NMR Methods to Study the Dynamics of SH2 Domain-Phosphopeptide Complexes.

Allostery Chemical exchange Nuclear magnetic resonance (NMR) spectroscopy Phosphopeptides Protein dynamics Spin relaxation Src-homology 2 (SH2) domain

Journal

Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969

Informations de publication

Date de publication:
2023
Historique:
medline: 6 9 2023
pubmed: 5 9 2023
entrez: 5 9 2023
Statut: ppublish

Résumé

Nuclear magnetic resonance (NMR) spectroscopy is the method of choice for studying the dynamics of biological macromolecules in solution. By exploiting the intricate interplay between the effects of protein motion (both overall rotational diffusion and internal mobility) and nuclear spin relaxation, NMR allows molecular motion to be probed at atomic resolution over a wide range of timescales, including picosecond (bond vibrations and methyl-group rotations), nanosecond (loop motions and rotational diffusion), and microsecond-millisecond (ligand binding, allostery). In this chapter, we describe different NMR pulse schemes (R

Identifiants

pubmed: 37668967
doi: 10.1007/978-1-0716-3393-9_2
doi:

Substances chimiques

Phosphopeptides 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

25-37

Informations de copyright

© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Références

Stoker AW (2005) Protein tyrosine phosphatases and signalling. J Endocrinol 185(1):19–33. https://doi.org/10.1677/joe.1.06069
doi: 10.1677/joe.1.06069 pubmed: 15817824
Eck MJ, Shoelson SE, Harrison SC (1993) Recognition of a high-affinity phosphotyrosyl peptide by the Src homology-2 domain of p56lck. Nature 362(6415):87–91. https://doi.org/10.1038/362087a0
doi: 10.1038/362087a0 pubmed: 7680435
Huang H, Li L, Wu C, Schibli D, Colwill K, Ma S, Li C, Roy P, Ho K, Songyang Z, Pawson T, Gao Y, Li SS (2008) Defining the specificity space of the human SRC homology 2 domain. Mol Cell Proteomics 7(4):768–784. https://doi.org/10.1074/mcp.M700312-MCP200
doi: 10.1074/mcp.M700312-MCP200 pubmed: 17956856
Marasco M, Carlomagno T (2020) Specificity and regulation of phosphotyrosine signaling through SH2 domains. J Struct Biol X 4:100026. https://doi.org/10.1016/j.yjsbx.2020.100026
doi: 10.1016/j.yjsbx.2020.100026 pubmed: 32647828 pmcid: 7337045
Hof P, Pluskey S, Dhe-Paganon S, Eck MJ, Shoelson SE (1998) Crystal structure of the tyrosine phosphatase SHP-2. Cell 92(4):441–450. https://doi.org/10.1016/s0092-8674(00)80938-1
doi: 10.1016/s0092-8674(00)80938-1 pubmed: 9491886
Marasco M, Kirkpatrick J, Nanna V, Sikorska J, Carlomagno T (2021) Phosphotyrosine couples peptide binding and SHP2 activation via a dynamic allosteric network. Comput Struct Biotechnol J 19:2398–2415. https://doi.org/10.1016/j.csbj.2021.04.040
doi: 10.1016/j.csbj.2021.04.040 pubmed: 34025932 pmcid: 8113834
Finerty PJ, Muhandiram R, Forman-Kay JD (2002) Side-chain dynamics of the SAP SH2 domain correlate with a binding hot spot and a region with conformational plasticity. J Mol Biol 322(3):605–620. https://doi.org/10.1016/s0022-2836(02)00803-3
doi: 10.1016/s0022-2836(02)00803-3 pubmed: 12225753
Kovermann M, Rogne P, Wolf-Watz M (2016) Protein dynamics and function from solution state NMR spectroscopy. Q Rev Biophys 49:e6. https://doi.org/10.1017/S0033583516000019
doi: 10.1017/S0033583516000019 pubmed: 27088887
Lipari G, Szabo A (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J Am Chem Soc 104(17):4546–4559. https://doi.org/10.1021/ja00381a009
doi: 10.1021/ja00381a009
Loria JP, Rance M, Palmer AG (1999) A relaxation-compensated Carr−Purcell−Meiboom−Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 121(10):2331–2332. https://doi.org/10.1021/ja983961a
doi: 10.1021/ja983961a
Marasco M, Berteotti A, Weyershaeuser J, Thorausch N, Sikorska J, Krausze J, Brandt HJ, Kirkpatrick J, Rios P, Schamel WW, Köhn M, Carlomagno T (2020) Molecular mechanism of SHP2 activation by PD-1 stimulation. Sci Adv 6(5):eaay4458. https://doi.org/10.1126/sciadv.aay4458
doi: 10.1126/sciadv.aay4458 pubmed: 32064351 pmcid: 6994217
Marasco M, Kirkpatrick JP, Carlomagno T (2020) 1H, 13C, 15N chemical shift assignments of SHP2 SH2 domains in complex with PD-1 immune-tyrosine motifs. Biomol NMR Assign 14(2):179–188. https://doi.org/10.1007/s12104-020-09941-y
doi: 10.1007/s12104-020-09941-y pubmed: 32236803 pmcid: 7462904
Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM (1990) Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J Am Chem Soc 112(12):4989–4991. https://doi.org/10.1021/ja00168a070
doi: 10.1021/ja00168a070
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6(3):277–293. https://doi.org/10.1007/BF00197809
doi: 10.1007/BF00197809 pubmed: 8520220
Vranken WF, Boucher W, Stevens TJ, Fogh RH, Pajon A, Llinas M, Ulrich EL, Markley JL, Ionides J, Laue ED (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59(4):687–696. https://doi.org/10.1002/prot.20449
doi: 10.1002/prot.20449 pubmed: 15815974
Hansen DF, Yang D, Feng H, Zhou Z, Wiesner S, Bai Y, Kay LE (2007) An exchange-free measure of 15N transverse relaxation: an NMR spectroscopy application to the study of a folding intermediate with pervasive chemical exchange. J Am Chem Soc 129(37):11468–11479. https://doi.org/10.1021/ja072717t
doi: 10.1021/ja072717t pubmed: 17722922
Dosset P, Hus JC, Blackledge M, Marion D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16(1):23–28. https://doi.org/10.1023/a:1008305808620
doi: 10.1023/a:1008305808620 pubmed: 10718609
Vallurupalli P, Bouvignies G, Kay LE (2012) Studying “invisible” excited protein states in slow exchange with a major state conformation. J Am Chem Soc 134(19):8148–8161. https://doi.org/10.1021/ja3001419
doi: 10.1021/ja3001419 pubmed: 22554188
Dayie KT, Wagner G (1994) Relaxation-rate measurements for 15N−1H groups with pulsed-field gradients and preservation of coherence pathways. J Magn Reson Ser A 111(1):121–126. https://doi.org/10.1006/jmra.1994.1236
doi: 10.1006/jmra.1994.1236
Farrow NA, Muhandiram R, Singer AU, Pascal SM, Kay CM, Gish G, Shoelson SE, Pawson T, Forman-Kay JD, Kay LE (1994) Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33(19):5984–6003. https://doi.org/10.1021/bi00185a040
doi: 10.1021/bi00185a040 pubmed: 7514039
Kay LE, Torchia DA, Bax A (1989) Backbone dynamics of proteins as studied by nitrogen-15 inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28(23):8972–8979. https://doi.org/10.1021/bi00449a003 , note = PMID: 2690953
doi: 10.1021/bi00449a003 pubmed: 2690953
Mulder FAA, de Graaf RA, Kaptein R, Boelens R (1998) An off-resonance rotating frame relaxation experiment for the investigation of macromolecular dynamics using adiabatic rotations. J Magn Reson 131(2):351–357. https://doi.org/10.1006/jmre.1998.1380
doi: 10.1006/jmre.1998.1380 pubmed: 9571112
Geen H, Freeman R (1991) Band-selective radiofrequency pulses. J Magn Reson (1969) 93(1):93–141. https://doi.org/10.1016/0022-2364(91)90034-Q
doi: 10.1016/0022-2364(91)90034-Q
Korzhnev DM, Skrynnikov NR, Millet O, Torchia DA, Kay LE (2002) An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J Am Chem Soc 124(36):10743–10753. https://doi.org/10.1021/ja0204776
doi: 10.1021/ja0204776 pubmed: 12207529
Hansen DF, Kay LE (2007) Improved magnetization alignment schemes for spin-lock relaxation experiments. J Biomol NMR 37(4):245–255. https://doi.org/10.1007/s10858-006-9126-6
doi: 10.1007/s10858-006-9126-6 pubmed: 17310328
Bax A, Clore GM, Gronenborn AM (1990) 1H-1H correlation via isotropic mixing of 13C magnetization, a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins. J Magn Reson (1969) 88(2):425–431. https://doi.org/10.1016/0022-2364(90)90202-K
doi: 10.1016/0022-2364(90)90202-K
Li YC, Montelione GT (1993) Solvent saturation-transfer effects in pulsed-field-gradient heteronuclear single-quantum-coherence (PFG-HSQC) spectra of polypeptides and proteins. J Magn Reson B 101(3):315–319. https://doi.org/10.1006/jmrb.1993.1049
doi: 10.1006/jmrb.1993.1049
Renner C, Schleicher M, Moroder L, Holak TA (2002) Practical aspects of the 2D 15N-[1h]-NOE experiment. J Biomol NMR 23(1):23–33. https://doi.org/10.1023/a:1015385910220
doi: 10.1023/a:1015385910220 pubmed: 12061715
Ferrage F, Cowburn D, Ghose R (2009) Accurate sampling of high-frequency motions in proteins by steady-state (15)N-{(1)H} nuclear Overhauser effect measurements in the presence of cross-correlated relaxation. J Am Chem Soc 131(17):6048–6049. https://doi.org/10.1021/ja809526q
doi: 10.1021/ja809526q pubmed: 19358609 pmcid: 3547682
Hansen DF, Vallurupalli P, Kay LE (2008) An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins. J Phys Chem B 112(19):5898–5904. https://doi.org/10.1021/jp074793o
doi: 10.1021/jp074793o pubmed: 18001083
Kozak S, Lercher L, Karanth MN, Meijers R, Carlomagno T, Boivin S (2016) Optimization of protein samples for NMR using thermal shift assays. J Biomol NMR 64(4):281–289. https://doi.org/10.1007/s10858-016-0027-z
doi: 10.1007/s10858-016-0027-z pubmed: 26984476 pmcid: 4869703
Carver JP, Richards RE (1972) A general two-site solution for the chemical exchange produced dependence of T2 upon the carr-Purcell pulse separation. J Magn Reson (1969) 6(1):89–105. https://doi.org/10.1016/0022-2364(72)90090-X
doi: 10.1016/0022-2364(72)90090-X
Palmer AG 3rd, Kroenke CD, Loria JP (2001) Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol 339:204–238. https://doi.org/10.1016/s0076-6879(01)39315-1
doi: 10.1016/s0076-6879(01)39315-1 pubmed: 11462813

Auteurs

Michelangelo Marasco (M)

Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

John P Kirkpatrick (JP)

School of Biosciences, University of Birmingham, Birmingham, UK.

Vittoria Nanna (V)

School of Biosciences, University of Birmingham, Birmingham, UK.
BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany.

Teresa Carlomagno (T)

School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK. t.carlomagno@bham.ac.uk.

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