The hydrophobic cluster on the surface of protein is the key structural basis for the SDS-resistance of chondroitinase VhChlABC

The application of chondroitinase requires consideration of the complex microenvironment of the target. Our previous research reported a marine-derived sodium dodecyl sulfate (SDS)-resistant chondroitinase VhChlABC. This study further investigated the mechanism of VhChlABC resistance to SDS. Focusing on the hydrophobic cluster on its strong hydrophilic surface, it was found that the reduction of hydrophobicity of surface residues Ala181, Met182, Met183, Ala184, Val185, and Ile305 significantly reduced the SDS resistance and stability. Molecular dynamics (MD) simulation and molecular docking analysis showed that I305G had more conformational flexibility around residue 305 than wild type (WT), which was more conducive to SDS insertion and binding. The affinity of A181G, M182A, M183A, V185A and I305G to SDS was significantly higher than that of WT. In conclusion, the surface hydrophobic microenvironment composed of six residues was the structural basis for SDS resistance. This feature could prevent the binding of SDS and the destruction of hydrophobic packaging by increasing the rigid conformation of protein and reducing the binding force of SDS-protein. The study provides a new idea for the rational design of SDS-resistant proteins and may further promote chondroitinase research in the targeted therapy of lung diseases under the pressure of pulmonary surfactant.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00201-1.

Using Surface Hydrophobicity Together with Empirical Potentials to Identify Protein-Protein Binding Sites: Application to the Interactions of E-cadherins

Studying the interactions within protein structures can inform about the details of how proteins of various types interact and aggregate. Empirical contact potentials have proven to be extremely important in the evaluation of individual modeled protein structures, but have found few applications to protein-protein interactions. In part, this is caused by a lack of properly formulated potentials with a proper reference state. Since the comparisons are made between different bound structures, the proper reference state should take into account other contacts. Therefore, a preferred reference state should be defined with respect to a given residue type interacting with an average residue instead of interacting with solvent as typically is used in derivation of statistical contact potentials. Here, a two-stage procedure for generating and evaluating interacting protein pairs is described, and an example of E-cadherin interactions is shown.