1
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McCoy KM, Fritzsching KJ, McDermott AE. GTP-Bound Escherichia coli FtsZ Filaments Are Composed of Tense Monomers: a Dynamic Nuclear Polarization-Nuclear Magnetic Resonance Study Using Interface Detection. mBio 2022; 13:e0235822. [PMID: 36214571 PMCID: PMC9765660 DOI: 10.1128/mbio.02358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
FtsZ filaments are the major structural component of the bacterial Z ring and are drivers of bacterial division. Crystal structures for FtsZ from some Gram-positive bacteria in the presence of GTP analogs suggest the possibility of a high-energy, "tense" conformation. It remains important to elucidate whether this tense form is the dominant form in filaments. Using dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) and differential isotopic labeling, we directly detected residues located at the intermonomer interface of GTP-bound wild-type (WT) Escherichia coli FtsZ filaments. We combined chemical shift prediction, homology modeling, and heteronuclear dipolar recoupling techniques to characterize the E. coli FtsZ filament interface and demonstrated that the monomers in active filaments assume a tense conformation. IMPORTANCE Bacterial replication is dependent on the cytoskeletal protein FtsZ, which forms filaments that scaffold and recruit other essential division proteins. While the FtsZ monomer is well studied across organisms, many questions remain about how the filaments form and function. Recently, a second monomer form was identified in Staphylococcus aureus that has far-reaching implications for FtsZ structure and function. However, to date, this form has not been directly observed outside S. aureus. In this study, we used solid-state NMR and dynamic nuclear polarization (DNP) to directly study the filaments of E. coli FtsZ to demonstrate that E. coli FtsZ filaments are primarily composed of this second, "tense" form of the monomer. This work is the first time GTP-bound, wild-type FtsZ filaments have been studied directly at atomic resolution and is an important step forward for the study of FtsZ filaments.
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Affiliation(s)
- Kelsey M. McCoy
- Department of Chemistry, Columbia University, New York, New York, USA
| | | | - Ann E. McDermott
- Department of Chemistry, Columbia University, New York, New York, USA
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2
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High-Resolution Magic Angle Spinning NMR of KcsA in Liposomes: The Highly Mobile C-Terminus. Biomolecules 2022; 12:biom12081122. [PMID: 36009016 PMCID: PMC9405666 DOI: 10.3390/biom12081122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/25/2022] Open
Abstract
The structure of the transmembrane domain of the pH-activated bacterial potassium channel KcsA has been extensively characterized, yet little information is available on the structure of its cytosolic, functionally critical N- and C-termini. This study presents high-resolution magic angle spinning (HR-MAS) and fractional deuteration as tools to study these poorly resolved regions for proteoliposome-embedded KcsA. Using 1H-detected HR-MAS NMR, we show that the C-terminus transitions from a rigid structure to a more dynamic structure as the solution is rendered acidic. We make previously unreported assignments of residues in the C-terminus of lipid-embedded channels. These data agree with functional models of the C-terminus-stabilizing KcsA tetramers at a neutral pH with decreased stabilization effects at acidic pH. We present evidence that a C-terminal truncation mutation has a destabilizing effect on the KcsA selectivity filter. Finally, we show evidence of hydrolysis of lipids in proteoliposome samples during typical experimental timeframes.
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3
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Sciolino N, Liu A, Breindel L, Burz DS, Sulchek T, Shekhtman A. Microfluidics delivery of DARPP-32 into HeLa cells maintains viability for in-cell NMR spectroscopy. Commun Biol 2022; 5:451. [PMID: 35551287 PMCID: PMC9098904 DOI: 10.1038/s42003-022-03412-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
High-resolution structural studies of proteins and protein complexes in a native eukaryotic environment present a challenge to structural biology. In-cell NMR can characterize atomic resolution structures but requires high concentrations of labeled proteins in intact cells. Most exogenous delivery techniques are limited to specific cell types or are too destructive to preserve cellular physiology. The feasibility of microfluidics transfection or volume exchange for convective transfer, VECT, as a means to deliver labeled target proteins to HeLa cells for in-cell NMR experiments is demonstrated. VECT delivery does not require optimization or impede cell viability; cells are immediately available for long-term eukaryotic in-cell NMR experiments. In-cell NMR-based drug screening using VECT was demonstrated by collecting spectra of the sensor molecule DARPP32, in response to exogenous administration of Forskolin.
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Affiliation(s)
- Nicholas Sciolino
- University at Albany, Department of Chemistry, Albany, NY, 12222, USA
| | - Anna Liu
- Georgia Tech, School of Mechanical Engineering, Atlanta, GA, 30332, USA
| | - Leonard Breindel
- University at Albany, Department of Chemistry, Albany, NY, 12222, USA
| | - David S Burz
- University at Albany, Department of Chemistry, Albany, NY, 12222, USA
| | - Todd Sulchek
- Georgia Tech, School of Mechanical Engineering, Atlanta, GA, 30332, USA
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4
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Luchinat E, Cremonini M, Banci L. Radio Signals from Live Cells: The Coming of Age of In-Cell Solution NMR. Chem Rev 2022; 122:9267-9306. [PMID: 35061391 PMCID: PMC9136931 DOI: 10.1021/acs.chemrev.1c00790] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
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A detailed knowledge
of the complex processes that make cells and
organisms alive is fundamental in order to understand diseases and
to develop novel drugs and therapeutic treatments. To this aim, biological
macromolecules should ideally be characterized at atomic resolution
directly within the cellular environment. Among the existing structural
techniques, solution NMR stands out as the only one able to investigate
at high resolution the structure and dynamic behavior of macromolecules
directly in living cells. With the advent of more sensitive NMR hardware
and new biotechnological tools, modern in-cell NMR approaches have
been established since the early 2000s. At the coming of age of in-cell
NMR, we provide a detailed overview of its developments and applications
in the 20 years that followed its inception. We review the existing
approaches for cell sample preparation and isotopic labeling, the
application of in-cell NMR to important biological questions, and
the development of NMR bioreactor devices, which greatly increase
the lifetime of the cells allowing real-time monitoring of intracellular
metabolites and proteins. Finally, we share our thoughts on the future
perspectives of the in-cell NMR methodology.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum−Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Matteo Cremonini
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Lucia Banci
- Magnetic Resonance Center, Università degli Studi di Firenze, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Italy
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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5
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Sparks S, Hayama R, Rout MP, Cowburn D. Analysis of Multivalent IDP Interactions: Stoichiometry, Affinity, and Local Concentration Effect Measurements. Methods Mol Biol 2020; 2141:463-475. [PMID: 32696372 PMCID: PMC10862351 DOI: 10.1007/978-1-0716-0524-0_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nuclear magnetic resonance (NMR) titration and isothermal titration calorimetry can be combined to provide an assessment of how multivalent intrinsically disordered protein (IDP) interactions can involve enthalpy-entropy balance. Here, we describe the underlying technical details and additional methods, such as dynamic light scattering analysis, needed to assess these reactions. We apply this to a central interaction involving the disordered regions of phe-gly nucleoporins (FG-Nups) that contain multiple phenylalanine-glycine repeats which are of particular interest, as their interactions with nuclear transport factors (NTRs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex (NPC). These analyses revealed that a combination of low per-FG motif affinity and the enthalpy-entropy balance prevents high-avidity interaction between FG-Nups and NTRs while the large number of FG motifs promotes frequent FG-NTR contacts, resulting in enhanced selectivity.
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Affiliation(s)
- Samuel Sparks
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Silicon Therapeutics, Boston, MA, USA
| | - Ryo Hayama
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Cowburn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA.
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6
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The Inescapable Effects of Ribosomes on In-Cell NMR Spectroscopy and the Implications for Regulation of Biological Activity. Int J Mol Sci 2019; 20:ijms20061297. [PMID: 30875837 PMCID: PMC6471074 DOI: 10.3390/ijms20061297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/05/2019] [Accepted: 03/09/2019] [Indexed: 12/16/2022] Open
Abstract
The effects of RNA on in-cell NMR spectroscopy and ribosomes on the kinetic activity of several metabolic enzymes are reviewed. Quinary interactions between labelled target proteins and RNA broaden in-cell NMR spectra yielding apparent megadalton molecular weights in-cell. The in-cell spectra can be resolved by using cross relaxation-induced polarization transfer (CRINEPT), heteronuclear multiple quantum coherence (HMQC), transverse relaxation-optimized, NMR spectroscopy (TROSY). The effect is reproduced in vitro by using reconstituted total cellular RNA and purified ribosome preparations. Furthermore, ribosomal binding antibiotics alter protein quinary structure through protein-ribosome and protein-mRNA-ribosome interactions. The quinary interactions of Adenylate kinase, Thymidylate synthase and Dihydrofolate reductase alter kinetic properties of the enzymes. The results demonstrate that ribosomes may specifically contribute to the regulation of biological activity.
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7
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Abstract
In-cell NMR spectroscopy is a powerful tool to study protein structures and interactions under near physiological conditions in both prokaryotic and eukaryotic living cells. The low sensitivity and resolution of in-cell NMR spectra and limited lifetime of cells over the course of an in-cell experiment have presented major hurdles to wide acceptance of the technique, limiting it to a few select systems. These issues are addressed by introducing the use of the CRINEPT pulse sequence to increase the sensitivity and resolution of in-cell NMR spectra and the use of a bioreactor to maintain cell viability for up to 24h. Application of advanced pulse sequences and bioreactor during in-cell NMR experiments will facilitate the exploration of a wide range of biological processes.
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8
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Breindel L, Burz DS, Shekhtman A. Interaction proteomics by using in-cell NMR spectroscopy. J Proteomics 2019; 191:202-211. [PMID: 29427760 PMCID: PMC6082733 DOI: 10.1016/j.jprot.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/31/2018] [Accepted: 02/04/2018] [Indexed: 12/17/2022]
Abstract
A synopsis of in-cell NMR spectroscopic approaches to study interaction proteomics in prokaryotic and eukaryotic cells is presented. We describe the use of in-cell NMR spectroscopy to resolve high resolution protein structures, discuss methodologies for determining and analyzing high and low affinity protein-target structural interactions, including intrinsically disordered proteins, and detail important functional interactions that result from these interactions. SIGNIFICANCE: The ultimate goal of structural and biochemical research is to understand how macromolecular interactions give rise to and regulate biological activity in living cells. The challenge is formidable due to the complexity that arises not only from the number of proteins (genes) expressed by the organism, but also from the combinatorial interactions between them. Despite ongoing efforts to decipher the complex nature of protein interactions, new methods for structurally characterizing protein complexes are needed to fully understand molecular networks. With the onset of in-cell NMR spectroscopy, molecular structures and interactions can be studied under physiological conditions shedding light on the structural underpinning of biological activity.
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Affiliation(s)
- Leonard Breindel
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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9
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Demers JP, Fricke P, Shi C, Chevelkov V, Lange A. Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:51-78. [PMID: 30527136 DOI: 10.1016/j.pnmrs.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 06/15/2018] [Accepted: 06/15/2018] [Indexed: 05/26/2023]
Abstract
In the cellular environment, biomolecules assemble in large complexes which can act as molecular machines. Determining the structure of intact assemblies can reveal conformations and inter-molecular interactions that are only present in the context of the full assembly. Solid-state NMR (ssNMR) spectroscopy is a technique suitable for the study of samples with high molecular weight that allows the atomic structure determination of such large protein assemblies under nearly physiological conditions. This review provides a practical guide for the first steps of studying biological supra-molecular assemblies using ssNMR. The production of isotope-labeled samples is achievable via several means, which include recombinant expression, cell-free protein synthesis, extraction of assemblies directly from cells, or even the study of assemblies in whole cells in situ. Specialized isotope labeling schemes greatly facilitate the assignment of chemical shifts and the collection of structural data. Advanced strategies such as mixed, diluted, or segmental subunit labeling offer the possibility to study inter-molecular interfaces. Detailed and practical considerations are presented with respect to first setting up magic-angle spinning (MAS) ssNMR experiments, including the selection of the ssNMR rotor, different methods to best transfer the sample and prepare the rotor, as well as common and robust procedures for the calibration of the instrument. Diagnostic spectra to evaluate the resolution and sensitivity of the sample are presented. Possible improvements that can reduce sample heterogeneity and improve the quality of ssNMR spectra are reviewed.
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Affiliation(s)
- Jean-Philippe Demers
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Laboratory of Cell Biology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Pascal Fricke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Veniamin Chevelkov
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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10
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Hayama R, Sparks S, Hecht LM, Dutta K, Karp JM, Cabana CM, Rout MP, Cowburn D. Thermodynamic characterization of the multivalent interactions underlying rapid and selective translocation through the nuclear pore complex. J Biol Chem 2018; 293:4555-4563. [PMID: 29374059 PMCID: PMC5868264 DOI: 10.1074/jbc.ac117.001649] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/19/2018] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe-Gly nucleoporins (FG Nups) that contain multiple phenylalanine-glycine repeats are of particular interest, as their interactions with transport factors (TFs) underlie the paradoxically rapid yet also highly selective transport of macromolecules mediated by the nuclear pore complex. Here, we used NMR and isothermal titration calorimetry to thermodynamically characterize these multivalent interactions. These analyses revealed that a combination of low per-FG motif affinity and the enthalpy-entropy balance prevents high-avidity interaction between FG Nups and TFs, whereas the large number of FG motifs promotes frequent FG-TF contacts, resulting in enhanced selectivity. Our thermodynamic model underlines the importance of functional disorder of FG Nups. It helps explain the rapid and selective translocation of TFs through the nuclear pore complex and further expands our understanding of the mechanisms of "fuzzy" interactions involving IDPs.
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Affiliation(s)
- Ryo Hayama
- From the Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York 10065
| | - Samuel Sparks
- the Departments of Biochemistry and of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and
| | - Lee M Hecht
- From the Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York 10065
| | - Kaushik Dutta
- the New York Structural Biology Center, New York, New York 10027
| | - Jerome M Karp
- the Departments of Biochemistry and of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and
| | - Christina M Cabana
- From the Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York 10065
| | - Michael P Rout
- From the Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York 10065,
| | - David Cowburn
- the Departments of Biochemistry and of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, and
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11
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Sparks S, Temel DB, Rout MP, Cowburn D. Deciphering the "Fuzzy" Interaction of FG Nucleoporins and Transport Factors Using Small-Angle Neutron Scattering. Structure 2018; 26:477-484.e4. [PMID: 29429880 PMCID: PMC5929991 DOI: 10.1016/j.str.2018.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 10/27/2017] [Accepted: 01/12/2018] [Indexed: 11/16/2022]
Abstract
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interacting with TFs. To selectively characterize conformational changes in FG Nups induced by TFs we performed small-angle neutron scattering (SANS) with contrast matching. Conformational-ensembles derived from SANS data indicated an increase in the overall size of FG Nups is associated with TF interaction. Moreover, the organization of the FG motif in the interacting state is consistent with prior experimental analyses defining that FG motifs undergo conformational restriction upon interacting with TFs. These results provide structural insights into a highly dynamic interaction and illustrate how functional disorder imparts rapid and selective FG Nup-TF interactions.
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Affiliation(s)
- Samuel Sparks
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deniz B Temel
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY, USA
| | - David Cowburn
- Departments of Biochemistry and of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, NY, USA.
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12
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Burz DS, DeMott CM, Aldousary A, Dansereau S, Shekhtman A. Quantitative Determination of Interacting Protein Surfaces in Prokaryotes and Eukaryotes by Using In-Cell NMR Spectroscopy. Methods Mol Biol 2018; 1688:423-444. [PMID: 29151221 DOI: 10.1007/978-1-4939-7386-6_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper describes three protocols for identifying interacting surfaces on 15N-labeled target proteins of known structure by using in-cell NMR spectroscopy. The first protocol describes how to identify protein quinary structure interaction surfaces in prokaryotes by using cross-relaxation-induced polarization transfer, CRIPT, based in-cell NMR. The second protocol describes how to introduce labeled protein into eukaryotic (HeLa) cells via electroporation for CRIPT-based in-cell studies. The third protocol describes how to quantitatively map protein interacting surfaces by utilizing singular value decomposition, SVD, analysis of STructural INTeractions by in-cell NMR, STINT-NMR, data.
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Affiliation(s)
- David S Burz
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Asma Aldousary
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Stephen Dansereau
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, CH 122, Albany, NY, 12222, USA.
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13
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Danmaliki GI, Liu PB, Hwang PM. Stereoselective Deuteration in Aspartate, Asparagine, Lysine, and Methionine Amino Acid Residues Using Fumarate as a Carbon Source for Escherichia coli in D2O. Biochemistry 2017; 56:6015-6029. [DOI: 10.1021/acs.biochem.7b00991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gaddafi I. Danmaliki
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta Canada T6G 2H7
| | - Philip B. Liu
- Department
of Medicine, University of Alberta, Edmonton, Alberta Canada T6G 2R3
| | - Peter M. Hwang
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta Canada T6G 2H7
- Department
of Medicine, University of Alberta, Edmonton, Alberta Canada T6G 2R3
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14
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DeMott CM, Majumder S, Burz DS, Reverdatto S, Shekhtman A. Ribosome Mediated Quinary Interactions Modulate In-Cell Protein Activities. Biochemistry 2017; 56:4117-4126. [PMID: 28715177 DOI: 10.1021/acs.biochem.7b00613] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosomes are present inside bacterial cells at micromolar concentrations and occupy up to 20% of the cell volume. Under these conditions, even weak quinary interactions between ribosomes and cytosolic proteins can affect protein activity. By using in-cell and in vitro NMR spectroscopy, and biophysical techniques, we show that the enzymes, adenylate kinase and dihydrofolate reductase, and the respective coenzymes, ATP and NADPH, bind to ribosomes with micromolar affinity, and that this interaction suppresses the enzymatic activities of both enzymes. Conversely, thymidylate synthase, which works together with dihydrofolate reductase in the thymidylate synthetic pathway, is activated by ribosomes. We also show that ribosomes impede diffusion of green fluorescent protein in vitro and contribute to the decrease in diffusion in vivo. These results strongly suggest that ribosome-mediated quinary interactions contribute to the differences between in vitro and in vivo protein activities and that ribosomes play a previously under-appreciated nontranslational role in regulating cellular biochemistry.
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Affiliation(s)
- Christopher M DeMott
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Subhabrata Majumder
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York at Albany , Albany, New York 12222, United States
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15
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Mohanty B, Williams ML, Doak BC, Vazirani M, Ilyichova O, Wang G, Bermel W, Simpson JS, Chalmers DK, King GF, Mobli M, Scanlon MJ. Determination of ligand binding modes in weak protein-ligand complexes using sparse NMR data. JOURNAL OF BIOMOLECULAR NMR 2016; 66:195-208. [PMID: 27778134 DOI: 10.1007/s10858-016-0067-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
We describe a general approach to determine the binding pose of small molecules in weakly bound protein-ligand complexes by deriving distance constraints between the ligand and methyl groups from all methyl-containing residues of the protein. We demonstrate that using a single sample, which can be prepared without the use of expensive precursors, it is possible to generate high-resolution data rapidly and obtain the resonance assignments of Ile, Leu, Val, Ala and Thr methyl groups using triple resonance scalar correlation data. The same sample may be used to obtain Met εCH3 assignments using NOESY-based methods, although the superior sensitivity of NOESY using [U-13C,15N]-labeled protein makes the use of this second sample more efficient. We describe a structural model for a weakly binding ligand bound to its target protein, DsbA, derived from intermolecular methyl-to-ligand nuclear Overhauser enhancements, and demonstrate that the ability to assign all methyl resonances in the spectrum is essential to derive an accurate model of the structure. Once the methyl assignments have been obtained, this approach provides a rapid means to generate structural models for weakly bound protein-ligand complexes. Such weak complexes are often found at the beginning of programs of fragment based drug design and can be challenging to characterize using X-ray crystallography.
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Affiliation(s)
- Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Martin L Williams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Mansha Vazirani
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Olga Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Geqing Wang
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- La Trobe Institute for Molecular Bioscience, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Wolfgang Bermel
- Bruker Biospin GmbH, Silberstreifen, 76287, Rheinstetten, Germany
| | - Jamie S Simpson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mehdi Mobli
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia.
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16
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Sethi A, Bruell S, Patil N, Hossain MA, Scott DJ, Petrie EJ, Bathgate RAD, Gooley PR. The complex binding mode of the peptide hormone H2 relaxin to its receptor RXFP1. Nat Commun 2016; 7:11344. [PMID: 27088579 PMCID: PMC4837482 DOI: 10.1038/ncomms11344] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/16/2016] [Indexed: 11/20/2022] Open
Abstract
H2 relaxin activates the relaxin family peptide receptor-1 (RXFP1), a class A G-protein coupled receptor, by a poorly understood mechanism. The ectodomain of RXFP1 comprises an N-terminal LDLa module, essential for activation, tethered to a leucine-rich repeat (LRR) domain by a 32-residue linker. H2 relaxin is hypothesized to bind with high affinity to the LRR domain enabling the LDLa module to bind and activate the transmembrane domain of RXFP1. Here we define a relaxin-binding site on the LDLa-LRR linker, essential for the high affinity of H2 relaxin for the ectodomain of RXFP1, and show that residues within the LDLa-LRR linker are critical for receptor activation. We propose H2 relaxin binds and stabilizes a helical conformation of the LDLa-LRR linker that positions residues of both the linker and the LDLa module to bind the transmembrane domain and activate RXFP1. The mechanism by which relaxin activates the relaxin family peptide receptor-1 is poorly understood. Here, Sethi et al. identify a relaxin binding site in an extracellular linker between the LDLa and LRR domains and propose that relaxin binding stabilizes a helical conformation that leads to receptor activation.
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Affiliation(s)
- Ashish Sethi
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Shoni Bruell
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Nitin Patil
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia.,School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Mohammed Akhter Hossain
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Emma J Petrie
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Ross A D Bathgate
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry &Molecular Biology, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
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17
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Ferrage F, Dutta K, Cowburn D. Identification of Hydrophobic Interfaces in Protein-Ligand Complexes by Selective Saturation Transfer NMR Spectroscopy. Molecules 2015; 20:21992-9. [PMID: 26690112 PMCID: PMC6332028 DOI: 10.3390/molecules201219824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/17/2015] [Accepted: 11/26/2015] [Indexed: 11/28/2022] Open
Abstract
The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase.
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Affiliation(s)
- Fabien Ferrage
- New York Structural Biology Center, New York, NY 10027, USA.
- Department of Chemistry, École Normale Supérieure-PSL Research University, 24 rue Lhomond, 75005 Paris, France.
- LBM, Sorbonne Universités, UPMC Univ Paris 06, 4 place Jussieu, F-75005 Paris, France.
- UMR 7203 LBM, CNRS, F-75005 Paris, France.
| | - Kaushik Dutta
- New York Structural Biology Center, New York, NY 10027, USA.
| | - David Cowburn
- New York Structural Biology Center, New York, NY 10027, USA.
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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18
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Baber JL, Louis JM, Clore GM. Dependence of distance distributions derived from double electron-electron resonance pulsed EPR spectroscopy on pulse-sequence time. Angew Chem Int Ed Engl 2015; 54:5336-9. [PMID: 25757985 PMCID: PMC4412742 DOI: 10.1002/anie.201500640] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 02/10/2015] [Indexed: 11/06/2022]
Abstract
Pulsed double electron-electron resonance (DEER) provides pairwise P(r) distance distributions in doubly spin labeled proteins. We report that in protonated proteins, P(r) is dependent on the length of the second echo period T owing to local environmental effects on the spin-label phase memory relaxation time Tm . For the protein ABD, this effect results in a 1.4 Å increase in the P(r) maximum from T=6 to 20 μs. Protein A has a bimodal P(r) distribution, and the relative height of the shorter distance peak at T=10 μs, the shortest value required to obtain a reliable P(r), is reduced by 40 % relative to that found by extrapolation to T=0. Our results indicate that data at a series of T values are essential for quantitative interpretation of DEER to determine the extent of the T dependence and to extrapolate the results to T=0. Complete deuteration (99 %) of the protein was accompanied by a significant increase in Tm and effectively abolished the P(r) dependence on T.
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Affiliation(s)
- James L. Baber
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - John M. Louis
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
| | - G. Marius Clore
- National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, U.S.A
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19
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Majumder S, Xue J, DeMott CM, Reverdatto S, Burz DS, Shekhtman A. Probing protein quinary interactions by in-cell nuclear magnetic resonance spectroscopy. Biochemistry 2015; 54:2727-38. [PMID: 25894651 DOI: 10.1021/acs.biochem.5b00036] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Historically introduced by McConkey to explain the slow mutation rate of highly abundant proteins, weak protein (quinary) interactions are an emergent property of living cells. The protein complexes that result from quinary interactions are transient and thus difficult to study biochemically in vitro. Cross-correlated relaxation-induced polarization transfer-based in-cell nuclear magnetic resonance allows the characterization of protein quinary interactions with atomic resolution inside live prokaryotic and eukaryotic cells. We show that RNAs are an important component of protein quinary interactions. Protein quinary interactions are unique to the target protein and may affect physicochemical properties, protein activity, and interactions with drugs.
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Affiliation(s)
- Subhabrata Majumder
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Jing Xue
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Sergey Reverdatto
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - David S Burz
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, State University of New York, Albany, New York 12222, United States
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20
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Baber JL, Louis JM, Clore GM. Dependence of Distance Distributions Derived from Double Electron-Electron Resonance Pulsed EPR Spectroscopy on Pulse-Sequence Time. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Choi YS, Lee YJ, Lee SY, Shi L, Ha JH, Cheong HK, Cheong C, Cohen RE, Ryu KS. Differential ubiquitin binding by the acidic loops of Ube2g1 and Ube2r1 enzymes distinguishes their Lys-48-ubiquitylation activities. J Biol Chem 2014; 290:2251-63. [PMID: 25471371 DOI: 10.1074/jbc.m114.624809] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ubiquitin E2 enzymes, Ube2g1 and Ube2r1, are able to synthesize Lys-48-linked polyubiquitins without an E3 ligase but how that is accomplished has been unclear. Although both E2s contain essential acidic loops, only Ube2r1 requires an additional C-terminal extension (184-196) for efficient Lys-48-ubiquitylation activity. The presence of Tyr-102 and Tyr-104 in the Ube2g1 acidic loop enhanced both ubiquitin binding and Lys-48-ubiquitylation and distinguished Ube2g1 from the otherwise similar truncated Ube2r1(1-183) (Ube2r1C). Replacement of Gln-105-Ser-106-Gly-107 in the acidic loop of Ube2r1C (Ube2r1C(YGY)) by the corresponding residues from Ube2g1 (Tyr-102-Gly-103-Tyr-104) increased Lys-48-ubiquitylation activity and ubiquitin binding. Two E2∼UB thioester mimics (oxyester and disulfide) were prepared to characterize the ubiquitin binding activity of the acidic loop. The oxyester but not the disulfide derivative was found to be a functional equivalent of the E2∼UB thioester. The ubiquitin moiety of the Ube2r1C(C93S)-[(15)N]UB(K48R) oxyester displayed two-state conformational exchange, whereas the Ube2r1C(C93S/YGY)-[(15)N]UB(K48R) oxyester showed predominantly one state. Together with NMR studies that compared UB(K48R) oxyesters of the wild-type and the acidic loop mutant (Y102G/Y104G) forms of Ube2g1, in vitro ubiquitylation assays with various mutation forms of the E2s revealed how the intramolecular interaction between the acidic loop and the attached donor ubiquitin regulates Lys-48-ubiquitylation activity.
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Affiliation(s)
- Yun-Seok Choi
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea, Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Yun-Ju Lee
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Seo-Yeon Lee
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Lei Shi
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, and
| | - Jung-Hye Ha
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea
| | - Hae-Kap Cheong
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883
| | - Chaejoon Cheong
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea
| | - Robert E Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870
| | - Kyoung-Seok Ryu
- From the Division of Magnetic Resonance, Korea Basic Science Institute Ochang Campus, Cheongwon-Gun, Ochang-Eup, Yangcheong-Ri 804-1, Chungcheongbuk-Do 363-883, Department of Bio-Analytical Science, University of Science and Technology, Daejon 305-333, South Korea,
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22
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Miyanoiri Y, Takeda M, Okuma K, Ono AM, Terauchi T, Kainosho M. Differential isotope-labeling for Leu and Val residues in a protein by E. coli cellular expression using stereo-specifically methyl labeled amino acids. JOURNAL OF BIOMOLECULAR NMR 2013; 57:237-249. [PMID: 24057411 DOI: 10.1007/s10858-013-9784-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/16/2013] [Indexed: 06/02/2023]
Abstract
The (1)H-(13)C HMQC signals of the (13)CH3 moieties of Ile, Leu, and Val residues, in an otherwise deuterated background, exhibit narrow line-widths, and thus are useful for investigating the structures and dynamics of larger proteins. This approach, named methyl TROSY, is economical as compared to laborious methods using chemically synthesized site- and stereo-specifically isotope-labeled amino acids, such as stereo-array isotope labeling amino acids, since moderately priced, commercially available isotope-labeled α-keto acid precursors can be used to prepare the necessary protein samples. The Ile δ1-methyls can be selectively labeled, using isotope-labeled α-ketobutyrates as precursors. However, it is still difficult to prepare a residue-selectively Leu and Val labeled protein, since these residues share a common biosynthetic intermediate, α-ketoisovalerate. Another hindering drawback in using the α-ketoisovalerate precursor is the lack of stereo-selectivity for Leu and Val methyls. Here we present a differential labeling method for Leu and Val residues, using four kinds of stereo-specifically (13)CH3-labeled [U-(2)H;(15)N]-leucine and -valine, which can be efficiently incorporated into a protein using Escherichia coli cellular expression. The method allows the differential labeling of Leu and Val residues with any combination of stereo-specifically isotope-labeled prochiral methyls. Since relatively small amounts of labeled leucine and valine are required to prepare the NMR samples; i.e., 2 and 10 mg/100 mL of culture for leucine and valine, respectively, with sufficient isotope incorporation efficiency, this approach will be a good alternative to the precursor methods. The feasibility of the method is demonstrated for 82 kDa malate synthase G.
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Affiliation(s)
- Yohei Miyanoiri
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
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23
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Hansen AL, Lundström P, Velyvis A, Kay LE. Quantifying millisecond exchange dynamics in proteins by CPMG relaxation dispersion NMR using side-chain 1H probes. J Am Chem Soc 2012; 134:3178-89. [PMID: 22300166 DOI: 10.1021/ja210711v] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for quantifying millisecond time-scale chemical exchange at side-chain (1)H positions in proteins. Such experiments are not possible in a fully protonated molecule because of magnetization evolution from homonuclear scalar couplings that interferes with the extraction of accurate transverse relaxation rates. It is shown, however, that by using a labeling strategy whereby proteins are produced using {(13)C,(1)H}-glucose and D(2)O a significant number of 'isolated' side-chain (1)H spins are generated, eliminating such effects. It thus becomes possible to record (1)H dispersion profiles at the β positions of Asx, Cys, Ser, His, Phe, Tyr, and Trp as well as the γ positions of Glx, in addition to the methyl side-chain moieties. This brings the total of amino acid side-chain positions that can be simultaneously probed using a single (1)H dispersion experiment to 16. The utility of the approach is demonstrated with an application to the four-helix bundle colicin E7 immunity protein, Im7, which folds via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. The extracted (1)H chemical shift differences at side-chain positions provide valuable restraints in structural studies of invisible, excited states, complementing backbone chemical shifts that are available from existing relaxation dispersion experiments.
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Affiliation(s)
- Alexandar L Hansen
- Department of Molecular Genetics, The University of Toronto, Toronto, Ontario M5S 1A8, Canada
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24
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Nand D, Cukkemane A, Becker S, Baldus M. Fractional deuteration applied to biomolecular solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2012; 52:91-101. [PMID: 22105305 PMCID: PMC3277825 DOI: 10.1007/s10858-011-9585-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/29/2011] [Indexed: 05/15/2023]
Abstract
Solid-state Nuclear Magnetic Resonance can provide detailed insight into structural and dynamical aspects of complex biomolecules. With increasing molecular size, advanced approaches for spectral simplification and the detection of medium to long-range contacts become of critical relevance. We have analyzed the protonation pattern of a membrane-embedded ion channel that was obtained from bacterial expression using protonated precursors and D(2)O medium. We find an overall reduction of 50% in protein protonation. High levels of deuteration at H(α) and H(β) positions reduce spectral congestion in ((1)H,(13)C,(15)N) correlation experiments and generate a transfer profile in longitudinal mixing schemes that can be tuned to specific resonance frequencies. At the same time, residual protons are predominantly found at amino-acid side-chain positions enhancing the prospects for obtaining side-chain resonance assignments and for detecting medium to long-range contacts. Fractional deuteration thus provides a powerful means to aid the structural analysis of complex biomolecules by solid-state NMR.
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Affiliation(s)
- Deepak Nand
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Abhishek Cukkemane
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Marc Baldus
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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25
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Breukels V, Konijnenberg A, Nabuurs SM, Doreleijers JF, Kovalevskaya NV, Vuister GW. Overview on the use of NMR to examine protein structure. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 17:Unit17.5. [PMID: 21488042 DOI: 10.1002/0471140864.ps1705s64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein-ligand interaction, protein dynamics, or protein folding is described.
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Affiliation(s)
- Vincent Breukels
- Protein Biophysics, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
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26
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Asami S, Schmieder P, Reif B. High resolution 1H-detected solid-state NMR spectroscopy of protein aliphatic resonances: access to tertiary structure information. J Am Chem Soc 2011; 132:15133-5. [PMID: 20939587 DOI: 10.1021/ja106170h] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biological magic angle spinning (MAS) solid-state nuclear magnetic resonance spectroscopy has developed rapidly over the past two decades. For the structure determination of a protein by solid-state NMR, routinely (13)C,(13)C distance restraints as well as dihedral restraints are employed. In protonated samples, this is achieved by growing the bacterium on a medium which contains [1,3]-(13)C glycerol or [2]-(13)C glycerol to dilute the (13)C spin system. Labeling schemes, which rely on heteronuclei, are insensitive both for detection and in terms of quantification of distances, since they are relying on low-γ nuclei. Proton detection can in principle provide a gain in sensitivity by a factor of 8 and 31, compared to the (13)C or (15)N detected version of the experiment. We report here a new labeling scheme, which enables (1)H-detection of aliphatic resonances with high resolution in MAS solid-state NMR spectroscopy. We prepared microcrystals of the SH3 domain of chicken α-spectrin with 5% protonation at nonexchangeable sites and obtained line widths on the order of 25 Hz for aliphatic (1)H resonances. We show further that (13)C resolved 3D-(1)H,(1)H correlation experiments yield access to long-range proton-proton distances in the protein.
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Affiliation(s)
- Sam Asami
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Roessle-Str. 10, 13125 Berlin, Germany
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27
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Otten R, Villali J, Kern D, Mulder FAA. Probing microsecond time scale dynamics in proteins by methyl (1)H Carr-Purcell-Meiboom-Gill relaxation dispersion NMR measurements. Application to activation of the signaling protein NtrC(r). J Am Chem Soc 2010; 132:17004-14. [PMID: 21058670 PMCID: PMC2991065 DOI: 10.1021/ja107410x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Indexed: 11/29/2022]
Abstract
To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ (1)H Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of microsecond to millisecond time scale dynamics of methyl groups in proteins, exploiting their high abundance and favorable relaxation properties. In our approach, protein samples are produced using [(1)H, (13)C]-d-glucose in ∼100% D(2)O, which yields CHD(2) methyl groups for alanine, valine, threonine, isoleucine, leucine, and methionine residues with high abundance, in an otherwise largely deuterated background. Methyl groups in such samples can be sequence-specifically assigned to near completion, using (13)C TOCSY NMR spectroscopy, as was recently demonstrated (Otten, R.; et al. J. Am. Chem. Soc. 2010, 132, 2952-2960). In this Article, NMR pulse schemes are presented to measure (1)H CPMG relaxation dispersion profiles for CHD(2) methyl groups, in a vein similar to that of backbone relaxation experiments. Because of the high deuteration level of methyl-bearing side chains, artifacts arising from proton scalar coupling during the CPMG pulse train are negligible, with the exception of Ile-δ1 and Thr-γ2 methyl groups, and a pulse scheme is described to remove the artifacts for those residues. Strong (13)C scalar coupling effects, observed for several leucine residues, are removed by alternative biochemical and NMR approaches. The methodology is applied to the transcriptional activator NtrC(r), for which an inactive/active state transition was previously measured and the motions in the microsecond time range were estimated through a combination of backbone (15)N CPMG dispersion NMR spectroscopy and a collection of experiments to determine the exchange-free component to the transverse relaxation rate. Exchange contributions to the (1)H line width were detected for 21 methyl groups, and these probes were found to collectively report on a local structural rearrangement around the phosphorylation site, with a rate constant of (15.5 ± 0.5) × 10(3) per second (i.e., τ(ex) = 64.7 ± 1.9 μs). The affected methyl groups indicate that, already before phosphorylation, a substantial, transient rearrangement takes place between helices 3 and 4 and strands 4 and 5. This conformational equilibrium allows the protein to gain access to the active, signaling state in the absence of covalent modification through a shift in a pre-existing dynamic equilibrium. Moreover, the conformational switching maps exactly to the regions that differ between the solution NMR structures of the fully inactive and active states. These results demonstrate that a cost-effective and quantitative study of protein methyl group dynamics by (1)H CPMG relaxation dispersion NMR spectroscopy is possible and can be applied to study functional motions on the microsecond time scale that cannot be accessed by backbone (15)N relaxation dispersion NMR. The use of methyl groups as dynamics probes extends such applications also to larger proteins.
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28
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Schwalbe M, Dutta K, Libich DS, Venugopal H, Claridge JK, Gell DA, Mackay JP, Edwards PJB, Pascal SM. Two-state conformational equilibrium in the Par-4 leucine zipper domain. Proteins 2010; 78:2433-49. [PMID: 20602362 DOI: 10.1002/prot.22752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Prostate apoptosis response factor-4 (Par-4) is a pro-apoptotic and tumor-suppressive protein. A highly conserved heptad repeat sequence at the Par-4 C-terminus suggests the presence of a leucine zipper (LZ). This C-terminal region is essential for Par-4 self-association and interaction with various effector proteins. We have used nuclear magnetic resonance (NMR) spectroscopy to fully assign the chemical shift resonances of a peptide comprising the LZ domain of Par-4 at neutral pH. Further, we have investigated the properties of the Par-4 LZ domain and two point mutants under a variety of conditions using NMR, circular dichroism (CD), light scattering, and bioinformatics. Results indicate an environment-dependent conformational equilibrium between a partially ordered monomer (POM) and a predominantly coiled coil dimer (CCD). The combination of techniques used allows the time scales of the equilibrium to be probed and also helps to identify features of the amino acid sequence that may influence the equilibrium.
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Affiliation(s)
- Martin Schwalbe
- Centre for Structural Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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29
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Otten R, Chu B, Krewulak KD, Vogel HJ, Mulder FAA. Comprehensive and cost-effective NMR spectroscopy of methyl groups in large proteins. J Am Chem Soc 2010; 132:2952-60. [PMID: 20148553 DOI: 10.1021/ja907706a] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An NMR approach is described which yields the methyl resonance assignments of alanine, threonine, valine, leucine, and isoleucine residues in proteins with high sensitivity and excellent resolution. The method relies on protein samples produced by bacterial expression using [(1)H,(13)C]-D-glucose and approximately 100% D(2)O, which is cost-effective and ensures the isotopic enrichment of all possible methyl groups. Magnetization transfer throughout the methyl-containing side chains is possible with this labeling scheme due to the high level of deuteration along the amino acid side chain, coupled with the selection of the favorable CHD(2) methyl isotopomer for detection. In an application to the 34 kDa periplasmic binding protein FepB 164 out of 195 methyl groups (85%) were assigned sequence-specifically and stereospecifically. This percentage increases to 91% when taking into account that not all backbone assignments are available for this system. The remaining unassigned methyl groups belong to six leucine residues, caused by low cross-peak intensities, and four alanine residues due to degeneracy of the (13)C(alpha)/(13)C(beta) frequencies. Our results demonstrate that NMR spectroscopic investigations of protein structure, dynamics, and interactions can be extended to include all methyl-containing amino acids also for larger proteins.
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Affiliation(s)
- Renee Otten
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Ferrage F, Dutta K, Shekhtman A, Cowburn D. Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density. JOURNAL OF BIOMOLECULAR NMR 2010; 47:41-54. [PMID: 20372977 PMCID: PMC3637030 DOI: 10.1007/s10858-010-9409-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Accepted: 03/10/2010] [Indexed: 05/02/2023]
Abstract
Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes.
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Affiliation(s)
| | | | | | - David Cowburn
- Corresponding author: David Cowburn, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, USA. Tel: 1 212 939 0660,
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Nakamura T, Takahashi H, Takahashi M, Shimba N, Suzuki EI, Shimada I. Direct Determination of the Insulin−Insulin Receptor Interface Using Transferred Cross-Saturation Experiments. J Med Chem 2010; 53:1917-22. [DOI: 10.1021/jm901099v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takefumi Nakamura
- The Institute of Life Sciences, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa, Japan
- Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
- Biomedicinal Information Research Center, National institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
| | - Hideo Takahashi
- Biomedicinal Information Research Center, National institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
| | - Mitsuo Takahashi
- The Institute of Life Sciences, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa, Japan
| | - Nobuhisa Shimba
- The Institute of Life Sciences, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa, Japan
- Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
- Biomedicinal Information Research Center, National institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
| | - Ei-ichiro Suzuki
- The Institute of Life Sciences, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki, Kanagawa, Japan
- Japan Biological Informatics Consortium, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
| | - Ichio Shimada
- Biomedicinal Information Research Center, National institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo, Japan
- The Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
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Guo C, Tugarinov V. Selective 1H- 13C NMR spectroscopy of methyl groups in residually protonated samples of large proteins. JOURNAL OF BIOMOLECULAR NMR 2010; 46:127-33. [PMID: 19957200 DOI: 10.1007/s10858-009-9393-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 11/25/2009] [Indexed: 05/23/2023]
Abstract
Methyl (13)CHD(2) isotopomers of all methyl-containing amino-acids can be observed in residually protonated samples of large proteins obtained from [U-(13)C,(1)H]-glucose/D(2)O-based bacterial media, with sensitivity sufficient for a number of NMR applications. Selective detection of some subsets of methyl groups (Ala(beta), Thr(gamma 2)) is possible using simple 'out-and-back' NMR methodology. Such selective methyl-detected 'out-and-back' NMR experiments allow complete assignments of threonine gamma 2 methyls in residually protonated, [U-(13)C,(1)H]-glucose/D(2)O-derived samples of an 82-kDa enzyme Malate Synthase G. [U-(13)C,(1)H]-glucose/D(2)O-derived protein samples are relatively inexpensive and are usually available at very early stages of any NMR study of high-molecular-weight systems.
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Affiliation(s)
- Chenyun Guo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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Eryilmaz E, Benach J, Su M, Seetharaman J, Dutta K, Wei H, Gottlieb P, Hunt JF, Ghose R. Structure and dynamics of the P7 protein from the bacteriophage phi 12. J Mol Biol 2008; 382:402-22. [PMID: 18647606 DOI: 10.1016/j.jmb.2008.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 06/20/2008] [Accepted: 07/03/2008] [Indexed: 12/15/2022]
Abstract
Cystoviruses are a class of enveloped double-stranded RNA viruses that use a multiprotein polymerase complex (PX) to replicate and transcribe the viral genome. Although the structures of the polymerase and ATPase components of the cystoviral PX are known and their functional behavior is understood to a large extent, no atomic-resolution structural information is available for the major capsid protein P1 that defines the overall structure and symmetry of the viral capsid and the essential protein P7. Toward obtaining a complete structural and functional understanding of the cystoviral PX, we have obtained the structure of P7 from the cystovirus phi 12 at a resolution of 1.8 A. The N-terminal core region (1-129) of P7 forms a novel homodimeric alpha/beta-fold having structural similarities with BRCT domains implicated in multiple protein-protein interactions in DNA repair proteins. Our results, combined with the known role of P7 in stabilizing the nucleation complex during capsid assembly, hint toward its participation in key protein-protein interactions within the cystoviral PX. Additionally, we have found through solution NMR studies that the C-terminal tail of P7 (130-169) that is essential for virus viability, although highly disordered, contains a nascent helix. We demonstrate for the first time, through NMR titrations, that P7 is capable of interacting with RNA. We find that both the N-terminal core and the dynamic C-terminal tail of P7 play a role in RNA recognition. This interaction leads to a significant reduction of the degree of disorder in the C-terminal tail. Given the requirement of P7 in maintaining genome packaging efficiency and transcriptional fidelity, our data suggest a central biological role for P7-RNA interactions.
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Affiliation(s)
- Ertan Eryilmaz
- Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA
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Abstract
We describe an in-cell NMR-based method for mapping the structural interactions (STINT-NMR) that underlie protein-protein complex formation. This method entails sequentially expressing two (or more) proteins within a single bacterial cell in a time-controlled manner and monitoring their interactions using in-cell NMR spectroscopy. The resulting NMR data provide a complete titration of the interaction and define structural details of the interacting surfaces at atomic resolution. Unlike the case where interacting proteins are simultaneously overexpressed in the labeled medium, in STINT-NMR the spectral complexity is minimized because only the target protein is labeled with NMR-active nuclei, which leaves the interactor protein(s) cryptic. This method can be combined with genetic and molecular screens to provide a structural foundation for proteomic studies. The protocol takes 4 d from the initial transformation of the bacterial cells to the acquisition of the NMR spectra.
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Affiliation(s)
- David S Burz
- State University of New York at Albany, Department of Chemistry, 1400 Washington Avenue, Albany, New York 12222, USA
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Horst R, Bertelsen EB, Fiaux J, Wider G, Horwich AL, Wüthrich K. Direct NMR observation of a substrate protein bound to the chaperonin GroEL. Proc Natl Acad Sci U S A 2005; 102:12748-53. [PMID: 16116078 PMCID: PMC1188259 DOI: 10.1073/pnas.0505642102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The reaction cycle and the major structural states of the molecular chaperone GroEL and its cochaperone, GroES, are well characterized. In contrast, very little is known about the nonnative states of the substrate polypeptide acted on by the chaperonin machinery. In this study, we investigated the substrate protein human dihydrofolate reductase (hDHFR) while bound to GroEL or to a single-ring analog, SR1, by NMR spectroscopy in solution under conditions where hDHFR was efficiently recovered as a folded, enzymatically active protein from the stable complexes upon addition of ATP and GroES. By using the NMR techniques of transverse relaxation-optimized spectroscopy (TROSY), cross-correlated relaxation-induced polarization transfer (CRIPT), and cross-correlated relaxation-enhanced polarization transfer (CRINEPT), bound hDHFR could be observed directly. Measurements of the buildup of hDHFR NMR signals by different magnetization transfer mechanisms were used to characterize the dynamic properties of the NMR-observable parts of the bound substrate. The NMR data suggest that the bound state includes random coil conformations devoid of stable native-like tertiary contacts and that the bound hDHFR might best be described as a dynamic ensemble of randomly structured conformers.
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Affiliation(s)
- Reto Horst
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
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