1
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Ixquiac M, Reynoso FJ, Schmidt M, Mazur TR, Zhao T, Gay HA, Hugo GD, Henke LE, Michalski JM, Velarde A, De Falla V, Reyes FE, Montenegro E, Ruiz Furlan EA, Sun B. Bridging the Gap of Radiotherapy Treatment Planning Quality between High-Income, and Low- and Middle-Income Countries Using Knowledge-Based Planning. Int J Radiat Oncol Biol Phys 2023; 117:e591. [PMID: 37785788 DOI: 10.1016/j.ijrobp.2023.06.1941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiotherapy departments in low- and middle-income countries (LMICs) like Guatemala have recently introduced intensity-modulated radiotherapy (IMRT). IMRT has become the standard of care in high-income countries (HIC) due to reduced toxicity and improved outcomes in some cancers. The purpose of this work is to show the feasibility of adapting knowledge-based (KB) models established in a HIC to a LMIC lacking experience in IMRT to improve plan quality and planning efficiency. MATERIALS/METHODS A Halcyon Linac was installed at our clinic in Guatemala in 2019 and has been used to treat approximately 90 patients daily with IMRT. A model developed on a cohort of head and neck cancer patients at a US academic radiotherapy center were applied at our center to create 20head and neck VMAT plans with different prescriptions, including simultaneous-integrated and sequential boosts. RESULTS The plans created using the KB models achieved similar coverage of the planning target volume for each plan KB plans showed better 1) Parotid sparing with a mean dose reduction between 5%-25% and spinal cord maximum dose reduction between 3%-15%. The time efficiency to create VMAT plans using KB model versus manual planning improved four-fold, on average one hour versus more than 4 hours, respectively. CONCLUSION Despite different prescriptions, guidelines and demographics of cancer patients between two institutions in a HIC and LMIC, this work demonstrates that KB planning can be used to generate better and more consistent VMAT plans versus manually created plans. In addition, KB planning has the potential to greatly increase planning efficiency higher efficiency and help address the shortage of medical physicists and dosimetrists in LMICs.
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Affiliation(s)
- M Ixquiac
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - F J Reynoso
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - M Schmidt
- Washington University in St. Louis, St. Louis, MO
| | - T R Mazur
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - T Zhao
- Washington University in St. Louis, St. Louis, MO
| | - H A Gay
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - G D Hugo
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - L E Henke
- University Hospitals, Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH
| | - J M Michalski
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - A Velarde
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - V De Falla
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - F E Reyes
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - E Montenegro
- Liga Nacional Contra el Cáncer / INCAN, Guatemala, Guatemala
| | - E A Ruiz Furlan
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - B Sun
- Baylor College of Medicine, Department of Radiation Oncology, Houston, TX
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2
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Ixquiac M, Montenegro E, Reynoso FJ, Schmidt M, Mazur TR, Zhao T, Gay HA, Hugo GD, Henke LE, Michalski JM, Velarde A, De Falla V, Reyes FE, Furlan EAR, Sun B. Standardizing LT Chest Wall Radiotherapy Treatment Planning in a Low- or Middle- Income Country Radiotherapy Clinic Using Knowledge Based Planning. Int J Radiat Oncol Biol Phys 2023; 117:e675-e676. [PMID: 37785990 DOI: 10.1016/j.ijrobp.2023.06.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiotherapy departments in low- or middle-income countries (LMICs) tend to lag behind introducing emerging technologies like intensity-modulated radiotherapy (IMRT). IMRT has become the standard of care in high-income countries (HIC) due to reduced toxicity and improved outcomes in a wide variety of cancers. The purpose of this work is showing the results of left Chest-Wall knowledge-based planning (KBP) standardization and implementation in a LMIC setting. MATERIALS/METHODS A Halcyon Linac was installed at our clinic in Guatemala in 2019 and currently used to treat ∼90 IMRT patients daily. The standardization of IMRT procedures has been difficult for complex sites like chest-wall. The steps for standardization included: AAPM TG-263 nomenclature implementation, and planning workflows within the TPS, creation of optimization structures, and plan quality evaluation following RTOG1005 protocol hypofractionation arm. 25 plans were created manually achieving all RTOG1005 protocol constraints. The statistics were analyzed trough the model analytics tool provided by KPB manufacturer. RESULTS The results show that more plans are needed to improve the KBP model. This initial model was used to create a standardized clinical protocol in the TPS in order to continue adding plans to the KBP model database. This approach ensures that we obtain consistent plan quality and standardize our planning. The manual planning objectives achieved: CONCLUSION: The experience using the TPS to standardize our treatment planning process achieved good consistency in our planning objectives. This approach will help create KBP models according to our own clinic-specific requirements. Future work will be made to compare our LMIC KBP models with those made at a HIC academic radiotherapy center.
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Affiliation(s)
- M Ixquiac
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - E Montenegro
- Liga Nacional Contra el Cáncer / INCAN, Guatemala, Guatemala
| | - F J Reynoso
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - M Schmidt
- Washington University in St. Louis, St. Louis, MO
| | - T R Mazur
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - T Zhao
- Washington University in St. Louis, St. Louis, MO
| | - H A Gay
- Washington University School of Medicine in St. Louis, Department of Radiation Oncology, St. Louis, MO
| | - G D Hugo
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - L E Henke
- University Hospitals, Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH
| | - J M Michalski
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - A Velarde
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - V De Falla
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - F E Reyes
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - E A Ruiz Furlan
- Liga Nacional Contra el Cáncer e Instituto de Cancerología LIGA-INCAN, Guatemala City, Guatemala
| | - B Sun
- Baylor College of Medicine, Department of Radiation Oncology, Houston, TX
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3
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Vicens Q, Mondragón E, Reyes FE, Coish P, Aristoff P, Berman J, Kaur H, Kells KW, Wickens P, Wilson J, Gadwood RC, Schostarez HJ, Suto RK, Blount KF, Batey RT. Structure-Activity Relationship of Flavin Analogues That Target the Flavin Mononucleotide Riboswitch. ACS Chem Biol 2018; 13:2908-2919. [PMID: 30107111 DOI: 10.1021/acschembio.8b00533] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The flavin mononucleotide (FMN) riboswitch is an emerging target for the development of novel RNA-targeting antibiotics. We previously discovered an FMN derivative, 5FDQD, that protects mice against diarrhea-causing Clostridium difficile bacteria. Here, we present the structure-based drug design strategy that led to the discovery of this fluoro-phenyl derivative with antibacterial properties. This approach involved the following stages: (1) structural analysis of all available free and bound FMN riboswitch structures; (2) design, synthesis, and purification of derivatives; (3) in vitro testing for productive binding using two chemical probing methods; (4) in vitro transcription termination assays; and (5) resolution of the crystal structures of the FMN riboswitch in complex with the most mature candidates. In the process, we delineated principles for productive binding to this riboswitch, thereby demonstrating the effectiveness of a coordinated structure-guided approach to designing drugs against RNA.
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Affiliation(s)
- Quentin Vicens
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Estefanía Mondragón
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Francis E. Reyes
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
| | - Philip Coish
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Paul Aristoff
- Aristoff Consulting LLC, 3726 Green Spring Drive, Fort Collins, Colorado 80528, United States
| | - Judd Berman
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Harpreet Kaur
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Kevin W. Kells
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Phil Wickens
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Jeffery Wilson
- Dalton Pharma Services, 349 Wildcat Road, Toronto, ON M3J 2S3, Canada
| | - Robert C. Gadwood
- Kalexsyn, Inc., 4502 Campus Drive, Kalamazoo, Michigan 49008, United States
| | | | - Robert K. Suto
- Xtal BioStructures, Inc., 12 Michigan Drive, Natick, Massachusetts 01760, United States
| | - Kenneth F. Blount
- BioRelix Inc., 124 Washington Street, Foxborough, Massachusetts 02035, United States
| | - Robert T. Batey
- Department of Chemistry and Biochemistry, University of Colorado, 596 UCB, Boulder, Colorado 80309, United States
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4
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Wright ZVF, McCarthy S, Dickman R, Reyes FE, Sanchez-Martinez S, Cryar A, Kilford I, Hall A, Takle AK, Topf M, Gonen T, Thalassinos K, Tabor AB. The Role of Disulfide Bond Replacements in Analogues of the Tarantula Toxin ProTx-II and Their Effects on Inhibition of the Voltage-Gated Sodium Ion Channel Na v1.7. J Am Chem Soc 2017; 139:13063-13075. [PMID: 28880078 PMCID: PMC5618157 DOI: 10.1021/jacs.7b06506] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Spider
venom toxins, such as Protoxin-II (ProTx-II), have recently
received much attention as selective Nav1.7 channel blockers,
with potential to be developed as leads for the treatment of chronic
nocioceptive pain. ProTx-II is a 30-amino acid peptide with three
disulfide bonds that has been reported to adopt a well-defined inhibitory
cystine knot (ICK) scaffold structure. Potential drawbacks with such
peptides include poor pharmacodynamics and potential scrambling of
the disulfide bonds in vivo. In order to address
these issues, in the present study we report the solid-phase synthesis
of lanthionine-bridged analogues of ProTx-II, in which one of the
three disulfide bridges is replaced with a thioether linkage, and
evaluate the biological properties of these analogues. We have also
investigated the folding and disulfide bridging patterns arising from
different methods of oxidation of the linear peptide precursor. Finally,
we report the X-ray crystal structure of ProTx-II to atomic resolution;
to our knowledge this is the first crystal structure of an ICK spider
venom peptide not bound to a substrate.
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Affiliation(s)
- Zoë V F Wright
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Stephen McCarthy
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Rachael Dickman
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia 20147, United States
| | - Silvia Sanchez-Martinez
- Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia 20147, United States
| | - Adam Cryar
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London , Gower Street, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - Ian Kilford
- European Knowledge Centre, Eisai Limited , Mosquito Way, Hatfield, Hertfordshire AL10 9SN, United Kingdom
| | - Adrian Hall
- European Knowledge Centre, Eisai Limited , Mosquito Way, Hatfield, Hertfordshire AL10 9SN, United Kingdom
| | - Andrew K Takle
- European Knowledge Centre, Eisai Limited , Mosquito Way, Hatfield, Hertfordshire AL10 9SN, United Kingdom
| | - Maya Topf
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute , Ashburn, Virginia 20147, United States
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London , Gower Street, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London , London WC1E 7HX, United Kingdom
| | - Alethea B Tabor
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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5
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Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Jiang L, Westermark GT, Gonen T, Eisenberg DS. The Cryo-EM Method Micro-ED Structure Determination of Type II Diabetes-Related Protein Segments. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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6
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Krotee P, Rodriguez JA, Sawaya MR, Cascio D, Reyes FE, Shi D, Hattne J, Nannenga BL, Oskarsson ME, Philipp S, Griner S, Jiang L, Glabe CG, Westermark GT, Gonen T, Eisenberg DS. Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity. eLife 2017; 6. [PMID: 28045370 PMCID: PMC5207774 DOI: 10.7554/elife.19273] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/01/2016] [Indexed: 01/09/2023] Open
Abstract
hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19-29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15-25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxic effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19-29 S20G may serve as a model for the toxic spine of hIAPP.
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Affiliation(s)
- Pascal Krotee
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Jose A Rodriguez
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Michael R Sawaya
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Duilio Cascio
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Marie E Oskarsson
- Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Stephan Philipp
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States
| | - Sarah Griner
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
| | - Lin Jiang
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States.,Brain Research Institute (BRI), University of California, Los Angeles, Los Angeles, United States
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, United States.,Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David S Eisenberg
- Department of Biological Chemistry, Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States.,UCLA-DOE Institute, University of California, Los Angeles, Los Angeles, United States
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7
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Liu S, Hattne J, Reyes FE, Sanchez-Martinez S, Jason de la Cruz M, Shi D, Gonen T. Atomic resolution structure determination by the cryo-EM method MicroED. Protein Sci 2016; 26:8-15. [PMID: 27452773 DOI: 10.1002/pro.2989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free-electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future.
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Affiliation(s)
- Shian Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Silvia Sanchez-Martinez
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20148
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8
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Hammel M, Amlanjyoti D, Reyes FE, Chen JH, Parpana R, Tang HYH, Larabell CA, Tainer JA, Adhya S. HU multimerization shift controls nucleoid compaction. Sci Adv 2016; 2:e1600650. [PMID: 27482541 PMCID: PMC4966879 DOI: 10.1126/sciadv.1600650] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/14/2016] [Indexed: 05/05/2023]
Abstract
Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasive Escherichia coli into an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. (M.H.); (J.A.T.)
| | - Dhar Amlanjyoti
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Francis E. Reyes
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jian-Hua Chen
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Rochelle Parpana
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henry Y. H. Tang
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Carolyn A. Larabell
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - John A. Tainer
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
- Corresponding author. (M.H.); (J.A.T.)
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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9
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Hattne J, Shi D, de la Cruz MJ, Reyes FE, Gonen T. Modeling truncated pixel values of faint reflections in MicroED images. J Appl Crystallogr 2016; 49:1029-1034. [PMID: 27275145 PMCID: PMC4886988 DOI: 10.1107/s1600576716007196] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/27/2016] [Indexed: 12/04/2022] Open
Abstract
The weak pixel counts surrounding the Bragg spots in a diffraction image are important for establishing a model of the background underneath the peak and estimating the reliability of the integrated intensities. Under certain circumstances, particularly with equipment not optimized for low-intensity measurements, these pixel values may be corrupted by corrections applied to the raw image. This can lead to truncation of low pixel counts, resulting in anomalies in the integrated Bragg intensities, such as systematically higher signal-to-noise ratios. A correction for this effect can be approximated by a three-parameter lognormal distribution fitted to the weakly positive-valued pixels at similar scattering angles. The procedure is validated by the improved refinement of an atomic model against structure factor amplitudes derived from corrected micro-electron diffraction (MicroED) images.
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Affiliation(s)
- Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - M. Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Francis E. Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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10
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Shi D, Nannenga BL, de la Cruz MJ, Liu J, Sawtelle S, Calero G, Reyes FE, Hattne J, Gonen T. The collection of MicroED data for macromolecular crystallography. Nat Protoc 2016; 11:895-904. [PMID: 27077331 PMCID: PMC5357465 DOI: 10.1038/nprot.2016.046] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.
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Affiliation(s)
- Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Jinyang Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Steven Sawtelle
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
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11
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Rodriguez JA, Ivanova MI, Sawaya MR, Cascio D, Reyes FE, Shi D, Sangwan S, Guenther EL, Johnson LM, Zhang M, Jiang L, Arbing MA, Nannenga BL, Hattne J, Whitelegge J, Brewster AS, Messerschmidt M, Boutet S, Sauter NK, Gonen T, Eisenberg DS. Structure of the toxic core of α-synuclein from invisible crystals. Nature 2015; 525:486-90. [PMID: 26352473 DOI: 10.1038/nature15368] [Citation(s) in RCA: 444] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/13/2015] [Indexed: 12/18/2022]
Abstract
The protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.
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Affiliation(s)
- Jose A Rodriguez
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Magdalena I Ivanova
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Michael R Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Duilio Cascio
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Francis E Reyes
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Dan Shi
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Smriti Sangwan
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Elizabeth L Guenther
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Lisa M Johnson
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Meng Zhang
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Lin Jiang
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Mark A Arbing
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
| | - Brent L Nannenga
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - Julian Whitelegge
- Box 42, NPI-Semel Institute, 760 Westwood Plaza, UCLA, Los Angeles, California 90024, USA
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA
| | - David S Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA
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12
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Hattne J, Reyes FE, Nannenga BL, Shi D, de la Cruz MJ, Leslie AGW, Gonen T. MicroED data collection and processing. Acta Crystallogr A Found Adv 2015; 71:353-60. [PMID: 26131894 PMCID: PMC4487423 DOI: 10.1107/s2053273315010669] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 06/02/2015] [Indexed: 11/30/2022]
Abstract
The collection and processing of MicroED data are presented. MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.
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Affiliation(s)
- Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - M Jason de la Cruz
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew G W Leslie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, England
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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13
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Abstract
MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. DOI:http://dx.doi.org/10.7554/eLife.03600.001
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Affiliation(s)
- Brent L Nannenga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Dan Shi
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Johan Hattne
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Francis E Reyes
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Tamir Gonen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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14
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Abstract
Structures of riboswitch receptor domains bound to their effector have revealed how mRNAs recognize diverse small molecules, but mechanistic details into its linkage with regulation of gene expression remain elusive1,2. To address this, we solved crystal structures of two different classes of cobalamin (vitamin B12) binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B12 derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin with relatively few hydrogen bonding interactions that typically govern RNA-small molecule recognition. We show that a composite cobalamin/RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.
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Affiliation(s)
- James E Johnson
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA
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15
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Trausch JJ, Ceres P, Reyes FE, Batey RT. The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer. Structure 2011; 19:1413-23. [PMID: 21906956 DOI: 10.1016/j.str.2011.06.019] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 12/16/2022]
Abstract
Transport and biosynthesis of folate and its derivatives are frequently controlled by the tetrahydrofolate (THF) riboswitch in Firmicutes. We have solved the crystal structure of the THF riboswitch aptamer in complex with folinic acid, a THF analog. Uniquely, this structure reveals two molecules of folinic acid binding to a single structured domain. These two sites interact with ligand in a similar fashion, primarily through recognition of the reduced pterin moiety. 7-deazaguanine, a soluble analog of guanine, binds the riboswitch with nearly the same affinity as its natural effector. However, 7-deazaguanine effects transcriptional termination to a substantially lesser degree than folinic acid, suggesting that the cellular guanine pool does not act upon the THF riboswitch. Under physiological conditions the ligands display strong cooperative binding, with one of the two sites playing a greater role in eliciting the regulatory response, which suggests that the second site may play another functional role.
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Affiliation(s)
- Jeremiah J Trausch
- Department of Chemistry and Biochemistry, University of Colorado, UCB 215, Boulder, CO 80309-0215, USA
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16
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Daldrop P, Reyes FE, Robinson DA, Hammond CM, Lilley DM, Batey RT, Brenk R. Novel ligands for a purine riboswitch discovered by RNA-ligand docking. ACTA ACUST UNITED AC 2011; 18:324-35. [PMID: 21439477 PMCID: PMC3119931 DOI: 10.1016/j.chembiol.2010.12.020] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/02/2010] [Accepted: 12/29/2010] [Indexed: 01/01/2023]
Abstract
The increasing number of RNA crystal structures enables a structure-based approach to the discovery of new RNA-binding ligands. To develop the poorly explored area of RNA-ligand docking, we have conducted a virtual screening exercise for a purine riboswitch to probe the strengths and weaknesses of RNA-ligand docking. Using a standard protein-ligand docking program with only minor modifications, four new ligands with binding affinities in the micromolar range were identified, including two compounds based on molecular scaffolds not resembling known ligands. RNA-ligand docking performed comparably to protein-ligand docking indicating that this approach is a promising option to explore the wealth of RNA structures for structure-based ligand design.
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Affiliation(s)
- Peter Daldrop
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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17
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Edwards AL, Reyes FE, Héroux A, Batey RT. Structural basis for recognition of S-adenosylhomocysteine by riboswitches. RNA 2010; 16:2144-55. [PMID: 20864509 PMCID: PMC2957054 DOI: 10.1261/rna.2341610] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 08/16/2010] [Indexed: 05/25/2023]
Abstract
S-adenosyl-(L)-homocysteine (SAH) riboswitches are regulatory elements found in bacterial mRNAs that up-regulate genes involved in the S-adenosyl-(L)-methionine (SAM) regeneration cycle. To understand the structural basis of SAH-dependent regulation by RNA, we have solved the structure of its metabolite-binding domain in complex with SAH. This structure reveals an unusual pseudoknot topology that creates a shallow groove on the surface of the RNA that binds SAH primarily through interactions with the adenine ring and methionine main chain atoms and discriminates against SAM through a steric mechanism. Chemical probing and calorimetric analysis indicate that the unliganded RNA can access bound-like conformations that are significantly stabilized by SAH to direct folding of the downstream regulatory switch. Strikingly, we find that metabolites bearing an adenine ring, including ATP, bind this aptamer with sufficiently high affinity such that normal intracellular concentrations of these compounds may influence regulation of the riboswitch.
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Affiliation(s)
- Andrea L Edwards
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
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18
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Abstract
A number of RNAs ranging from small helices to large megadalton ribonucleoprotein complexes have been solved to atomic resolution using X-ray crystallography. As with proteins, RNA crystallography involves a number of screening trials in which the concentration of macromolecule, precipitant, salt, and temperature are varied, an approach known as searching "condition space." In contrast to proteins, the nature of base pairing in nucleic acids creates predictable secondary structure that facilitates the rational design of RNA variants, allowing "sequence space" to be screened in parallel. This chapter reviews RNA-specific techniques and considerations for RNA crystallography and presents a complete workflow used by our laboratory for solving RNA structures starting with initial library construction, methods to investigate and improve RNA crystal quality, and finally phase determination and structure solution.
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Affiliation(s)
- Francis E Reyes
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, USA
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19
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Gilbert SD, Reyes FE, Edwards AL, Batey RT. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure 2009; 17:857-68. [PMID: 19523903 DOI: 10.1016/j.str.2009.04.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 04/01/2009] [Accepted: 04/02/2009] [Indexed: 12/30/2022]
Abstract
Purine riboswitches discriminate between guanine and adenine by at least 10,000-fold based on the identity of a single pyrimidine (Y74) that forms a Watson-Crick base pair with the ligand. To understand how this high degree of specificity for closely related compounds is achieved through simple pairing, we investigated their interaction with purine analogs with varying functional groups at the 2- and 6-positions that have the potential to alter interactions with Y74. Using a combination of crystallographic and calorimetric approaches, we find that binding these purines is often facilitated by either small structural changes in the RNA or tautomeric changes in the ligand. This work also reveals that, along with base pairing, conformational restriction of Y74 significantly contributes to nucleobase selectivity. These results reveal that compounds that exploit the inherent local flexibility within riboswitch binding pockets can alter their ligand specificity.
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Affiliation(s)
- Sunny D Gilbert
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO 80309-0215, USA
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20
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Hardin JW, Reyes FE, Batey RT. Analysis of a critical interaction within the archaeal box C/D small ribonucleoprotein complex. J Biol Chem 2009; 284:15317-24. [PMID: 19336398 PMCID: PMC2685712 DOI: 10.1074/jbc.m901368200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 11/06/2022] Open
Abstract
In archaea and eukarya, box C/D ribonucleoprotein (RNP) complexes are responsible for 2'-O-methylation of tRNAs and rRNAs. The archaeal box C/D small RNP complex requires a small RNA component (sRNA) possessing Watson-Crick complementarity to the target RNA along with three proteins: L7Ae, Nop5p, and fibrillarin. Transfer of a methyl group from S-adenosylmethionine to the target RNA is performed by fibrillarin, which by itself has no affinity for the sRNA-target duplex. Instead, it is targeted to the site of methylation through association with Nop5p, which in turn binds to the L7Ae-sRNA complex. To understand how Nop5p serves as a bridge between the targeting and catalytic functions of the box C/D small RNP complex, we have employed alanine scanning to evaluate the interaction between the Pyrococcus horikoshii Nop5p domain and an L7Ae box C/D RNA complex. From these data, we were able to construct an isolated RNA-binding domain (Nop-RBD) that folds correctly as demonstrated by x-ray crystallography and binds to the L7Ae box C/D RNA complex with near wild type affinity. These data demonstrate that the Nop-RBD is an autonomously folding and functional module important for protein assembly in a number of complexes centered on the L7Ae-kinkturn RNP.
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Affiliation(s)
- John W Hardin
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
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