1
|
Buchko GW, Zhou M, Craig JK, Van Voorhis WC, Myler PJ. Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms - μs) dynamics in the C-terminal helix at the dimer interface. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:107-116. [PMID: 33392924 PMCID: PMC7779335 DOI: 10.1007/s12104-020-09992-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein's backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation studies, the backbone 1H, 13C, and 15N NMR chemical shifts for Nsp9 have been extensively assigned. These assignments were assisted by the preparation of an ~ 70% deuterated sample and residue-specific, 15N-labelled samples (V, L, M, F, and K). A major feature of the assignments was the "missing" amide resonances for N96-L106 in the 1H-15N HSQC spectrum, a region that comprises almost the complete C-terminal α-helix that forms a major part of the homodimer interface in the crystal structure of SARS-CoV-2 Nsp9, suggesting this region either undergoes intermediate motion in the ms to μs timescale and/or is heterogenous. These "missing" amide resonances do not unambiguously appear in the 1H-15N HSQC spectrum of SARS-CoV-2 Nsp9 collected at a concentration of 0.0007 mM. At this concentration, at the detection limit, native mass spectrometry indicates the protein is exclusively in the monomeric state, suggesting the intermediate motion in the C-terminal of Nsp9 may be due to intramolecular dynamics. Perhaps this intermediate ms to μs timescale dynamics is the physical basis for a previously suggested "fluidity" of the C-terminal helix that may be responsible for homophilic (Nsp9-Nsp9) and postulated heterophilic (Nsp9-Unknown) protein-protein interactions.
Collapse
Affiliation(s)
- Garry W Buchko
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA.
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA.
- School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - Mowei Zhou
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Justin K Craig
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease, Seattle, USA
- Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, Department of Medical Education and Biomedical Informatics, Department of Global Health, University of Washington, Seattle, Washington, USA
| |
Collapse
|
2
|
Shaheen S, Barrett KF, Subramanian S, Arnold SLM, Laureanti JA, Myler PJ, Van Voorhis WC, Buchko GW. Solution structure for an Encephalitozoon cuniculi adrenodoxin-like protein in the oxidized state. Protein Sci 2020; 29:809-817. [PMID: 31912584 DOI: 10.1002/pro.3818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
Encephalitozoon cuniculi is a unicellular, obligate intracellular eukaryotic parasite in the Microsporidia family and one of the agents responsible for microsporidosis infections in humans. Like most Microsporidia, the genome of E. cuniculi is markedly reduced and the organism contains mitochondria-like organelles called mitosomes instead of mitochondria. Here we report the solution NMR structure for a protein physically associated with mitosome-like organelles in E. cuniculi, the 128-residue, adrenodoxin-like protein Ec-Adx (UniProt ID Q8SV19) in the [2Fe-2S] ferredoxin superfamily. Oxidized Ec-Adx contains a mixed four-strand β-sheet, β2-β1-β4-β3 (↓↑↑↓), loosely encircled by three α-helices and two 310 -helices. This fold is similar to the structure observed in other adrenodoxin and adrenodoxin-like proteins except for the absence of a fifth anti-parallel β-strand next to β3 and the position of α3. Cross peaks are missing or cannot be unambiguously assigned for 20 amide resonances in the 1 H-15 N HSQC spectrum of Ec-Adx. These missing residues are clustered primarily in two regions, G48-V61 and L94-L98, containing the four cysteine residues predicted to ligate the paramagnetic [2Fe-2S] cluster. Missing amide resonances in 1 H-15 N HSQC spectra are detrimental to NMR-based solution structure calculations because 1 H-1 H NOE restraints are absent (glass half-empty) and this may account for the absent β-strand (β5) and the position of α3 in oxidized Ec-Adx. On the other hand, the missing amide resonances unambiguously identify the presence, and immediate environment, of the paramagnetic [2Fe-2S] cluster in oxidized Ec-Adx (glass half-full).
Collapse
Affiliation(s)
- Shareef Shaheen
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington
| | - Kayleigh F Barrett
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington
| | - Sandhya Subramanian
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington
| | - Samuel L M Arnold
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington
| | - Joseph A Laureanti
- Physical Chemistry Directorate, Pacific Northwest National Laboratory, Richland, Washington
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Medical Education and Biomedical Informatics & Department of Global Health, University of Washington, Seattle, Washington
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Disease, Center for Emerging and Re-emerging Infectious Disease, University of Washington, Seattle, Washington.,Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington
| | - Garry W Buchko
- Seattle Structural Genomics Center for Infectious Diseases, Seattle, Washington.,Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,School of Molecular Biosciences, Washington State University, Pullman, Washington
| |
Collapse
|