1D Motifs Research Articles

Supramolecular manganese(II) compounds influenced by conformational flexibility and rigidity of bis(4-pyridyl) containing bridging ligands

A covalent-bonded one-dimensional (1D) chain, [Mn(bpe)2(SCN)2]n (1) [bpe=1,2-bis(4-pyridyl)ethane], and a hydrogen-bonded two-dimensional (2D) sheet, [Mn(tbp)2(H2O)2(SCN)2] (2) [tbp=trans-1,2-bis(4-pyridyl)ethylene], have been prepared. Complex 1 can be viewed as a purely coordinative-bonded 1D motif doubly bridged by the bpe ligand that is a gauche conformational isomer with a large dihedral angle of 73.9°. The two bridging bpe ligands feature a shape of square with a dimension of 10.064 Å × 9.776 Å. The compound 2 possesses non-covalent bonding forces of hydrogen bonds and π–π interactions responsible for the fabrication of the 2D architecture. Magnetic susceptibility data for 1 were fitted by employing the infinite chain model (H=−J∑Si·Si+1) to give parameters of J=−0.052 cm−1 and g=2.00, indicating the presence of a weak anti-ferromagnetic coupling.

5-(4-Pyridyl)-1,3,4-oxadiazole-2(3H)-thione

In the crystal structure of the title compound, C7H5N3OS, the H atom of the thiol group is transferred to the neighboring N atom of the five-membered oxa­diazo­le ring. Intermolecular N—H⋯N interactions exist between adjacent mol­ecules, resulting in a one-dimensional (1D) supramolecular structure; π–π stacking interactions also exist between these 1D motifs.

Protein functional-group 3D motif and its applications

Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called “functional-group 3D motif”, based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and α/β hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.