Computational prediction and validation of specific EmbR binding site on PknH

Insung Na; Huanqin Dai; Hantian Li; Anvita Gupta; David Kreda; Powell Zhang; Xiangyin Chen; Lixin Zhang; Gil Alterovitz

doi:10.1016/j.synbio.2021.11.006

Computational prediction and validation of specific EmbR binding site on PknH

Synth Syst Biotechnol. 2021 Nov 26;6(4):429-436. doi: 10.1016/j.synbio.2021.11.006. eCollection 2021 Dec.

Authors

Insung Na¹, Huanqin Dai^{1

2}, Hantian Li^{2

3}, Anvita Gupta⁴, David Kreda⁵, Powell Zhang⁶, Xiangyin Chen⁷, Lixin Zhang⁷, Gil Alterovitz⁸

Affiliations

¹ Computational Health Informatics Program, Boston Children's Hospital/Harvard Medical School, Boston, MA 02115, USA.
² State Key Laboratory of Mycology, Institute of Microbiology, Beijing, 100101 China.
³ Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
⁴ Department of Computer Sciences, Stanford University, Stanford CA 94305, USA.
⁵ Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
⁶ Lexington High School, Boston, MA 02115, USA.
⁷ State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
⁸ Department of Medicine, Brigham and Women's Hospital/Harvard Medical School, Boston, MA 02115, USA.

Abstract

Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear. Ethambutol (EMB), one of the well-known first - line drugs in tuberculosis treatment is, unfortunately, not free from drug resistance problems. Genomic studies have shown that some genetic mutations in Mycobacterium tuberculosis (Mtb) EmbR, and EmbC/A/B genes cause EMB resistance. EmbR-PknH pair controls embC/A/B operon, which encodes EmbC/A/B genes, and EMB interacts with EmbA/B proteins. However, the EmbR binding site on PknH was unknown. We conducted molecular simulation on the EmbR- peptides binding structures and discovered phosphorylated PknH 273-280 (N'-HEALS^PDPD-C') makes β strand with the EmbR FHA domain, as β-MoRF (MoRF; molecular recognition feature) does at its binding site. Hydrogen bond number analysis also supported the peptides' β-MoRF forming activity at the EmbR FHA domain. Also, we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation status. The discovery validated that Mtb PknH 273-280 (N'-HEALSDPD-C') has reliable EmbR binding affinity. This approach is revolutionary in the computer-aided drug discovery field, because it is the first trial to discover the protein-protein interaction site, and find binding partner in nature from this site.

Keywords: Binding site prediction; Disorder-to-order transition; Drug resistance; Molecular simulation; Protein intrinsic disorder.