Protein thermal denaturation is modulated by central residues in the protein structure network

Abstract

Network structural analysis, known as residue interaction networks or graphs (RIN or RIG, respectively) or protein structural networks or graphs (PSN or PSG, respectively), comprises a useful tool for detecting important residues for protein function, stability, folding and allostery. In RIN, the tertiary structure is represented by a network in which residues (nodes) are connected by interactions (edges). Such structural networks have consistently presented a few central residues that are important for shortening the pathways linking any two residues in a protein structure. To experimentally demonstrate that central residues effectively participate in protein properties, mutations were directed to seven central residues of the bglucosidase Sfbgly (b-D-glucoside glucohydrolase; EC 3.2.1.21). These mutations reduced the thermal stability of the enzyme, as evaluated by changes in transition temperature (T m ) and the denaturation rate at 45°C. Moreover, mutations directed to the vicinity of a central residue also caused significant decreases in the T m of Sfbgly and clearly increased the unfolding rate constant at 45°C. However, mutations at noncentral residues or at surrounding residues did not affect the thermal stability of Sfbgly. Therefore, the data reported in the present study suggest that the perturbation of the central residues reduced the stability of the native structure of Sfbgly. These results are in agreement with previous findings showing that networks are robust, whereas attacks on central nodes cause network failure. Finally, the present study demonstrates that central residues underlie the functional properties of proteins.

Using the Amino Acid Network to Modulate the Hydrolytic Activity of β-Glycosidases

“…While negative changes present ratios between 0 and 1, positive effects yield ratios higher than 1. Unless otherwise stated, all mutants tested here are correctly folded and present structural features similar to the wild-type enzyme, as seen by tryptophan fluorescence spectra or thermal shifting assays [9,14,28]. …”

Insight into the mechanism of protein thermostability based on the residue interaction degrees

“…For example, the T4 lysozyme mutant Ser 117 → Phe was isolated fortuitously and found to be more thermostable than wild-type by 1.1–1.4 kcal/mol [34]. While, the perturbation of the central residue (Phe 251) reduced the stability of the native structure of β-glucosidase [35].…”

Molecular mechanism of carbon nanotube to activate Subtilisin Carlsberg in polar and non-polar organic media

“…The method can provide network features (e.g., nodes, hubs, and links) and gain insight into the global properties of protein dynamics, topological rearrangements and functionally important residues. Consequently, it has been widely applied to study protein folding, protein stability, internal communications, allosterism and so on424344.…”