Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry

Efficient and reliable method for the simulation of scanning tunneling images and spectra with local basis sets

Based on Bardeen's perturbative approach to tunneling, we have found an expression for the current between tip and sample, which can be efficiently coded in order to perform fast ab initio simulations of STM images. Under the observation that the potential between the electrodes should be nearly flat at typical tunnel gaps, we have addressed the difficulty in the computation of the tunneling matrix elements by considering a vacuum region of constant potential delimited by two surfaces (each of them close to tip and sample respectively), then propagating tip and sample wave functions by means of the vacuum Green's function, to finally obtain a closed form in terms of convolutions. The current is then computed for every tip-sample relative position and for every bias voltage in one shot. The electronic structure of tip and sample is calculated at the same footing, within density functional theory, and independently. This allows us to carry out multiple simulations for a given surface with a database of different tips. We have applied this method to the Si(111)-(7x7) and Ge(111)-c(2x8) surfaces. Topographies and spectroscopic data, showing a very good agreement with experiments, are presented.Comment: 10 pages, 11 figure

A solution-processable dissymmetric porous organic cage

A dissymmetric, soluble, porous organic cage from a low-cost racemic precursor.</p

The pneumococcal divisome: dynamic control of streptococcus pneumoniae cell division

Cell division in Streptococcus pneumoniae (pneumococcus) is performed and regulated by a protein complex consisting of at least 14 different protein elements; known as the divisome. Recent findings have advanced our understanding of the molecular events surrounding this process and have provided new understanding of the mechanisms that occur during the division of pneumococcus. This review will provide an overview of the key protein complexes and how they are involved in cell division. We will discuss the interaction of proteins in the divisome complex that underpin the control mechanisms for cell division and cell wall synthesis and remodelling that are required in S. pneumoniae, including the involvement of virulence factors and capsular polysaccharides

Cage doubling: solvent-mediated re-equilibration of a [3+6] prismatic organic cage to a large [6+12] truncated tetrahedron

We show that a [3 + 6] trigonal prismatic imine (a) cage can rearrange stoichiometrically and structurally to form a [6 + 12] trigonal prismatic imine (a) cage can rearrange stoichiometrically and structurally to form a [6 + 12 cage (b) with a truncated tetrahedral shape. Molecular simulations rationalize why this rearrangement was only observed for the prismatic [3 + 6] cage TCC1 but not for the analogous [3 + 6] cages, TCC2 and TCC3. Solvent was found to be a dominant factor in driving this rearrangement