MD simulations and trajectory analyses motivated by the fact that new structural information about the TMEM16 scramblases is emerging from cryo-EM determinations in lipid nanodiscs. Because the functional environment of these proteins in in vivo and in in vitro is closer to flat membranes, we studied comparatively the responses of the membrane to the TMEM16 proteins in flat membranes and nanodiscs. We find that bilayer shapes in the nanodiscs are very different from those observed in the flat membrane systems, but the function-related slanting of the membrane observed at the nhTMEM16 boundary with the protein is similar in the nanodiscs and in the flat bilayers. This changes, however, in the bilayer composed of longer-tail lipids, which is thicker near the phospholipid translocation pathway, which may reflect an enhanced tendency of the long tails to penetrate the pathway and create, as shown previously, a nonconductive environment. These findings support the correspondence between the mechanistic involvement of the lipid environment in the flat membranes, and the nanodiscs. © 2019 Wiley Periodicals, Inc.     

Highly efficient visible-light driven photochromism: developments towards a solid-state molecular switch operating through a triplet-sensitised pathway

We introduce a new highly efficient photochromic organometallic dithienylethene (DTE) complex, the first instance of a DTE core symmetrically modified by two Pt(II) chromophores [Pt(PEt(3))(2)(C≡C)(DTE)(C≡C)Pt(PEt(3))(2)Ph] (1), which undergoes ring-closure when activated by visible light in solvents of different polarity, in thin films and even in the solid state. Complex 1 has been synthesised and fully photophysically characterised by (resonance) Raman and transient absorption spectroscopy complemented by calculations. The ring-closing photoconversion in a single crystal of 1 has been followed by X-ray crystallography. This process occurs with the extremely high yield of 80%--considerably outperforming the other DTE derivatives. Remarkably, the photocyclisation of 1 occurs even under visible light (>400 nm), which is not absorbed by the non-metallated DTE core HC≡C(DTE)C≡CH (2) itself. This unusual behaviour and the high photocyclisation yields in solution are attributed to the presence of a heavy atom in 1 that enables a triplet-sensitised photocyclisation pathway, elucidated by transient absorption spectroscopy and DFT calculations. The results of resonance Raman investigation confirm the involvement of the alkynyl unit in the frontier orbitals of both closed and open forms of 1 in the photocyclisation process. The changes in the Raman spectra upon cyclisation have permitted the identification of Raman marker bands, which include the acetylide stretching vibration. Importantly, these bands occur in the spectral region unobstructed by other vibrations and can be used for non-destructive monitoring of photocyclisation/photoreversion processes and for optical readout in this type of efficiently photochromic thermally stable systems. This study indicates a strategy for generating efficient solid-state photoswitches in which modification of the Pt(II) units has the potential to tune absorption properties and hence operational wavelength across the visible range.     

Analytical calculation of atomic and molecular electrostatic potentials from the Poisson equation

An analytic formulation is given for the total potential in atomic and molecular systems, based on the electrostatic approach from the Hellmann-Feynman theorem. The potential function is obtained from the analytic solution of the Poisson equation using charge densities expressed as a superposition of gaussian functions. The method is independent of the specific LCAO approximation used for the calculation of the charge distribution function. The calculation of the potential and its derivatives to a rapid algorithm form, which can be used for the evaluation of various electronic properties and the treatment of experimental situation, even for large molecular systems.     

Improved measurement of the form factors in the decay lambda+c-->lambda + nue

Using the CLEO detector at the Cornell Electron Storage Ring, we have studied the distribution of kinematic variables in the decay lambda(+)(c)lambda--> e(+)nu(e). By performing a four-dimensional maximum likelihood fit, we determine the form factor ratio, R= f(2)/f(1) = -0.31 +/- 0.05(stat) +/- 0.04(syst), the pole mass, M(pole) = [2.21 +/- 0.08(stat) +/- 0.14(syst)] GeV/c(2), and the decay asymmetry parameter of the lambda(+)(c), alpha (lambda(c)) = -0.86 +/-0.03(stat) +/- 0.02(syst), for q(2) = 0.67 (GeV/c(2))(2). We compare the angular distributions of the lambda(+)(c) and lambda(-)(c) and find no evidence for CP violation: A(lambda(c)) = (alpha(lambda(c)) + alpha (lambda(c)))/(alpha(lambda(c))-alpha(lambda(c))) = 0.00 +/- 0.03(stat) +/- 0.01(syst) +/- 0.02, where the third error is from the uncertainty in the world average of the CP-violating parameter, A(lambda), for ppi(-).     

Observation of eta'c production in gammagamma fusion at CLEO

We report on the observation of the eta(')(c)(2(1)S0), the radial excitation of the eta(c)(1(1)S0) ground state of charmonium, in the two-photon fusion reaction gammagamma-->eta(')(c)-->K(0)(S)K+/-pi(-/+) in 13.6 fb(-1) of CLEO II/II.V data and 13.1 fb(-1) of CLEO III data. We obtain M(eta(')(c))=3642.9+/-3.1(stat)+/-1.5(syst) MeV and M(eta(c))=2981.8+/-1.3(stat)+/-1.5(syst) MeV. The corresponding values of hyperfine splittings between 1S0 and 3S1 states are DeltaM(hf)(1S)=115.1+/-2.0 MeV and DeltaM(hf)(2S)=43.1+/-3.4 MeV. Assuming that the eta(c) and eta(')(c) have equal branching fractions to K(S)Kpi, we obtain Gamma(gammagamma)(eta(')(c))=1.3+/-0.6 keV.