How does Sec63 affect the conformation of Sec61 in yeast?

The Sec complex catalyzes the translocation of proteins of the secretory pathway into the endoplasmic reticulum and the integration of membrane proteins into the endoplasmic reticulum membrane. Some substrate peptides require the presence and involvement of accessory proteins such as Sec63. Recently, a structure of the Sec complex from Saccharomyces cerevisiae, consisting of the Sec61 channel and the Sec62, Sec63, Sec71 and Sec72 proteins was determined by cryo-electron microscopy (cryo-EM). Here, we show by co-precipitation that the accessory membrane protein Sec62 is not required for formation of stable Sec63-Sec61 contacts. Molecular dynamics simulations started from the cryo-EM conformation of Sec61 bound to Sec63 and of unbound Sec61 revealed how Sec63 affects the conformation of Sec61 lateral gate, plug, pore region and pore ring diameter via three intermolecular contact regions. Molecular docking of SRP-dependent vs. SRP-independent peptide chains into the Sec61 channel showed that the pore regions affected by presence/absence of Sec63 play a crucial role in positioning the signal anchors of SRP-dependent substrates nearby the lateral gate.

Discovery of two types of new porphyrin–C70 co-crystals: influence of intermolecular contact on the inherent resistance

Two types of supramolecular aggregates based on C70 were synthesised and their inherent resistances were analysed.

Improving intermolecular contact prediction through protein-protein interaction prediction using coevolutionary analysis with expectation-maximization

Predicting residue-residue contacts between interacting proteins is an important problem in bioinformatics. The growing wealth of sequence data can be used to infer these contacts through correlated mutation analysis on multiple sequence alignments of interacting homologs of the proteins of interest. This requires correct identification of pairs of interacting proteins for many species, in order to avoid introducing noise (i.e. non-interacting sequences) in the analysis that will decrease predictive performance. We have designed Ouroboros, a novel algorithm to reduce such noise in intermolecular contact prediction. Our method iterates between weighting proteins according to how likely they are to interact based on the correlated mutations signal, and predicting correlated mutations based on the weighted sequence alignment. We show that this approach accurately discriminates between protein interaction versus noninteraction and simultaneously improves the prediction of intermolecular contact residues compared to a naive application of correlated mutation analysis. Furthermore, the method relaxes the assumption of one-to-one interaction of previous approaches, allowing for the study of many-to-many interactions. Source code and test data are available at www.bif.wur.nl/

Comparison of the structural motifs and packing arrangements of six novel derivatives and one polymorph of 2-(1-phenyl-1H-1,2,3-triazol-4-yl)pyridine

The crystal structures of a new polymorph and seven new derivatives of 2-(1-phenyl-1H-1,2,3-triazol-4-yl)pyridine have been characterized and examined along with three structures from the literature to identify trends in their intermolecular contact patterns and packing arrangements in order to develop an insight into the crystallization behaviour of this class of compound. Seven unique C—H...Xcontacts were identified in the structures and three of these are present in four or more structures, indicating that these are reliable supramolecular synthons. Analysis of the packing arrangements of the molecules usingXPacidentified two closely related supramolecular constructs that are present in eight of the 11 structures; in all cases, the structures feature at least one of the three most common intermolecular contacts, suggesting a clear relationship between the intermolecular contacts and the packing arrangements of the structures. Both the intermolecular contacts and packing arrangements appear to be remarkably consistent between structures featuring different functional groups, with the expected exception of the carboxylic acid derivative 4-(4-(pyridin-2-yl)-1H-1,2,3-triazol-1-yl) benzoic acid (L11), where the introduction of a strong hydrogen-bonding group results in a markedly different supramolecular structure being adopted. The occurrence of these structural features has been compared with the packing efficiency of the structures and their melting points in order to assess the relative favourability of the supramolecular structural features in stabilizing the crystal structures.

4-Hydroxy-5-methoxy-N,1-dimethyl-2-oxo-N-[4-(trifluoromethyl)phenyl]-1,2-dihydroquinoline-3-carboxamide

The title compound, C20H17F3N2O4, named tasquinimod, is a second-generation oral quinoline-3-carboxamide analogue, which is currently in phase III clinical trials for the treatment of metastatic prostate cancer. The quinoline unit is almost planar (r.m.s. deviation of fitted atoms = 0.0075 Å). The carboxamide side chain, substituted at position 3, is tilted by 88.07 (7)° to the quinoline plane. Both the methyl and carbonyl groups of this carboxamide side chain are in asynconformation. The 4-(trifluoromethyl)phenyl plane is inclined at 50.62 (17)° to the plane of the carboxamide side chain, and at 87.14 (4)° to the plane of the quinoline ring system. The 4-hydroxy H atom acts as a double proton donor in an intramolecular hydrogen bond to the 5-position methoxy O atom and in an intermolecular contact to the 2-oxo group, generating a chain along [010] in the crystal structure.

3-(3-Methoxyphenyl)benzo[d]thiazolo[3,2-a]imidazol-9-ium hydrogen sulfate

In the title molecular salt, C16H13N2OS+·HSO4−, the thiazolo[3,2-a]benzimidazolium ring system is roughly planar [maximum deviation = 0.046 (3) Å] and makes a dihedral angle of 58.22 (11)° with the benzene ring. The methoxy group is almost coplanar with its attached benzene ring [Cmethyl—O—C—C = −1.6 (5)°]. In the crystal, the cation is linked to the anion by a bifurcated N—H...(O,O) hydrogen bond, generating anR12(4) ring motif. The ion pairs are then connected by a C—H...O hydrogen bond into inversion dimers and these dimers are further linked by O—H...O hydrogen bonds into an infinite tape along [100]. A π–π stacking interaction [centroid-to-centroid distance = 3.5738 (18) Å] and a short intermolecular contact [S...O = 2.830 (3) Å] are also observed.