A threonine zipper that mediates protein–protein interactions: Structure and prediction

Abstract

We present the structure of an engineered protein-protein interface between two beta barrel proteins, which is mediated by interactions between threonine (Thr) residues. This Thr zipper structure suggests that the protein interface is stabilized by close-packing of the Thr residues, with only one intermonomer hydrogen bond (H-bond) between two of the Thr residues. This Thr-rich interface provides a unique opportunity to study the behavior of Thr in the context of many other Thr residues. In previous work, we have shown that the side chain (χ ) dihedral angles of interface and core Thr residues can be predicted with high accuracy using a hard sphere plus stereochemical constraint (HS) model. Here, we demonstrate that in the Thr-rich local environment of the Thr zipper structure, we are able to predict the χ dihedral angles of most of the Thr residues. Some, however, are not well predicted by the HS model. We therefore employed explicitly solvated molecular dynamics (MD) simulations to further investigate the side chain conformations of these residues. The MD simulations illustrate the role that transient H-bonding to water, in combination with steric constraints, plays in determining the behavior of these Thr side chains. Broader Audience Statement: Protein-protein interactions are critical to life and the search for ways to disrupt adverse protein-protein interactions involved in disease is an ongoing area of drug discovery. We must better understand protein-protein interfaces, both to be able to disrupt existing ones and to engineer new ones for a variety of biotechnological applications. We have discovered and characterized an artificial Thr-rich protein-protein interface. This novel interface demonstrates a heretofore unknown property of Thr-rich surfaces: mediating protein-protein interactions.

The R882H substitution in the human de novo DNA methyltransferase DNMT3A disrupts allosteric regulation by the tumor supressor p53

“…The ability of partner proteins to impact DNMT3A function depends on the formation of a complex, although this may not be sufficient. Anisotropy measurements are widely employed to assess protein-DNA, protein-protein interactions, and estimate the oligomeric state of proteins (51)(52)(53)(54)(55)(56)(57)(58). We previously used a 30-bp 5Ј 6-FAM-labeled duplex DNA (GCbox30), which contains a single recognition site for DNMT3A, to resolve the oligomeric state of DNMT3A (28,41).…”

Red fluorescent proteins engineered from green fluorescent proteins

“…We determined the crystal structures of AR1.0 and AG at 1.84 and 1.62 Å resolution, respectively. Although our AG contains three amino acid differences from the AG mutant whose structure is known (PDB ID 6ciu) ( 26 ), no significant structural difference was observed between them. The asymmetric unit of the AR1.0 crystal contains six molecules (one and a half tetramers), and that of the AG crystal four (one tetramer).…”

Insecticidal and Potato Growth Stimulation Activity of Bacillus thuringiensis kurstaki HD-1

“…Even polar groups can bind hydrogen to backbone peptide groups and inhibit hydrogen bonding of α-helices; these connections are established at the end of α-helices due to the presence of carbonyl oxygens or -NH groups, which are not related to hydrogen bonding of helix [39]. Recently, a protein-protein interaction mediated by beta barrel-based Ts has been described as follows: these Ts are packaged as a one-piece component, and the T-T H-bonds have relevance to structure stabilization [42]. E has various torsion angles whose stability is affected by the environment, and the zwitterionic form is stable; the carboxyl group of its side chain is ionized and polar (pKa = 4.3).…”