1
|
Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Pedroza Romo MJ, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. Structure 2023; 31:1589-1603.e6. [PMID: 37776857 PMCID: PMC10843481 DOI: 10.1016/j.str.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1 ubiquitin-associated (UBA) domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. No experimentally determined molecular structure of this unusual UBA domain is available. We fused the UBA domain to the 1TEL variant of the translocation ETS leukemia protein sterile alpha motif (TELSAM) crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and crystallize at protein concentrations as low as 0.2 mg/mL. Our studies support a mechanism of 1TEL fusion crystallization and show that 1TEL fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
Collapse
Affiliation(s)
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Wisdom O Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christina M Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA; Fritz B. Burns Cancer Research Laboratory, Brigham Young University, Provo, UT, USA.
| | - James D Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
| |
Collapse
|
2
|
Gajjar PL, Pedroza Romo MJ, Litchfield CM, Callahan M, Redd N, Nawarathnage S, Soleimani S, Averett J, Wilson E, Lewis A, Stewart C, Tseng YJ, Doukov T, Lebedev A, Moody JD. Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits. Acta Crystallogr D Struct Biol 2023; 79:925-943. [PMID: 37747038 PMCID: PMC10565734 DOI: 10.1107/s2059798323007246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
TELSAM-fusion crystallization has the potential to become a revolutionary tool for the facile crystallization of proteins. TELSAM fusion can increase the crystallization rate and enable crystallization at low protein concentrations, in some cases with minimal crystal contacts [Nawarathnage et al. (2022), Open Biol. 12, 210271]. Here, requirements for the linker composition between 1TEL and a fused CMG2 vWa domain were investigated. Ala-Ala, Ala-Val, Thr-Val and Thr-Thr linkers were evaluated, comparing metrics for crystallization propensity and crystal order. The effect on crystallization of removing or retaining the purification tag was then tested. It was discovered that increasing the linker bulk and retaining the 10×His purification tag improved the diffraction resolution, likely by decreasing the number of possible vWa-domain orientations in the crystal. Additionally, it was discovered that some vWa-domain binding modes are correlated with scrambling of the 1TEL polymer orientation in crystals and an effective mitigation strategy for this pathology is presented.
Collapse
Affiliation(s)
- Parag L. Gajjar
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Maria J. Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Celeste M. Litchfield
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Miles Callahan
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Nathan Redd
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Supeshala Nawarathnage
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Jacob Averett
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Elijah Wilson
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Andrew Lewis
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Yi-Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, USA
| | - Andrey Lebedev
- Scientific Computing, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, 701 East University Parkway, Provo, UT 84602, USA
| |
Collapse
|
3
|
Kottur J, White KM, Rodriguez ML, Rechkoblit O, Quintana-Feliciano R, Nayar A, García-Sastre A, Aggarwal AK. Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. PLoS Pathog 2023; 19:e1011546. [PMID: 37523415 PMCID: PMC10414583 DOI: 10.1371/journal.ppat.1011546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/10/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
Collapse
Affiliation(s)
- Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - M. Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Richard Quintana-Feliciano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ahana Nayar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| |
Collapse
|
4
|
Nawarathnage S, Tseng YJ, Soleimani S, Smith T, Romo MJP, Abiodun WO, Egbert CM, Madhusanka D, Bunn D, Woods B, Tsubaki E, Stewart C, Brown S, Doukov T, Andersen JL, Moody JD. Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544429. [PMID: 37398013 PMCID: PMC10312729 DOI: 10.1101/2023.06.14.544429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 Å. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.
Collapse
Affiliation(s)
- Supeshala Nawarathnage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Yi Jie Tseng
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
- These authors contributed equally to this work
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Maria J Pedroza Romo
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Wisdom Oshireku Abiodun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Christina M. Egbert
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Deshan Madhusanka
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Derick Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Bridger Woods
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Evan Tsubaki
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, California, United States of America
| | - Joshua L. Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, United States of America
| |
Collapse
|
5
|
Gajjar PL, Romo MJP, Litchfield CM, Callahan M, Redd N, Nawarathnage S, Soleimani S, Averett J, Wilson E, Lewis A, Stewart C, Tseng YJJ, Doukov T, Lebedev A, Moody JD. Decreasing the flexibility of the TELSAM-target protein linker and omitting the cleavable fusion tag improves crystal order and diffraction limits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540586. [PMID: 37293010 PMCID: PMC10245584 DOI: 10.1101/2023.05.12.540586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
TELSAM crystallization promises to become a revolutionary tool for the facile crystallization of proteins. TELSAM can increase the rate of crystallization and form crystals at low protein concentrations without direct contact between TELSAM polymers and, in some cases, with very minimal crystal contacts overall (Nawarathnage et al ., 2022). To further understand and characterize TELSAM-mediated crystallization, we sought to understand the requirements for the composition of the linker between TELSAM and the fused target protein. We evaluated four different linkers Ala-Ala, Ala-Val, Thr-Val, and Thr-Thr, between 1TEL and the human CMG2 vWa domain. We compared the number of successful crystallization conditions, the number of crystals, the average and best diffraction resolution, and the refinement parameters for the above constructs. We also tested the effect of the fusion protein SUMO on crystallization. We discovered that rigidification of the linker improved diffraction resolution, likely by decreasing the number of possible orientations of the vWa domains in the crystal, and that omitting the SUMO domain from the construct also improved the diffraction resolution. Synopsis We demonstrate that the TELSAM protein crystallization chaperone can enable facile protein crystallization and high-resolution structure determination. We provide evidence to support the use of short but flexible linkers between TELSAM and the protein of interest and to support the avoidance of cleavable purification tags in TELSAM-fusion constructs.
Collapse
|
6
|
High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development. Nat Struct Mol Biol 2022; 29:850-853. [PMID: 36075969 PMCID: PMC10388636 DOI: 10.1038/s41594-022-00828-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/28/2022] [Indexed: 11/08/2022]
Abstract
Emergence of SARS-CoV-2 coronavirus has led to millions of deaths globally. We present three high-resolution crystal structures of the SARS-CoV-2 nsp14 N7-methyltransferase core bound to S-adenosylmethionine (1.62 Å), S-adenosylhomocysteine (1.55 Å) and sinefungin (1.41 Å). We identify features of the methyltransferase core that are crucial for the development of antivirals and show SAH as the best scaffold for the design of antivirals against SARS-CoV-2 and other pathogenic coronaviruses.
Collapse
|
7
|
Nawarathnage S, Soleimani S, Mathis MH, Bezzant BD, Ramírez DT, Gajjar P, Bunn DR, Stewart C, Smith T, Pedroza Romo MJ, Brown S, Doukov T, Moody JD. Crystals of TELSAM-target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts. Open Biol 2022; 12:210271. [PMID: 35232248 PMCID: PMC8889177 DOI: 10.1098/rsob.210271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/05/2022] [Indexed: 01/09/2023] Open
Abstract
While conducting pilot studies into the usefulness of fusion to TELSAM polymers as a potential protein crystallization strategy, we observed novel properties in crystals of two TELSAM-target protein fusions, as follows. (i) A TELSAM-target protein fusion can crystallize more rapidly and with greater propensity than the same target protein alone. (ii) TELSAM-target protein fusions can be crystallized at low protein concentrations. This unprecedented observation suggests a route to crystallize proteins that can only be produced in microgram amounts. (iii) The TELSAM polymers themselves need not directly contact one another in the crystal lattice in order to form well-diffracting crystals. This novel observation is important because it suggests that TELSAM may be able to crystallize target proteins too large to allow direct inter-polymer contacts. (iv) Flexible TELSAM-target protein linkers can allow target proteins to find productive binding modes against the TELSAM polymer. (v) TELSAM polymers can adjust their helical rise to allow fused target proteins to make productive crystal contacts. (vi). Fusion to TELSAM polymers can stabilize weak inter-target protein crystal contacts. We report features of these TELSAM-target protein crystal structures and outline future work needed to validate TELSAM as a crystallization chaperone and determine best practices for its use.
Collapse
Affiliation(s)
| | - Sara Soleimani
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Moriah H. Mathis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Braydan D. Bezzant
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Diana T. Ramírez
- Department of Natural Sciences, California State University Chico, Chico, CA, USA
| | - Parag Gajjar
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Derick R. Bunn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Cameron Stewart
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tobin Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | | | - Seth Brown
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Tzanko Doukov
- Macromolecular Crystallography Group, Structural Molecular Biology Resource, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - James D. Moody
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| |
Collapse
|