Proteomics

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Targeted in situ cross-linking for determination of structure and interactions of SARS-CoV-2 proteins in the cellular context

ABSTRACT: Cross-linking mass spectrometry (XL-MS) has progressed from studying purified protein assemblies in-vitro towards investigating the same assemblies in intact cells, tissues, and even whole organisms (so called “in situ XL-MS”). In situ XL-MS offers the great advantage of reporting on the architectures of protein complexes as they occur inside cells and tissues. Here we developed a complete workflow of in-situ XL-MS followed by purification, and employ it to investigate SARS-CoV2 protein inside the host cell. We focused on three Sars-Cov-2 proteins for which the structural information is either missing or incomplete: NSP1, NSP2, and the Nucleocapsid protein (N protein). Relatively little is known about the structures of these specific proteins, which was our motivation for choosing them. We were able to identify considerable cross-link sets, of in-situ origin. Integration of the cross-links with additional structural information allowed us to build almost complete models for NSP2 and the N protein.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Severe Acute Respiratory Syndrome

SUBMITTER: Moriya Slavin  

LAB HEAD: Nir Kalisman

PROVIDER: PXD023487 | Pride | 2021-10-06

REPOSITORIES: Pride

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Dataset's files

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Action DRS
2020_09_09_02_NSP2_DSS_10cc_P2.raw Raw
2020_09_09_03_NSP2_DSS_10cc_P4.raw Raw
2020_09_23_01_DSS_NSP2_08_09_20_MiniS_B6.raw Raw
2020_09_23_02_DSS_NSP2_08_09_20_MiniS_B5.raw Raw
2020_09_23_03_DSS_NSP2_08_09_20_MiniS_B4.raw Raw
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Publications

Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2.

Slavin Moriya M   Zamel Joanna J   Zohar Keren K   Eliyahu Tsiona T   Braitbard Merav M   Brielle Esther E   Baraz Leah L   Stolovich-Rain Miri M   Friedman Ahuva A   Wolf Dana G DG   Rouvinski Alexander A   Linial Michal M   Schneidman-Duhovny Dina D   Kalisman Nir N  

Proceedings of the National Academy of Sciences of the United States of America 20210801 34

Atomic structures of several proteins from the coronavirus family are still partial or unavailable. A possible reason for this gap is the instability of these proteins outside of the cellular context, thereby prompting the use of in-cell approaches. In situ cross-linking and mass spectrometry (in situ CLMS) can provide information on the structures of such proteins as they occur in the intact cell. Here, we applied targeted in situ CLMS to structurally probe Nsp1, Nsp2, and nucleocapsid (N) prot  ...[more]

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