45 research outputs found
Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius
This is the author accepted manuscript. The final version is available from eLife Sciences Publications via the DOI in this recordData availability:
The atomic coordinates of SlaA were deposited in the Protein Data Bank (https://www.rcsb.org/) with accession numbers PDB-7ZCX, PDDB-8AN3, and PDB-8AN3 for pH 4, 7 and 10, respectively. The electron density maps were deposited in the EM DataResource (https://www.emdataresource.org/) with accession numbers EMD-14635, EMD-15531 and EMD-15531 for pH 4, 7 and 10, respectively. Sub-tomogram averaging map of the S-layer has been deposited in the EMDB (EMD-18127) and models of the hexameric and trimeric pores in the Protein Databank under accession codes PDB-8QP0 and PDB-8QOX, respectivelyOther structural data used in this study are: H. volcanii csg (PDB ID: 7PTR, http://dx.doi.org/10.2210/pdb7ptr/pdb), and C. crescentus RsaA ((N-terminus PDB ID: 6T72, http://dx.doi.org/10.2210/pdb6t72/pdb, C-terminus PDB ID: 5N8P, http://dx.doi.org/10.2210/pdb5n8p/pdb).Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single particle cryo electron microscopy (cryoEM), cryo electron tomography (cryoET) and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes, changes play important roles in S-layer assembly.European Research CouncilWellcome TrustWellcome TrustAgence Nationale de la RechercheAgence Nationale de la RechercheLeverhulme TrustBiotechnology and Biological Sciences Research Council (BBSRC
Introduction to technical communications of the 26th Int'l. Conference on logic programming (ICLP'10)
Abstract is not available
The Dynamical Ensemble of the Posner Molecule is not Symmetric
The Posner molecule, , has long been recognized
to have biochemical relevance in various physiological processes. It has found
recent attention for its possible role as a biological quantum information
processor, whereby the molecule purportedly maintains long-lived nuclear spin
coherences among its nuclei (presumed to be symmetrically
arranged), allowing it to function as a room temperature qubit. The structure
of the molecule has been of much dispute in the literature, although the
point group symmetry has often been assumed and exploited in
calculations. Using a variety of simulation techniques (including ab initio
molecular dynamics and structural relaxation), rigorous data analysis tools and
by exploring thousands of individual configurations, we establish that the
molecule predominantly assumes low symmetry structures ( and
) at room temperature, as opposed to the higher symmetry
configurations explored previously. Our findings have important implications on
the viability of this molecule as a qubit
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The Biological Qubit: Calcium Phosphate Dimers, not Trimers
The Posner molecule (calcium phosphate trimer), has been hypothesized to
function as a biological quantum information processor due to its supposedly
long-lived entangled P nuclear spin states. This hypothesis was
challenged by our recent finding that the molecule lacks a well-defined
rotational axis of symmetry -- an essential assumption in the proposal for
Posner-mediated neural processing -- and exists as an asymmetric dynamical
ensemble. Following up, we investigate here the spin dynamics of the molecule's
entangled P nuclear spins within the asymmetric ensemble. Our
simulations show that entanglement between two nuclear spins prepared in a Bell
state in separate Posner molecules decays on a sub-second timescale -- much
faster than previously hypothesized, and not long enough for super-cellular
neuronal processing. Calcium phosphate dimers however, are found to be
surprisingly resilient to decoherence and are able to preserve entangled
nuclear spins for hundreds of seconds, suggesting that neural processing might
occur through them instead
Driven spin dynamics enhances cryptochrome magnetoreception: Towards live quantum sensing
The mechanism underlying magnetoreception has long eluded explanation. A
popular hypothesis attributes this sense to the quantum coherent spin dynamics
of spin-selective recombination reactions of radical pairs in the protein
cryptochrome. However, concerns about the validity of the hypothesis have been
raised as unavoidable inter-radical interactions, such as strong
electron-electron dipolar coupling, appear to suppress its sensitivity. We
demonstrate that this can be overcome by driving the spin system through a
modulation of the inter-radical distance. It is shown that this dynamical
process markedly enhances geomagnetic field sensitivity in strongly coupled
radical pairs via a Landau-Zener type transition between singlet and triplet
states. These findings suggest that a "live" harmonically driven
magnetoreceptor can be more sensitive than its "dead" static counterpart.Comment: 7 pages, 4 figures, in addition to Supporting Material of 15 pages
and 12 figure