479 research outputs found
Folding and insertion thermodynamics of the transmembrane WALP peptide
The anchor of most integral membrane proteins consists of one or several
helices spanning the lipid bilayer. The WALP peptide, GWW(LA)(L)WWA, is a
common model helix to study the fundamentals of protein insertion and folding,
as well as helix-helix association in the membrane. Its structural properties
have been illuminated in a large number of experimental and simulation studies.
In this combined coarse-grained and atomistic simulation study, we probe the
thermodynamics of a single WALP peptide, focusing on both the insertion across
the water-membrane interface, as well as folding in both water and a membrane.
The potential of mean force characterizing the peptide's insertion into the
membrane shows qualitatively similar behavior across peptides and three force
fields. However, the Martini force field exhibits a pronounced secondary
minimum for an adsorbed interfacial state, which may even become the global
minimum---in contrast to both atomistic simulations and the alternative PLUM
force field. Even though the two coarse-grained models reproduce the free
energy of insertion of individual amino acids side chains, they both
underestimate its corresponding value for the full peptide (as compared with
atomistic simulations), hinting at cooperative physics beyond the residue
level. Folding of WALP in the two environments indicates the helix as the most
stable structure, though with different relative stabilities and chain-length
dependence.Comment: 12 pages, 5 figure
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[Ge<sub>2</sub>]<sup>4â</sup>Dumbbells with Very Short GeâGe Distances in the Zintl Phase Li<sub>3</sub>NaGe<sub>2</sub>: A Solid-State Equivalent to Molecular O<sub>2</sub>
The novel ternary Zintl phase Li3NaGe2 comprises alkali-metal cations and [Ge2]4â dumbbells. The diatomic [Ge2]4â unit is characterized by the shortest GeâGe distance (2.390(1)â
Ă
) ever observed in a Zintl phase and thus represents the first Ge=Ge double bond under such conditions, as also suggested by the (8âN) rule. Raman measurements support these findings. The multiple-bond character is confirmed by electronic-structure calculations, and an upfield 6Li NMR shift of â10.0âppm, which was assigned to the Li cations surrounded by the Ïâ
systems of three Ge dumbbells, further underlines this interpretation. For the unperturbed, ligand-free dumbbell in Li3NaGe2, the Ï-âbonding py and pz orbitals are degenerate as in molecular oxygen, which has singly occupied orbitals. The partially filled Ï-type bands of the neat solid Li3NaGe2 cross the Fermi level, resulting in metallic properties. Li3NaGe2 was synthesized from the elements as well as from binary reactants and subsequently characterized crystallographically.O.P. acknowledges
support from a Marie SkĆodowska-Curie Individual Fellowship.
L.M.S. is further grateful to the Fonds der Chemischen Industrie
and the Studienstiftung des deutschen Volkes for her fellowships.
A.J.K. gratefully acknowledges funding from the Alfred Kordelin
Foundation and computational resources from CSC â the Finnish
IT Center for Science.This is the accepted manuscript. The final version is available at http://onlinelibrary.wiley.com/wol1/doi/10.1002/ange.201508044/abstract
Electrokinetic behavior of two touching inhomogeneous biological cells and colloidal particles: Effects of multipolar interactions
We present a theory to investigate electro-kinetic behavior, namely,
electrorotation and dielectrophoresis under alternating current (AC) applied
fields for a pair of touching inhomogeneous colloidal particles and biological
cells. These inhomogeneous particles are treated as graded ones with physically
motivated model dielectric and conductivity profiles. The mutual polarization
interaction between the particles yields a change in their respective dipole
moments, and hence in the AC electrokinetic spectra. The multipolar
interactions between polarized particles are accurately captured by the
multiple images method. In the point-dipole limit, our theory reproduces the
known results. We find that the multipolar interactions as well as the spatial
fluctuations inside the particles can affect the AC electrokinetic spectra
significantly.Comment: Revised version with minor changes: References added and discussion
extende
Lithiumâion mobility in Li6B18(Li3N) and Li vacancy tuning in the solid solution Li6B18(Li3N)1âx(Li2O)x
All-solid-state batteries are promising candidates for safe energy-storage systems due to non-flammable solid electrolytes and the possibility to use metallic lithium as an anode. Thus, there is a challenge to design new solid electrolytes and to understand the principles of ion conduction on an atomic scale. We report on a new concept for compounds with high lithium ion mobility based on a rigid open-framework boron structure. The hostâguest structure Li6B18(Li3N) comprises large hexagonal pores filled with urn:x-wiley:14337851:media:anie202213962:anie202213962-math-0001 Li7N] strands that represent a perfect cutout from the structure of α-Li3N. Variable-temperature 7Liâ
NMR spectroscopy reveals a very high Li mobility in the template phase with a remarkably low activation energy below 19â
kJâmolâ1 and thus much lower than pristine Li3N. The formation of the solid solution of Li6B18(Li3N) and Li6B18(Li2O) over the complete compositional range allows the tuning of lithium defects in the template structure that is not possible for pristine Li3N and Li2O
Experimental and Computational Observations of Immunogenic Cobalt Porphyrin Lipid Bilayers: Nanodomain-Enhanced Antigen Association.
Cobalt porphyrin phospholipid (CoPoP) can incorporate within bilayers to enable non-covalent surface-display of antigens on liposomes by mixing with proteins bearing a polyhistidine tag (his-tag); however, the mechanisms for how this occurs are poorly understood. These were investigated using the his-tagged model antigen Pfs25, a protein antigen candidate for malaria transmission-blocking vaccines. Pfs25 was found to associate with the small molecule aquocobalamin, a form of vitamin B12 and a cobalt-containing corrin macrocycle, but without particle formation, enabling comparative assessment. Relative to CoPoP liposomes, binding and serum stability studies indicated a weaker association of Pfs25 to aquocobalamin or cobalt nitrilotriacetic acid (Co-NTA) liposomes, which have cobalt displayed in the aqueous phase on lipid headgroups. Antigen internalization by macrophages was enhanced with Pfs25 bound to CoPoP liposomes. Immunization in mice with Pfs25 bound to CoPoP liposomes elicited antibodies that recognized ookinetes and showed transmission-reducing activity. To explore the physical mechanisms involved, we employed molecular dynamics (MD) simulations of bilayers containing phospholipid, cholesterol, as well as either CoPoP or NTA-functionalized lipids. The results show that the CoPoP-containing bilayer creates nanodomains that allow access for a limited but sufficient amount of water molecules that could be replaced by his-tags due to their favorable free energy properties allowing for stabilization. The position of the metal center within the NTA liposomes was much more exposed to the aqueous environment, which could explain its limited capacity for stabilizing Pfs25. This study illustrates the impact of CoPoP-induced antigen particleization in enhancing vaccine efficacy, and provides molecular insights into the CoPoP bilayer properties that enable this
Dynamics of driven interfaces near isotropic percolation transition
We consider the dynamics and kinetic roughening of interfaces embedded in
uniformly random media near percolation treshold. In particular, we study
simple discrete ``forest fire'' lattice models through Monte Carlo simulations
in two and three spatial dimensions. An interface generated in the models is
found to display complex behavior. Away from the percolation transition, the
interface is self-affine with asymptotic dynamics consistent with the
Kardar-Parisi-Zhang universality class. However, in the vicinity of the
percolation transition, there is a different behavior at earlier times. By
scaling arguments we show that the global scaling exponents associated with the
kinetic roughening of the interface can be obtained from the properties of the
underlying percolation cluster. Our numerical results are in good agreement
with theory. However, we demonstrate that at the depinning transition, the
interface as defined in the models is no longer self-affine. Finally, we
compare these results to those obtained from a more realistic
reaction-diffusion model of slow combustion.Comment: 7 pages, 9 figures, to appear in Phys. Rev. E (1998
The source ambiguity problem: Distinguishing the effects of grammar and processing on acceptability judgments
Judgments of linguistic unacceptability may theoretically arise from either grammatical deviance or significant processing difficulty. Acceptability data are thus naturally ambiguous in theories that explicitly distinguish formal and functional constraints. Here, we consider this source ambiguity problem in the context of Superiority effects: the dispreference for ordering a wh-phrase in front of a syntactically âsuperiorâ wh-phrase in multiple wh-questions, e.g., What did who buy? More specifically, we consider the acceptability contrast between such examples and so-called D-linked examples, e.g., Which toys did which parents buy? Evidence from acceptability and self-paced reading experiments demonstrates that (i) judgments and processing times for Superiority violations vary in parallel, as determined by the kind of wh-phrases they contain, (ii) judgments increase with exposure, while processing times decrease, (iii) reading times are highly predictive of acceptability judgments for the same items, and (iv) the effects of the complexity of the wh-phrases combine in both acceptability judgments and reading times. This evidence supports the conclusion that D-linking effects are likely reducible to independently motivated cognitive mechanisms whose effects emerge in a wide range of sentence contexts. This in turn suggests that Superiority effects, in general, may owe their character to differential processing difficulty
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