Effects of boundary walls on the properties of settling spheres

Numerical Simulations are performed, using Eulerian two fluid model (TFM) to investigate the effects of solid volume fraction and no-slip side walls on the settling particles. It is found that average settling velocity decreases with increasing volume fraction for both gas-solid (GS) and liquid-solid (LS) systems, in good agreement with the Richardson-Zaki 1 − ϕ n ${\left(1-\phi \right)}^{n}$ law. It was also noted that average velocity is independent of the boundary condition for both gas-solid (GS) and liquid-solid (LS) systems. The root mean square value of the solid volume fraction shows the increasing trend with volume fraction, caused by the many particle interactions. Furthermore, no-slip sidewalls were found to damp the velocity fluctuations quantitively, while following the well-known ϕ 1 / 2 ${\phi }^{1/2}$ scaling with volume fraction. Side walls were found to act as kinetic trap for the particles, damping the fluctuation near the walls and plateauing in the mid plane. These simulations showed that the GS system shows the higher solid fraction fluctuations that the LS system at the same Reynolds number, mainly because of the higher collision frequency (higher Stokes number) among the particles.

Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate

Although more than 75% of the proteome is composed of multidomain proteins, current knowledge of protein folding is based primarily on studies of isolated domains. In this work, we describe the folding mechanism of a multidomain tandem construct comprising two distinct covalently bound PDZ domains belonging to a protein called Whirlin, a scaffolding protein of the hearing apparatus. In particular, via a synergy between NMR and kinetic experiments, we demonstrate the presence of a misfolded intermediate that competes with productive folding. In agreement with the view that tandem domain swapping is a potential source of transient misfolding, we demonstrate that such a kinetic trap retains native-like functional activity, as shown by the preserved ability to bind its physiological ligand. Thus, despite the general knowledge that protein misfolding is intimately associated with dysfunction and diseases, we provide a direct example of a functionally competent misfolded state. Remarkably, a bioinformatics analysis of the amino acidic sequence of Whirlin from different species suggests that the tendency to perform tandem domain swapping between PDZ1 and PDZ2 is highly conserved, as demonstrated by their unexpectedly high sequence identity. On the basis of these observations, we discuss on a possible physiological role of such misfolded intermediate.

Group II intron as cold sensor for self-preservation and bacterial conjugation

Group II introns are self-splicing ribozymes and mobile genetic elements. Splicing is required for both expression of the interrupted host gene and intron retromobility. For the pRS01 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intron's host relaxase protein. Relaxase, in turn, initiates horizontal transfer of the conjugative pRS01 plasmid and stimulates retrotransposition of the intron. Little is known about how splicing of bacterial group II introns is influenced by environmental conditions. Here, we show that low temperatures can inhibit Ll.LtrB intron splicing. Whereas autocatalysis is abolished in the cold, splicing is partially restored by the intron-encoded protein (IEP). Structure profiling reveals cold-induced disruptions of key tertiary interactions, suggesting that a kinetic trap prevents the intron RNA from assuming its native state. Interestingly, while reduced levels of transcription and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread by conjugal transfer. Taken together, this study demonstrates not only the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress adaptation, but also maintenance of horizontal plasmid and intron transfer under cold-shock.

TAPBPR Promotes Antigen Loading on MHC-I Molecules Using a Peptide Trap

Chaperones tapasin and TAP-binding protein related (TAPBPR) perform the important functions of stabilizing nascent MHC-I molecules (chaperoning) and selecting high affinity peptides in the MHC-I groove (editing). While X-ray and cryo-EM snapshots of MHC-I in complex with TAPBPR and tapasin, respectively, have provided important insights into the peptide-deficient MHC-I groove structure, the molecular mechanism through which these chaperones influence the selection of specific amino acid sequences remains incompletely characterized. Of particular importance is a 16 residue loop in TAPBPR (corresponding to 11 residues in tapasin), which has been proposed to actively compete with incoming peptides by forming direct contacts in the F-pocket of the empty MHC-I groove. Using a deep mutational scanning functional analysis of TAPBPR, we find that important residues for the chaperoning activity are located on the major interaction surfaces with nascent MHC-I molecules, excluding the loop. However, interactions with properly conformed molecules toward peptide editing are influenced by loop mutations, in an MHC-I allele- and peptide-dependent manner. Detailed biophysical characterization by ITC, FP and NMR reveals that the loop does not interact with the peptide-deficient MHC-I groove to compete with incoming peptides, but instead promotes peptide loading by acting as a kinetic trap. Our results suggest that the longer loop of TAPBPR lowers the affinity threshold for peptide selection, to promote loading within subcellular compartments of reduced peptide concentration and to prevent disassembly of high affinity peptide-MHC-I complexes that are transiently interrogated by TAPBPR during editing.

High-affinity agonist binding to C5aR results from a cooperative two-site binding mechanism

A current challenge in the field of life sciences is to decipher, in their native environment, the functional activation of cell surface receptors upon binding of complex ligands. Lack of suitable nanoscopic methods has hampered our ability to meet this challenge in an experimental manner. Here, we use for the first time the interplay between atomic force microscopy, steered molecular dynamics and functional assays to elucidate the complex ligand-binding mechanism of C5a with the human G protein-coupled C5a receptor (C5aR). We have identified two independent binding sites acting in concert where the N-terminal C5aR serves as kinetic trap and the transmembrane domain as functional site. Our results corroborate the two-site binding model and clearly identify a cooperative effect between two binding sites within the C5aR. We anticipate that our methodology could be used for development and design of new therapeutic agents to negatively modulate C5aR activity.

Correction: Can aromaticity be a kinetic trap? Example of mechanically interlocked aromatic [2-5]catenanes built from cyclo[18]carbon

Correction for ‘Can aromaticity be a kinetic trap? Example of mechanically interlocked aromatic [2-5]catenanes built from cyclo[18]carbon’ by Nikita Fedik et al., Chem. Commun., 2020, 56, 2711–2714.

Can aromaticity be a kinetic trap? Example of mechanically interlocked aromatic [2-5]catenanes built from cyclo[18]carbon

Aromaticity serves as a kinetic trap for mechanically interlocked cyclo[18]carbon rings.

Triple Self-Sorting in Constitutional Dynamic Networks: Parallel Generation of Cu(I), Fe(II) and Zn(II) Imine-Based Metal Complexes

<div>Three imine-based metal complexes, having no overlap in terms of their compositions, have been simultaneously generated from the self-sorting of a constitutional dynamic library (CDL) containing three amines, three aldehydes and three metal salts. The hierarchical ordering of the stability of three metal complexes assembled and the leveraging of the antagonistic and agonistic relationships existing between the constituents within the constitutional dynamic network corresponding to the CDL were pivotal in achieving the desired sorting. The mechanism and the driving forces underlying the self-sorting process have been studied by NMR. The self-sorting of the Fe(II) and Zn(II) complexes was found to depend on an interplay between the thermodynamic driving forces and a kinetic trap involved in their assembling. These results also exemplify the concept of “simplexity” –the fact that the output of a self-assembling system may be simplified by increasing its initial compositional complexity—as the two complexes could self-sort only in the presence of the third pair of organic components, those of the Cu(I) complex.</div><br>

Triple Self-Sorting in Constitutional Dynamic Networks: Parallel Generation of Cu(I), Fe(II) and Zn(II) Imine-Based Metal Complexes

<div>Three imine-based metal complexes, having no overlap in terms of their compositions, have been simultaneously generated from the self-sorting of a constitutional dynamic library (CDL) containing three amines, three aldehydes and three metal salts. The hierarchical ordering of the stability of three metal complexes assembled and the leveraging of the antagonistic and agonistic relationships existing between the constituents within the constitutional dynamic network corresponding to the CDL were pivotal in achieving the desired sorting. The mechanism and the driving forces underlying the self-sorting process have been studied by NMR. The self-sorting of the Fe(II) and Zn(II) complexes was found to depend on an interplay between the thermodynamic driving forces and a kinetic trap involved in their assembling. These results also exemplify the concept of “simplexity” –the fact that the output of a self-assembling system may be simplified by increasing its initial compositional complexity—as the two complexes could self-sort only in the presence of the third pair of organic components, those of the Cu(I) complex.</div><br>