Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability

• Published in: Biochimica et biophysica acta. General subjects Vol. 1865; no. 7; p. 129895
• Main Authors: Borges, Bruno, Gallo, Gloria, Coelho, Camila, Negri, Naiane, Maiello, Fernando, Hardy, Leon, Würtele, Martin
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.07.2021
• Subjects: Alkaline phosphatase; Crystal structure; Dynamic cross correlation; Molecular dynamics; Principal component analysis; Residue interaction network; Rotamer analysis; selection pressure; Shewanella; temperature; thermal stability; Thermus thermophilus; Vibrio; X-ray diffraction; Alkaline phosphatase; BC; SAP; Molecular dynamics; SsAP; CFU; MD; Residue interaction network; Crystal structure; KL; NMA; VsAP; DCC; TtAP; PME; pNPP; RMSD; AP; PCA; Thermus thermophilus; PC; pNP; PMSF; RIN; IPTG; Rotamer analysis; Dynamic cross correlation; Principal component analysis
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2021.129895

Understanding the determinants of protein thermostability is very important both from the theoretical and applied perspective. One emerging view in thermostable enzymes seems to indicate that a salt bridge/charged residue network plays a fundamental role in their thermostability. The structure of alkaline phosphatase (AP) from Thermus thermophilus HB8 was solved by X-ray crystallography at 2.1 Å resolution. The obtained structure was further analyzed by molecular dynamics studies at different temperatures (303 K, 333 K and 363 K) and compared to homologous proteins from the cold-adapted organisms Shewanella sp. and Vibrio strain G15–21. To analyze differences in measures of dynamic variation, several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis were used. Using hierarchical clustering, the obtained results were combined to determine residues showing high degree dynamical variations due to temperature jumps. Furthermore, dynamic cross correlation (DCC) analysis was carried out to characterize networks of charged residues. Top clustered residues showed a higher propensity for thermostabilizing mutations, indicating evolutionary pressure acting on thermophilic organisms. The description of rotamer distributions by Gini coefficients and Kullback–Leibler (KL) divergence both revealed significant correlations with temperature. DCC analysis revealed a significant trend to de-correlation of the movement of charged residues at higher temperatures. The de-correlation of charged residues detected in Thermus thermophilus AP, highlights the importance of dynamic electrostatic network interactions for the thermostability of this enzyme. •Crystal structure of alkaline phosphatase from Thermus thermophilus was solved.•Molecular dynamics analysis was performed with novel measures of dynamic variation.•Comparative analysis allows identification of thermostabilizing mutations.•Rotamer distribution modeled by KL-divergence correlates with temperature.•Dynamic cross correlation analysis shows energy dispersion effects upon heating.