1
|
Ferrari ÁJR, Dixit SM, Thibeault J, Garcia M, Houliston S, Ludwig RW, Notin P, Phoumyvong CM, Martell CM, Jung MD, Tsuboyama K, Carter L, Arrowsmith CH, Guttman M, Rocklin GJ. Large-scale discovery, analysis, and design of protein energy landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.20.644235. [PMID: 40196533 PMCID: PMC11974690 DOI: 10.1101/2025.03.20.644235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
All folded proteins continuously fluctuate between their low-energy native structures and higher energy conformations that can be partially or fully unfolded. These rare states influence protein function, interactions, aggregation, and immunogenicity, yet they remain far less understood than protein native states. Although native protein structures are now often predictable with impressive accuracy, conformational fluctuations and their energies remain largely invisible and unpredictable, and experimental challenges have prevented large-scale measurements that could improve machine learning and physics-based modeling. Here, we introduce a multiplexed experimental approach to analyze the energies of conformational fluctuations for hundreds of protein domains in parallel using intact protein hydrogen-deuterium exchange mass spectrometry. We analyzed 5,778 domains 28-64 amino acids in length, revealing hidden variation in conformational fluctuations even between sequences sharing the same fold and global folding stability. Site-resolved hydrogen exchange NMR analysis of 13 domains showed that these fluctuations often involve entire secondary structural elements with lower stability than the overall fold. Computational modeling of our domains identified structural features that correlated with the experimentally observed fluctuations, enabling us to design mutations that stabilized low-stability structural segments. Our dataset enables new machine learning-based analysis of protein energy landscapes, and our experimental approach promises to reveal these landscapes at unprecedented scale.
Collapse
Affiliation(s)
- Állan J. R. Ferrari
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sugyan M. Dixit
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jane Thibeault
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mario Garcia
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Robert W. Ludwig
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pascal Notin
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Claire M. Phoumyvong
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Cydney M. Martell
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michelle D. Jung
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kotaro Tsuboyama
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Current address: Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Lauren Carter
- Department of Biochemistry, University of Washington, Seattle, WA, USA. Current address: Bill & Melinda Gates Medical Research Institute
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Gabriel J. Rocklin
- Department of Pharmacology & Center for Synthetic Biology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
2
|
Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [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: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
Collapse
Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| |
Collapse
|
3
|
Bhandari V, Reichheld SE, Houliston S, Lemak A, Arrowsmith CH, Sharpe S, Houry WA. The RavA-ViaA chaperone complex modulates bacterial persistence through its association with the fumarate reductase enzyme. J Biol Chem 2023; 299:105199. [PMID: 37660904 PMCID: PMC10585395 DOI: 10.1016/j.jbc.2023.105199] [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: 06/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
Regulatory ATPase variant A (RavA) is a MoxR AAA+ protein that functions together with a partner protein termed von Willebrand factor type A interacting with AAA+ ATPase (ViaA). RavA-ViaA are functionally associated with anaerobic respiration in Escherichia coli through interactions with the fumarate reductase (Frd) electron transport complex. Through this association, RavA and ViaA modulate the activity of the Frd complex and, hence, are proposed to have chaperone-like activity. However, the functional role of RavA-ViaA in the cell is not yet well established. We had demonstrated that RavA-ViaA can sensitize E. coli cells to sublethal concentrations of the aminoglycoside class of antibiotics. Since Frd has been associated with bacterial persistence against antibiotics, the relationship of RavA-ViaA and Frd was explored within this context. Experiments performed here reveal a function of RavA-ViaA in bacterial persistence upon treatment with antibiotics through the association of the chaperone complex with Frd. As part of this work, the NMR structure of the N-terminal domain of ViaA was solved. The structure reveals a novel alpha helical fold, which we name the VAN fold, that has not been observed before. We show that this domain is required for the function of the chaperone complex. We propose that modulating the levels of RavA-ViaA could enhance the susceptibility of Gram-negative bacteria to antibiotics.
Collapse
Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sean E Reichheld
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Structural Genomics Consortium, Toronto, Ontario, Canada
| | - Simon Sharpe
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Molecular Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
4
|
Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E. De novo design of immunoglobulin-like domains. Nat Commun 2022; 13:5661. [PMID: 36192397 PMCID: PMC9530121 DOI: 10.1038/s41467-022-33004-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding loops and constitute the largest growing class of drugs. Current engineering strategies for this class of compounds rely on naturally existing Ig frameworks, which can be hard to modify and have limitations in manufacturability, designability and range of action. Here, we develop design rules for the central feature of the Ig fold architecture—the non-local cross-β structure connecting the two β-sheets—and use these to design highly stable Ig domains de novo, confirm their structures through X-ray crystallography, and show they can correctly scaffold functional loops. Our approach opens the door to the design of antibody-like scaffolds with tailored structures and superior biophysical properties. The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to scaffold functional loops.
Collapse
Affiliation(s)
- Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.,Novartis Institutes for BioMedical Research Inc., San Diego, CA, 92121, USA
| | - Soraia R Mendes
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jason C Klima
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Encodia, Inc., San Diego, CA, 92121, USA
| | - Marta Nadal
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jorge Roel-Touris
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Hugh K Haddox
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Adam Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
| | - Enrique Marcos
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
| |
Collapse
|
5
|
Payliss BJ, Tse YWE, Reichheld SE, Lemak A, Yun HY, Houliston S, Patel A, Arrowsmith CH, Sharpe S, Wyatt HD. Phosphorylation of the DNA repair scaffold SLX4 drives folding of the SAP domain and activation of the MUS81-EME1 endonuclease. Cell Rep 2022; 41:111537. [DOI: 10.1016/j.celrep.2022.111537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 11/03/2022] Open
|
6
|
Wei Y, Redel C, Ahlner A, Lemak A, Johansson-Åkhe I, Houliston S, Kenney TMG, Tamachi A, Morad V, Duan S, Andrews DW, Wallner B, Sunnerhagen M, Arrowsmith CH, Penn LZ. The MYC oncoprotein directly interacts with its chromatin cofactor PNUTS to recruit PP1 phosphatase. Nucleic Acids Res 2022; 50:3505-3522. [PMID: 35244724 PMCID: PMC8989513 DOI: 10.1093/nar/gkac138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Despite MYC dysregulation in most human cancers, strategies to target this potent oncogenic driver remain an urgent unmet need. Recent evidence shows the PP1 phosphatase and its regulatory subunit PNUTS control MYC phosphorylation, chromatin occupancy, and stability, however the molecular basis remains unclear. Here we demonstrate that MYC interacts directly with PNUTS through the MYC homology Box 0 (MB0), a highly conserved region recently shown to be important for MYC oncogenic activity. By NMR we identified a distinct peptide motif within MB0 that interacts with PNUTS residues 1–148, a functional unit, here termed PNUTS amino-terminal domain (PAD). Using NMR spectroscopy we determined the solution structure of PAD, and characterised its MYC-binding patch. Point mutations of residues at the MYC-PNUTS interface significantly weaken their interaction both in vitro and in vivo, leading to elevated MYC phosphorylation. These data demonstrate that the MB0 region of MYC directly interacts with the PAD of PNUTS, which provides new insight into the control mechanisms of MYC as a regulator of gene transcription and a pervasive cancer driver.
Collapse
Affiliation(s)
- Yong Wei
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada
| | - Cornelia Redel
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Alexandra Ahlner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Alexander Lemak
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Isak Johansson-Åkhe
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Scott Houliston
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada
| | - Tristan M G Kenney
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Aaliya Tamachi
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada
| | - Vivian Morad
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | | | - David W Andrews
- Sunnybrook Research Institute, 2075 Bayview Ave. Toronto, ON, M4N 3M5, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Björn Wallner
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry, and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Structural Genomics Consortium (SGC), University of Toronto, 101 College St., Suite 700, Toronto, ON, M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| | - Linda Z Penn
- Princess Margaret Cancer Centre, University Health Network, 101 College St, Toronto, ON M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, 101 College St, Toronto, ON M5G 1L7, Canada
| |
Collapse
|
7
|
Tauber M, Kreuz S, Lemak A, Mandal P, Yerkesh Z, Veluchamy A, Al-Gashgari B, Aljahani A, Cortés-Medina LV, Azhibek D, Fan L, Ong MS, Duan S, Houliston S, Arrowsmith CH, Fischle W. Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1. Nucleic Acids Res 2020; 48:7728-7747. [PMID: 32609811 PMCID: PMC7430637 DOI: 10.1093/nar/gkaa520] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/01/2020] [Accepted: 06/08/2020] [Indexed: 12/29/2022] Open
Abstract
UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.
Collapse
Affiliation(s)
- Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Papita Mandal
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Zhadyra Yerkesh
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Alaguraj Veluchamy
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Bothayna Al-Gashgari
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Abrar Aljahani
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lorena V Cortés-Medina
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Dulat Azhibek
- Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Lixin Fan
- Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core Facility of the National Cancer Institute, Frederick, MD 21702, USA
| | - Michelle S Ong
- Structural Genomics Consortium, University of Toronto, Toronto M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto M5G 1L7, Canada
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| |
Collapse
|
8
|
Taylor KC, Kang PW, Hou P, Yang ND, Kuenze G, Smith JA, Shi J, Huang H, White KM, Peng D, George AL, Meiler J, McFeeters RL, Cui J, Sanders CR. Structure and physiological function of the human KCNQ1 channel voltage sensor intermediate state. eLife 2020; 9:e53901. [PMID: 32096762 PMCID: PMC7069725 DOI: 10.7554/elife.53901] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/24/2020] [Indexed: 12/14/2022] Open
Abstract
Voltage-gated ion channels feature voltage sensor domains (VSDs) that exist in three distinct conformations during activation: resting, intermediate, and activated. Experimental determination of the structure of a potassium channel VSD in the intermediate state has previously proven elusive. Here, we report and validate the experimental three-dimensional structure of the human KCNQ1 voltage-gated potassium channel VSD in the intermediate state. We also used mutagenesis and electrophysiology in Xenopus laevisoocytes to functionally map the determinants of S4 helix motion during voltage-dependent transition from the intermediate to the activated state. Finally, the physiological relevance of the intermediate state KCNQ1 conductance is demonstrated using voltage-clamp fluorometry. This work illuminates the structure of the VSD intermediate state and demonstrates that intermediate state conductivity contributes to the unusual versatility of KCNQ1, which can function either as the slow delayed rectifier current (IKs) of the cardiac action potential or as a constitutively active epithelial leak current.
Collapse
Affiliation(s)
- Keenan C Taylor
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Po Wei Kang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Panpan Hou
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Nien-Du Yang
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Departments of Chemistry and Pharmacology, Vanderbilt UniversityNashvilleUnited States
| | - Jarrod A Smith
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Jingyi Shi
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Hui Huang
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
| | - Kelli McFarland White
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Dungeng Peng
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University Medical CenterNashvilleUnited States
| | - Alfred L George
- Department of Pharmacology, Northwestern University Feinberg School of MedicineChicagoUnited States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Departments of Chemistry and Pharmacology, Vanderbilt UniversityNashvilleUnited States
- Department of Bioinformatics, Vanderbilt University Medical CenterNashvilleUnited States
| | - Robert L McFeeters
- Department of Chemistry, University of Alabama in HuntsvilleHuntsvilleUnited States
| | - Jianmin Cui
- Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, and Cardiac Bioelectricity, and Arrhythmia Center, Washington University in St. LouisSt. LouisUnited States
| | - Charles R Sanders
- Department of Biochemistry, Vanderbilt UniversityNashvilleUnited States
- Center for Structural Biology, Vanderbilt UniversityNashvilleUnited States
- Department of Medicine, Vanderbilt University Medical CenterNashvilleUnited States
| |
Collapse
|
9
|
Kaustov L, Lemak A, Wu H, Faini M, Fan L, Fang X, Zeng H, Duan S, Allali-Hassani A, Li F, Wei Y, Vedadi M, Aebersold R, Wang Y, Houliston S, Arrowsmith CH. The MLL1 trimeric catalytic complex is a dynamic conformational ensemble stabilized by multiple weak interactions. Nucleic Acids Res 2019; 47:9433-9447. [PMID: 31400120 PMCID: PMC6755125 DOI: 10.1093/nar/gkz697] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/22/2019] [Accepted: 07/31/2019] [Indexed: 11/14/2022] Open
Abstract
Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with additional conserved proteins, but the structural basis for subunit assembly and the mechanism of regulation is not well understood. We used a hybrid methods approach to study the assembly and biochemical function of the minimally active MLL1 complex (MLL1, WDR5 and RbBP5). A combination of small angle X-ray scattering, cross-linking mass spectrometry, nuclear magnetic resonance spectroscopy and computational modeling were used to generate a dynamic ensemble model in which subunits are assembled via multiple weak interaction sites. We identified a new interaction site between the MLL1 SET domain and the WD40 β-propeller domain of RbBP5, and demonstrate the susceptibility of the catalytic function of the complex to disruption of individual interaction sites.
Collapse
Affiliation(s)
- Lilia Kaustov
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Department of Anesthesia, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Marco Faini
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Lixin Fan
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Xianyang Fang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Abdellah Allali-Hassani
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Yong Wei
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
- Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Yunxing Wang
- The Small-Angel X-ray Scattering Core Facility, Center for Cancer Research of National Cancer Institute, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc. Frederick, MD 21702, USA
| | - Scott Houliston
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, ON M5G 2M9, Canada
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS Centre, South Tower, Toronto, ON M5G 1L7, Canada
| |
Collapse
|
10
|
Chen H, Pan J, Gandhi DM, Dockendorff C, Cui Q, Chanda B, Henzler-Wildman KA. NMR Structural Analysis of Isolated Shaker Voltage-Sensing Domain in LPPG Micelles. Biophys J 2019; 117:388-398. [PMID: 31301804 DOI: 10.1016/j.bpj.2019.06.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
The voltage-sensing domain (VSD) is a conserved structural module that regulates the gating of voltage-dependent ion channels in response to a change in membrane potential. Although the structures of many VSD-containing ion channels are now available, our understanding of the structural dynamics associated with gating transitions remains limited. To probe dynamics with site-specific resolution, we utilized NMR spectroscopy to characterize the VSD derived from Shaker potassium channel in 1-palmitoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol) (LPPG) micelles. The backbone dihedral angles predicted based on secondary chemical shifts using torsion angle likeliness obtained from shift (TALOS+) showed that the Shaker-VSD shares many structural features with the homologous Kv1.2/2.1 chimera, including a transition from α-helix to 310 helix in the C-terminal portion of the fourth transmembrane helix. Nevertheless, there are clear differences between the Shaker-VSD and Kv1.2/2.1 chimera in the S2-S3 linker and S3 transmembrane region, where the organization of secondary structure elements in Shaker-VSD appears to more closely resemble the KvAP-VSD. Comparison of microsecond-long molecular dynamics simulations of Kv 1.2-VSD in LPPG micelles and a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) bilayer showed that LPPG micelles do not induce significant structural distortion in the isolated voltage sensor. To assess the integrity of the tertiary fold, we directly probed the binding of BrMT analog 2-[2-({[3-(2-amino-ethyl)-6-bromo-1H-indol-2-yl]methoxy}k7methyl)-6-bromo-1H-indol-3-yl]ethan-1-amine (BrET), a gating modifier toxin, and identified the location of the putative binding site. Our results suggest that the Shaker-VSD in LPPG micelles is in a native-like fold and is likely to provide valuable insights into the dynamics of voltage-gating and its regulation.
Collapse
Affiliation(s)
- Hongbo Chen
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Junkun Pan
- Department of Neuroscience, Madison, Wisconsin; Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin
| | - Disha M Gandhi
- Departments of Chemistry, Marquette University, Milwaukee, Wisconsin
| | - Chris Dockendorff
- Departments of Chemistry, Marquette University, Milwaukee, Wisconsin
| | - Qiang Cui
- Departments of Chemistry, Physics, Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Baron Chanda
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Neuroscience, Madison, Wisconsin; Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin.
| | - Katherine A Henzler-Wildman
- Graduate Program in Biophysics, Madison, Wisconsin; Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin.
| |
Collapse
|
11
|
Rocklin GJ, Chidyausiku TM, Goreshnik I, Ford A, Houliston S, Lemak A, Carter L, Ravichandran R, Mulligan VK, Chevalier A, Arrowsmith CH, Baker D. Global analysis of protein folding using massively parallel design, synthesis, and testing. Science 2018; 357:168-175. [PMID: 28706065 PMCID: PMC5568797 DOI: 10.1126/science.aan0693] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022]
Abstract
Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.
Collapse
Affiliation(s)
- Gabriel J Rocklin
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Tamuka M Chidyausiku
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Inna Goreshnik
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Alex Ford
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.,Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada
| | - Lauren Carter
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Rashmi Ravichandran
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Vikram K Mulligan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Aaron Chevalier
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - David Baker
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
12
|
Reed B, Yakovleva L, Shuman S, Ghose R. Characterization of DNA Binding by the Isolated N-Terminal Domain of Vaccinia Virus DNA Topoisomerase IB. Biochemistry 2017; 56:3307-3317. [PMID: 28570045 DOI: 10.1021/acs.biochem.7b00042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vaccinia TopIB (vTopIB), a 314-amino acid eukaryal-type IB topoisomerase, recognizes and transesterifies at the DNA sequence 5'-(T/C)CCTT↓, leading to the formation of a covalent DNA-(3'-phosphotyrosyl274)-enzyme intermediate in the supercoil relaxation reaction. The C-terminal segment of vTopIB (amino acids 81-314), which engages the DNA minor groove at the scissile phosphodiester, comprises an autonomous catalytic domain that retains cleavage specificity, albeit with a cleavage site affinity lower than that of the full-length enzyme. The N-terminal domain (amino acids 1-80) engages the major groove on the DNA face opposite the scissile phosphodiester. Whereas DNA contacts of the N-terminal domain have been implicated in the DNA site affinity of vTopIB, it was not known whether the N-terminal domain per se could bind DNA. Here, using isothermal titration calorimetry, we demonstrate the ability of the isolated N-terminal domain to bind a CCCTT-containing 24-mer duplex with an apparent affinity that is ∼2.2-fold higher than that for an otherwise identical duplex in which the pentapyrimidine sequence is changed to ACGTG. Analyses of the interactions of the isolated N-terminal domain with duplex DNA via solution nuclear magnetic resonance methods are consistent with its DNA contacts observed in DNA-bound crystal structures of full-length vTopIB. The chemical shift perturbations and changes in hydrodynamic properties triggered by CCCTT DNA versus non-CCCTT DNA suggest differences in DNA binding dynamics. The importance of key N-terminal domain contacts in the context of full-length vTopIB is underscored by assessing the effects of double-alanine mutations on DNA transesterification and its sensitivity to ionic strength.
Collapse
Affiliation(s)
- Benjamin Reed
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Lyudmila Yakovleva
- Molecular Biology Program, Sloan-Kettering Institute , New York, New York 10021, United States
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute , New York, New York 10021, United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| |
Collapse
|
13
|
Nguyen LT, Vogel HJ. Staphylokinase has distinct modes of interaction with antimicrobial peptides, modulating its plasminogen-activation properties. Sci Rep 2016; 6:31817. [PMID: 27554435 PMCID: PMC4995489 DOI: 10.1038/srep31817] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022] Open
Abstract
Staphylokinase (Sak) is a plasminogen activator protein that is secreted by many Staphylococcus aureus strains. Sak also offers protection by binding and inhibiting specific antimicrobial peptides (AMPs). Here, we evaluate Sak as a more general interaction partner for AMPs. Studies with melittin, mCRAMP, tritrpticin and bovine lactoferricin indicate that the truncation of the first ten residues of Sak (SakΔN10), which occurs in vivo and uncovers important residues in a bulge region, improves its affinity for AMPs. Melittin and mCRAMP have a lower affinity for SakΔN10, and in docking studies, they bind to the N-terminal segment and bulge region of SakΔN10. By comparison, lactoferricin and tritrpticin form moderately high affinity 1:1 complexes with SakΔN10 and their cationic residues form several electrostatic interactions with the protein's α-helix. Overall, our work identifies two distinct AMP binding surfaces on SakΔN10 whose occupation would lead to either inhibition or promotion of its plasminogen activating properties.
Collapse
Affiliation(s)
- Leonard T Nguyen
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hans J Vogel
- Biochemistry Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
14
|
Langelaan DN, Liburd J, Yang Y, Miller E, Chitayat S, Crawley SW, Côté GP, Smith SP. Structure of the Single-lobe Myosin Light Chain C in Complex with the Light Chain-binding Domains of Myosin-1C Provides Insights into Divergent IQ Motif Recognition. J Biol Chem 2016; 291:19607-17. [PMID: 27466369 DOI: 10.1074/jbc.m116.746313] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Indexed: 01/06/2023] Open
Abstract
Myosin light chains are key regulators of class 1 myosins and typically comprise two domains, with calmodulin being the archetypal example. They bind IQ motifs within the myosin neck region and amplify conformational changes in the motor domain. A single lobe light chain, myosin light chain C (MlcC), was recently identified and shown to specifically bind to two sequentially divergent IQ motifs of the Dictyostelium myosin-1C. To provide a molecular basis of this interaction, the structures of apo-MlcC and a 2:1 MlcC·myosin-1C neck complex were determined. The two non-functional EF-hand motifs of MlcC pack together to form a globular four-helix bundle that opens up to expose a central hydrophobic groove, which interacts with the N-terminal portion of the divergent IQ1 and IQ2 motifs. The N- and C-terminal regions of MlcC make critical contacts that contribute to its specific interactions with the myosin-1C divergent IQ motifs, which are contacts that deviate from the traditional mode of calmodulin-IQ recognition.
Collapse
Affiliation(s)
- David N Langelaan
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Janine Liburd
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Yidai Yang
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Emily Miller
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Seth Chitayat
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Scott W Crawley
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Graham P Côté
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Steven P Smith
- From the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| |
Collapse
|
15
|
Hough LE, Dutta K, Sparks S, Temel DB, Kamal A, Tetenbaum-Novatt J, Rout MP, Cowburn D. The molecular mechanism of nuclear transport revealed by atomic-scale measurements. eLife 2015; 4. [PMID: 26371551 PMCID: PMC4621360 DOI: 10.7554/elife.10027] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/07/2015] [Indexed: 12/29/2022] Open
Abstract
Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the reason that transport can be both fast and specific remains undetermined, through lack of atomic-scale information on the behavior of FGs and their interaction with TFs. We used nuclear magnetic resonance spectroscopy to address these issues. We show that FG repeats are highly dynamic IDPs, stabilized by the cellular environment. Fast transport of TFs is supported because the rapid motion of FG motifs allows them to exchange on and off TFs extremely quickly through transient interactions. Because TFs uniquely carry multiple pockets for FG repeats, only they can form the many frequent interactions needed for specific passage between FG repeats to cross the NPC. DOI:http://dx.doi.org/10.7554/eLife.10027.001 Eukaryotic cells have a nucleus that contains most of the organism's genetic material. Two layers of membrane form an envelope around the nucleus and protect its contents from the rest of the cell's interior. However, this protective barrier must also allow certain proteins and nucleic acids(collectively called ‘cargo’) to move in and out of the nucleus. Cargo molecules can pass through channel-like structures called nuclear pore complexes, which are embedded in the nuclear envelope. However, transport across this barrier is highly selective. While small molecules can pass freely through nuclear pore complexes, larger cargo can only be transported when they are bound to so-called transport factors. The nuclear pore complex is a large structure made up of more than 30 different proteins called nucleoporins. Like all proteins, nucleoporins are built from amino acids. Many nucleoporins contain repeating units of two amino acids, namely phenylalanine (which is often referred to as ‘F’) and glycine (or ‘G’). These ‘FG nucleoporins’ are found on the inside of the nuclear pore complex and interact with transport factors to allow them to transit across the nuclear envelope. Several models have been put forward to explain how FG nucleoporins block the passage of most molecules. But it was unclear from these models how these nucleoporins could do this while simultaneously allowing the selective and fast transport of nuclear transport receptors. There was also a major lack of experimental data that probed the behavior of FG nucleoporins in detail. Hough, Dutta et al. have now used a technique called nuclear magnetic resonance spectroscopy (or NMR for short) to address this issue. NMR can be used to analyze the structure of proteins and how they interact with other molecules. This analysis revealed that FG nucleoporins never adopt an ordered three-dimensional shape, even briefly; instead they remain unfolded or disordered, moving constantly. Nevertheless, and unlike many other unfolded proteins, FG nucleoporins do not aggregate into clumps. This is because they are constantly changing and continuously interacting with other molecules present inside the cell, which prevents them from aggregating. Hough, Dutta et al. also observed that the repeating units in the FG nucleoporins engaged briefly with a large number of sites or pockets present on the transport factors. These FG repeats can bind and then release the transport factors at unusually high speeds, which enables the transport factors to move quickly through the nuclear pore complex. This transit is specific because only transport factors have a high capacity for interacting with the FG repeats. These findings provide an explanation for how the nuclear pore complex achieves fast and selective transport. Further work is needed to see whether certain FG nucleoporins specifically interact with a particular type of transport factor, to provide preferred transport routes through the nuclear pore complex. DOI:http://dx.doi.org/10.7554/eLife.10027.002
Collapse
Affiliation(s)
| | - Kaushik Dutta
- New York Structural Biology Center, New York, United States
| | - Samuel Sparks
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Deniz B Temel
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| | - Alia Kamal
- The Rockefeller University, New York, United States
| | | | | | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, United States
| |
Collapse
|
16
|
Rosato A, Vranken W, Fogh RH, Ragan TJ, Tejero R, Pederson K, Lee HW, Prestegard JH, Yee A, Wu B, Lemak A, Houliston S, Arrowsmith CH, Kennedy M, Acton TB, Xiao R, Liu G, Montelione GT, Vuister GW. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013. JOURNAL OF BIOMOLECULAR NMR 2015; 62:413-24. [PMID: 26071966 PMCID: PMC4569658 DOI: 10.1007/s10858-015-9953-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 05/28/2015] [Indexed: 05/21/2023]
Abstract
The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.
Collapse
Affiliation(s)
- Antonio Rosato
- Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Wim Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- (IB)2 Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium
| | - Rasmus H Fogh
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Timothy J Ragan
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK
| | - Roberto Tejero
- Departamento de Química Física, Universidad de Valencia, Avda. Dr. Moliner 50, 46100, Burjassot (Valencia), Spain
| | - Kari Pederson
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium, University of Georgia, Athens, GA, 30602, USA
| | - Adelinda Yee
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Bin Wu
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alexander Lemak
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Scott Houliston
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Michael Kennedy
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, OH, 45056, USA
| | - Thomas B Acton
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaohua Liu
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK.
| |
Collapse
|
17
|
Structural Insight into the Complex of Ferredoxin and [FeFe] Hydrogenase fromChlamydomonas reinhardtii. Chembiochem 2015; 16:1663-9. [DOI: 10.1002/cbic.201500130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Indexed: 01/01/2023]
|
18
|
Hong JH, Kaustov L, Coyaud E, Srikumar T, Wan J, Arrowsmith C, Raught B. KCMF1 (potassium channel modulatory factor 1) Links RAD6 to UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4) and lysosome-mediated degradation. Mol Cell Proteomics 2015; 14:674-85. [PMID: 25582440 DOI: 10.1074/mcp.m114.042168] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RAD6 is a ubiquitin E2 protein with roles in a number of different biological processes. Here, using affinity purification coupled with mass spectrometry, we identify a number of new RAD6 binding partners, including the poorly characterized ubiquitin E3 ligases KCMF1 (potassium channel modulatory factor 1) and UBR4 (ubiquitin N-recognin domain-containing E3 ligase 4), a protein that can bind N-end rule substrates, and which was recently linked to lysosome-mediated degradation and autophagy. NMR, combined with in vivo and in vitro interaction mapping, demonstrate that the KCMF1 C terminus binds directly to RAD6, whereas N-terminal domains interact with UBR4 and other intracellular vesicle- and mitochondria-associated proteins. KCMF1 and RAD6 colocalize at late endosomes and lysosomes, and cells disrupted for KCMF1 or RAD6 function display defects in late endosome vesicle dynamics. Notably, we also find that two different RAD6A point mutants (R7W and R11Q) found in X-linked intellectual disability (XLID) patients specifically lose the interaction with KCMF1 and UBR4, but not with other previously identified RAD6 interactors. We propose that RAD6-KCMF1-UBR4 represents a unique new E2-E3 complex that targets unknown N-end rule substrates for lysosome-mediated degradation, and that disruption of this complex via RAD6A mutations could negatively affect neuronal function in XLID patients.
Collapse
Affiliation(s)
- Jenny H Hong
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto
| | - Lilia Kaustov
- §Structural Genomics Consortium, Toronto, Ontario Canada
| | - Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto
| | - Tharan Srikumar
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto
| | - Janet Wan
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto
| | - Cheryl Arrowsmith
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto; §Structural Genomics Consortium, Toronto, Ontario Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network and Department of Medical Biophysics, University of Toronto;
| |
Collapse
|
19
|
Dutta K, Varshney AK, Franklin MC, Goger M, Wang X, Fries BC. Mechanisms mediating enhanced neutralization efficacy of staphylococcal enterotoxin B by combinations of monoclonal antibodies. J Biol Chem 2015; 290:6715-30. [PMID: 25572397 DOI: 10.1074/jbc.m114.630715] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Staphylococcal enterotoxin B (SEB) is a superantigen that cross-links the major histocompatibility complex class II and specific V-β chains of the T-cell receptor, thus forming a ternary complex. Developing neutralizing mAb to disrupt the ternary complex and abrogate the resulting toxicity is a major therapeutic challenge because SEB is effective at very low concentrations. We show that combining two SEB-specific mAbs enhances their efficacy, even though one of the two mAbs by itself has no effect on neutralization. Crystallography was employed for fine-mapping conformational epitopes in binary and ternary complexes between SEB and Fab fragments. NMR spectroscopy was used to validate and identify subtle allosteric changes induced by mAbs binding to SEB. The mapping of epitopes established that a combination of different mAbs can enhance efficacy of mAb-mediated protection from SEB induced lethal shock by two different mechanisms: one mAb mixture promoted clearance of the toxin both in vitro and in vivo by FcR-mediated cross-linking and clearance, whereas the other mAb mixture induced subtle allosteric conformational changes in SEB that perturbed formation of the SEB·T-cell receptor·major histocompatibility complex class II trimer. Finally structural information accurately predicted mAb binding to other superantigens that share conformational epitopes with SEB. Fine mapping of conformational epitopes is a powerful tool to establish the mechanism and optimize the action of synergistic mAb combinations.
Collapse
Affiliation(s)
- Kaushik Dutta
- From the New York Structural Biology Center, New York, New York 10027,
| | - Avanish K Varshney
- the Department of Medicine and Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11790, and the Department of Medicine, Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | | | - Michael Goger
- From the New York Structural Biology Center, New York, New York 10027
| | - Xiaobo Wang
- the Department of Medicine, Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Bettina C Fries
- the Department of Medicine and Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11790, and the Department of Medicine, Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461
| |
Collapse
|
20
|
Lemak A, Wu B, Yee A, Houliston S, Lee HW, Gutmanas A, Fang X, Garcia M, Semesi A, Wang YX, Prestegard JH, Arrowsmith CH. Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data. Structure 2014; 22:1862-1874. [PMID: 25456817 PMCID: PMC5046226 DOI: 10.1016/j.str.2014.09.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 01/09/2023]
Abstract
Multidomain proteins in which individual domains are connected by linkers often possess inherent interdomain flexibility that significantly complicates their structural characterization in solution using either nuclear magnetic resonance (NMR) spectroscopy or small-angle X-ray scattering (SAXS) alone. Here, we report a protocol for joint refinement of flexible multidomain protein structures against NMR distance and angular restraints, residual dipolar couplings, and SAXS data. The protocol is based on the ensemble optimization method principle (Bernadó et al., 2007) and is compared with different refinement strategies for the structural characterization of the flexible two-domain protein sf3636 from Shigella flexneri 2a. The results of our refinement suggest the existence of a dominant population of configurational states in solution possessing an overall elongated shape and restricted relative twisting of the two domains.
Collapse
Affiliation(s)
- Alexander Lemak
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Bin Wu
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Adelinda Yee
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Scott Houliston
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Aleksandras Gutmanas
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - Maite Garcia
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Anthony Semesi
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, MD 21702, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada.
| |
Collapse
|
21
|
Structural and functional characterization of DUF1471 domains of Salmonella proteins SrfN, YdgH/SssB, and YahO. PLoS One 2014; 9:e101787. [PMID: 25010333 PMCID: PMC4092069 DOI: 10.1371/journal.pone.0101787] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/07/2014] [Indexed: 11/20/2022] Open
Abstract
Bacterial species in the Enterobacteriaceae typically contain multiple paralogues of a small domain of unknown function (DUF1471) from a family of conserved proteins also known as YhcN or BhsA/McbA. Proteins containing DUF1471 may have a single or three copies of this domain. Representatives of this family have been demonstrated to play roles in several cellular processes including stress response, biofilm formation, and pathogenesis. We have conducted NMR and X-ray crystallographic studies of four DUF1471 domains from Salmonella representing three different paralogous DUF1471 subfamilies: SrfN, YahO, and SssB/YdgH (two of its three DUF1471 domains: the N-terminal domain I (residues 21–91), and the C-terminal domain III (residues 244–314)). Notably, SrfN has been shown to have a role in intracellular infection by Salmonella Typhimurium. These domains share less than 35% pairwise sequence identity. Structures of all four domains show a mixed α+β fold that is most similar to that of bacterial lipoprotein RcsF. However, all four DUF1471 sequences lack the redox sensitive cysteine residues essential for RcsF activity in a phospho-relay pathway, suggesting that DUF1471 domains perform a different function(s). SrfN forms a dimer in contrast to YahO and SssB domains I and III, which are monomers in solution. A putative binding site for oxyanions such as phosphate and sulfate was identified in SrfN, and an interaction between the SrfN dimer and sulfated polysaccharides was demonstrated, suggesting a direct role for this DUF1471 domain at the host-pathogen interface.
Collapse
|
22
|
Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, Gutmanas A. An overview of tools for the validation of protein NMR structures. JOURNAL OF BIOMOLECULAR NMR 2014; 58:259-285. [PMID: 23877928 DOI: 10.1007/s10858-013-9750-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).
Collapse
Affiliation(s)
- Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK,
| | | | | | | | | |
Collapse
|
23
|
Helander S, Montecchio M, Lemak A, Farès C, Almlöf J, Yi Y, Yee A, Arrowsmith C, DhePaganon S, Sunnerhagen M. Basic Tilted Helix Bundle - a new protein fold in human FKBP25/FKBP3 and HectD1. Biochem Biophys Res Commun 2014; 447:26-31. [PMID: 24667607 DOI: 10.1016/j.bbrc.2014.03.068] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 11/18/2022]
Abstract
In this paper, we describe the structure of a N-terminal domain motif in nuclear-localized FKBP251-73, a member of the FKBP family, together with the structure of a sequence-related subdomain of the E3 ubiquitin ligase HectD1 that we show belongs to the same fold. This motif adopts a compact 5-helix bundle which we name the Basic Tilted Helix Bundle (BTHB) domain. A positively charged surface patch, structurally centered around the tilted helix H4, is present in both FKBP25 and HectD1 and is conserved in both proteins, suggesting a conserved functional role. We provide detailed comparative analysis of the structures of the two proteins and their sequence similarities, and analysis of the interaction of the proposed FKBP25 binding protein YY1. We suggest that the basic motif in BTHB is involved in the observed DNA binding of FKBP25, and that the function of this domain can be affected by regulatory YY1 binding and/or interactions with adjacent domains.
Collapse
Affiliation(s)
- Sara Helander
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Meri Montecchio
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Alexander Lemak
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Christophe Farès
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Jonas Almlöf
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Yanjun Yi
- Structural Genomics Consortium, Northeast Structural Genomics Consortium, Ontario, Canada
| | - Adelinda Yee
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, Northeast Structural Genomics Consortium, Ontario, Canada
- Cancer Institute and Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Sirano DhePaganon
- Structural Genomics Consortium, Northeast Structural Genomics Consortium, Ontario, Canada
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| |
Collapse
|
24
|
Mayzel M, Rosenlöw J, Isaksson L, Orekhov VY. Time-resolved multidimensional NMR with non-uniform sampling. JOURNAL OF BIOMOLECULAR NMR 2014; 58:129-39. [PMID: 24435565 PMCID: PMC3929766 DOI: 10.1007/s10858-013-9811-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/30/2013] [Indexed: 05/11/2023]
Abstract
Time-resolved experiments demand high resolution both in spectral dimensions and in time of the studied kinetic process. The latter requirement traditionally prohibits applications of the multidimensional experiments, which, although capable of providing invaluable information about structure and dynamics and almost unlimited spectral resolution, require too lengthy data collection. Our work shows that the problem has a solution in using modern methods of NMR data collection and signal processing. A continuous fast pulsing three-dimensional experiment is acquired using non-uniform sampling during full time of the studied reaction. High sensitivity and time-resolution of a few minutes is achieved by simultaneous processing of the full data set with the multi-dimensional decomposition. The method is verified and illustrated in realistic simulations and by measuring deuterium exchange rates of amide protons in ubiquitin. We applied the method for characterizing kinetics of in vitro phosphorylation of two tyrosine residues in an intrinsically disordered cytosolic domain of the B cell receptor protein CD79b. Signals of many residues including tyrosines in both phosphorylated and unmodified forms of CD79b are found in a heavily crowded region of 2D ¹H-¹⁵N correlation spectrum and the significantly enhanced spectral resolution provided by the 3D time-resolved approach was essential for the quantitative site-specific analysis.
Collapse
Affiliation(s)
- Maxim Mayzel
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Joakim Rosenlöw
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Linnéa Isaksson
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| | - Vladislav Y. Orekhov
- The Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Göteborg, Sweden
| |
Collapse
|
25
|
Abstract
NMR spectroscopy is a valuable tool in structural genomics. Identification of protein samples that are amenable to structure determination by NMR spectroscopy requires efficient screening. The preparation of multiple samples in parallel and screening by NMR is described. The method described is applicable to large structural genomics projects but can easily be scaled down for application to small structural biology projects. All the equipment used is commonly found in any NMR structural biology laboratory.
Collapse
Affiliation(s)
- Adelinda A Yee
- Division of Cancer Genomics and Proteomics, and Northeast Structural Genomics Consortium (NESG), Ontario Cancer Institute, Toronto, ON, Canada
| | | | | | | |
Collapse
|
26
|
Lemak A, Yee A, Wu H, Yap D, Zeng H, Dombrovski L, Houliston S, Aparicio S, Arrowsmith CH. Solution NMR structure and histone binding of the PHD domain of human MLL5. PLoS One 2013; 8:e77020. [PMID: 24130829 PMCID: PMC3793974 DOI: 10.1371/journal.pone.0077020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/26/2013] [Indexed: 12/13/2022] Open
Abstract
Mixed Lineage Leukemia 5 (MLL5) is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. In addition to its catalytic domain, MLL5 contains a PHD finger domain, a protein module that is often involved in binding to the N-terminus of histone H3. Here we report the NMR solution structure of the MLL5 PHD domain showing a variant of the canonical PHD fold that combines conserved H3 binding features from several classes of other PHD domains (including an aromatic cage) along with a novel C-terminal α-helix, not previously seen. We further demonstrate that the PHD domain binds with similar affinity to histone H3 tail peptides di- and tri-methylated at lysine 4 (H3K4me2 and H3K4me3), the former being the putative product of the MLL5 catalytic reaction. This work establishes the PHD domain of MLL5 as a bone fide ‘reader’ domain of H3K4 methyl marks suggesting that it may guide the spreading or further methylation of this site on chromatin.
Collapse
Affiliation(s)
- Alexander Lemak
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Adelinda Yee
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, Ontario, Canada
| | - Damian Yap
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hong Zeng
- Structural Genomics Consortium, University of Toronto, Ontario, Canada
| | | | - Scott Houliston
- Northeast Structural Genomics Consortium and Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, Northeast Structural Genomics Consortium, Ontario, Canada
- Cancer Institute and Department of Medical Biophysics, University of Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
27
|
Tikole S, Jaravine V, Orekhov VY, Güntert P. Effects of NMR spectral resolution on protein structure calculation. PLoS One 2013; 8:e68567. [PMID: 23874675 PMCID: PMC3713035 DOI: 10.1371/journal.pone.0068567] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.
Collapse
Affiliation(s)
- Suhas Tikole
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Victor Jaravine
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | | | - Peter Güntert
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
- Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
- * E-mail:
| |
Collapse
|
28
|
Temel DB, Dutta K, Alphonse S, Nourikyan J, Grangeasse C, Ghose R. Regulatory interactions between a bacterial tyrosine kinase and its cognate phosphatase. J Biol Chem 2013; 288:15212-28. [PMID: 23543749 DOI: 10.1074/jbc.m113.457804] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The cyclic process of autophosphorylation of the C-terminal tyrosine cluster (YC) of a bacterial tyrosine kinase and its subsequent dephosphorylation following interactions with a counteracting tyrosine phosphatase regulates diverse physiological processes, including the biosynthesis and export of polysaccharides responsible for the formation of biofilms or virulence-determining capsules. We provide here the first detailed insight into this hitherto uncharacterized regulatory interaction at residue-specific resolution using Escherichia coli Wzc, a canonical bacterial tyrosine kinase, and its opposing tyrosine phosphatase, Wzb. The phosphatase Wzb utilizes a surface distal to the catalytic elements of the kinase, Wzc, to dock onto its catalytic domain (WzcCD). WzcCD binds in a largely YC-independent fashion near the Wzb catalytic site, inducing allosteric changes therein. YC dephosphorylation is proximity-mediated and reliant on the elevated concentration of phosphorylated YC near the Wzb active site resulting from WzcCD docking. Wzb principally recognizes the phosphate of its phosphotyrosine substrate and further stabilizes the tyrosine moiety through ring stacking interactions with a conserved active site tyrosine.
Collapse
Affiliation(s)
- Deniz B Temel
- Department of Chemistry, City College of New York, New York, New York 10031, USA
| | | | | | | | | | | |
Collapse
|
29
|
Hendrickx PMS, Gutmanas A, Kleywegt GJ. Vivaldi: visualization and validation of biomacromolecular NMR structures from the PDB. Proteins 2013. [PMID: 23180575 PMCID: PMC3618379 DOI: 10.1002/prot.24213] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe Vivaldi (VIsualization and VALidation DIsplay; http://pdbe.org/vivaldi), a web-based service for the analysis, visualization, and validation of NMR structures in the Protein Data Bank (PDB). Vivaldi provides access to model coordinates and several types of experimental NMR data using interactive visualization tools, augmented with structural annotations and model-validation information. The service presents information about the modeled NMR ensemble, validation of experimental chemical shifts, residual dipolar couplings, distance and dihedral angle constraints, as well as validation scores based on empirical knowledge and databases. Vivaldi was designed for both expert NMR spectroscopists and casual non-expert users who wish to obtain a better grasp of the information content and quality of NMR structures in the public archive. © Proteins 2013. © 2012 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Pieter M S Hendrickx
- Protein Data Bank in Europe, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | | |
Collapse
|
30
|
Ramelot TA, Rossi P, Forouhar F, Lee HW, Yang Y, Ni S, Unser S, Lew S, Seetharaman J, Xiao R, Acton TB, Everett JK, Prestegard JH, Hunt JF, Montelione GT, Kennedy MA. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations. Biochemistry 2012; 51:7239-49. [PMID: 22876860 DOI: 10.1021/bi300546b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.
Collapse
Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Andresen C, Helander S, Lemak A, Farès C, Csizmok V, Carlsson J, Penn LZ, Forman-Kay JD, Arrowsmith CH, Lundström P, Sunnerhagen M. Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res 2012; 40:6353-66. [PMID: 22457068 PMCID: PMC3401448 DOI: 10.1093/nar/gks263] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The crucial role of Myc as an oncoprotein and as a key regulator of cell growth makes it essential to understand the molecular basis of Myc function. The N-terminal region of c-Myc coordinates a wealth of protein interactions involved in transformation, differentiation and apoptosis. We have characterized in detail the intrinsically disordered properties of Myc-1–88, where hierarchical phosphorylation of S62 and T58 regulates activation and destruction of the Myc protein. By nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements and NOE analysis, we show that although Myc occupies a very heterogeneous conformational space, we find transiently structured regions in residues 22–33 and in the Myc homology box I (MBI; residues 45–65); both these regions are conserved in other members of the Myc family. Binding of Bin1 to Myc-1–88 as assayed by NMR and surface plasmon resonance (SPR) revealed primary binding to the S62 region in a dynamically disordered and multivalent complex, accompanied by population shifts leading to altered intramolecular conformational dynamics. These findings expand the increasingly recognized concept of intrinsically disordered regions mediating transient interactions to Myc, a key transcriptional regulator of major medical importance, and have important implications for further understanding its multifaceted role in gene regulation.
Collapse
Affiliation(s)
- Cecilia Andresen
- Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, SE-58183 Linköping, Sweden
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Stevens TJ, Fogh RH, Boucher W, Higman VA, Eisenmenger F, Bardiaux B, van Rossum BJ, Oschkinat H, Laue ED. A software framework for analysing solid-state MAS NMR data. JOURNAL OF BIOMOLECULAR NMR 2011; 51:437-47. [PMID: 21953355 PMCID: PMC3222832 DOI: 10.1007/s10858-011-9569-2] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 09/05/2011] [Indexed: 05/10/2023]
Abstract
Solid-state magic-angle-spinning (MAS) NMR of proteins has undergone many rapid methodological developments in recent years, enabling detailed studies of protein structure, function and dynamics. Software development, however, has not kept pace with these advances and data analysis is mostly performed using tools developed for solution NMR which do not directly address solid-state specific issues. Here we present additions to the CcpNmr Analysis software package which enable easier identification of spinning side bands, straightforward analysis of double quantum spectra, automatic consideration of non-uniform labelling schemes, as well as extension of other existing features to the needs of solid-state MAS data. To underpin this, we have updated and extended the CCPN data model and experiment descriptions to include transfer types and nomenclature appropriate for solid-state NMR experiments, as well as a set of experiment prototypes covering the experiments commonly employed by solid-sate MAS protein NMR spectroscopists. This work not only improves solid-state MAS NMR data analysis but provides a platform for anyone who uses the CCPN data model for programming, data transfer, or data archival involving solid-state MAS NMR data.
Collapse
Affiliation(s)
- Tim J. Stevens
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
| | - Rasmus H. Fogh
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
| | - Wayne Boucher
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
| | - Victoria A. Higman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Frank Eisenmenger
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Benjamin Bardiaux
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Barth-Jan van Rossum
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Hartmut Oschkinat
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Ernest D. Laue
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA UK
| |
Collapse
|
33
|
Velankar S, Alhroub Y, Best C, Caboche S, Conroy MJ, Dana JM, Fernandez Montecelo MA, van Ginkel G, Golovin A, Gore SP, Gutmanas A, Haslam P, Hendrickx PMS, Heuson E, Hirshberg M, John M, Lagerstedt I, Mir S, Newman LE, Oldfield TJ, Patwardhan A, Rinaldi L, Sahni G, Sanz-García E, Sen S, Slowley R, Suarez-Uruena A, Swaminathan GJ, Symmons MF, Vranken WF, Wainwright M, Kleywegt GJ. PDBe: Protein Data Bank in Europe. Nucleic Acids Res 2011; 40:D445-52. [PMID: 22110033 PMCID: PMC3245096 DOI: 10.1093/nar/gkr998] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi).
Collapse
Affiliation(s)
- S Velankar
- Protein Data Bank in Europe, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Orekhov VY, Jaravine VA. Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:271-92. [PMID: 21920222 DOI: 10.1016/j.pnmrs.2011.02.002] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 02/21/2011] [Indexed: 05/04/2023]
Affiliation(s)
- Vladislav Yu Orekhov
- Swedish NMR Centre, University of Gothenburg, Box 465, 40530 Gothenburg, Sweden.
| | | |
Collapse
|
35
|
Lemak A, Yee A, Bezsonova I, Dhe-Paganon S, Arrowsmith CH. Zn-binding AZUL domain of human ubiquitin protein ligase Ube3A. JOURNAL OF BIOMOLECULAR NMR 2011; 51:185-190. [PMID: 21947926 DOI: 10.1007/s10858-011-9552-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Accepted: 06/22/2011] [Indexed: 05/31/2023]
Abstract
Ube3A (also referred to as E6AP for E6 Associated Protein) is a E3 ubiquitin-protein ligase implicated in the development of Angelman syndrome by controlling degradation of synaptic protein Arc and oncogenic papilloma virus infection by controlling degradation of p53. This article describe the solution NMR structure of the conserved N-terminal domain of human Ube3A (residues 24-87) that contains two residues (Cys44 and Arg62) found to be mutated in patients with Angelman syndrome. The structure of this domain adopts a novel Zn-binding fold we called AZUL (Amino-terminal Zn-finger of Ube3a Ligase). The AZUL domain has a helix-loop-helix architecture with a Zn ion coordinated by four Cys residues arranged in Cys-X(4)-Cys-X(4)-Cys-X(28)-Cys motif. Three of the Zn-bound residues are located in a 23-residue long and well structured loop that connects two α-helicies.
Collapse
Affiliation(s)
- Alexander Lemak
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, and Northeast Structural Genomics Consortium, 101 College Street, Toronto, ON M5G 1L7, Canada
| | | | | | | | | |
Collapse
|
36
|
Warner LR, Varga K, Lange OF, Baker SL, Baker D, Sousa MC, Pardi A. Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set. J Mol Biol 2011; 411:83-95. [PMID: 21624375 PMCID: PMC3182476 DOI: 10.1016/j.jmb.2011.05.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 10/18/2022]
Abstract
The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein β-barrel assembly machine in E. coli. The first 100 residues in BamC were disordered in solution. The Rosetta calculations showed that BamC₁₀₁₋₃₄₄ forms two well-defined domains connected by an ~18-residue linker, where the relative orientation of the domains was not defined. Both domains adopt a helix-grip fold previously observed in the Bet v 1 superfamily. ¹⁵N relaxation data indicated a high degree of conformational flexibility for the linker connecting the N-terminal domain and the C-terminal domain in BamC. The results here show that CS-RDC-NOE Rosetta is robust and has a high tolerance for misassigned nuclear Overhauser effect restraints, greatly simplifying NMR structure determinations.
Collapse
Affiliation(s)
- Lisa R. Warner
- Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309, USA
| | - Krisztina Varga
- Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309, USA
| | - Oliver F. Lange
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Susan L. Baker
- Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Marcelo C. Sousa
- Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309, USA
| | - Arthur Pardi
- Department of Chemistry and Biochemistry University of Colorado, Boulder Boulder, CO 80309, USA
| |
Collapse
|
37
|
Zeng J, Zhou P, Donald BR. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data. JOURNAL OF BIOMOLECULAR NMR 2011; 50:371-95. [PMID: 21706248 PMCID: PMC3155202 DOI: 10.1007/s10858-011-9522-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 05/19/2011] [Indexed: 05/31/2023]
Abstract
One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called NASCA: (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), NASCA: extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that NASCA: assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by NASCA: have backbone RMSD 0.8-1.5 Å from the reference structures determined by traditional NMR approaches.
Collapse
Affiliation(s)
- Jianyang Zeng
- Department of Computer Science, Duke University, Durham NC 27708
| | - Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| | - Bruce Randall Donald
- Department of Computer Science, Duke University, Durham NC 27708
- Department of Biochemistry, Duke University Medical Center, Durham NC 27710
| |
Collapse
|