Backbone assignment of crystalline E. coli maltose binding protein
Tóm tắt
The E.coli maltose binding protein (MBP) is a 42.5 kDa molecule widely employed in many biotechnology applications. Because of its molecular size, it has become the main model system for the development of solution NMR methods adapted to large biomolecular targets. Here, we report virtually complete (~ 90%) backbone resonance assignments obtained on a microcrystalline sample of MBP with 1H-detected solid-state NMR at fast (> 100 kHz) magic-angle spinning. We additionally present the detailed description of the methodology employed for the preparation of the sample and the acquisition and analysis of the NMR spectra. The chemical shifts, obtained with a single uniformly 15N, 13C-labelled and fully-protonated sample and about 2 weeks on a 800 MHz NMR spectrometer, have been deposited to the BMRB under the accession number 50089.
Tài liệu tham khảo
Böckmann A, Lange A, Galinier A, Luca S, Giraud N, Juy M, Heise H, Montserret R, Penin F, Baldus M (2003) Solid state NMR sequential resonance assignments and conformational analysis of the 2 × 10.4 kDa dimeric form of the Bacillus subtilis protein Crh. J Biomol NMR 27:323–339
Bonaccorsi M, Knight MJ, Le Marchand T, Dannatt HRW, Schubeis T, Salmon L, Felli IC, Emsley L, Pierattelli R, Pintacuda G (2020) Multimodal response to copper binding in superoxide dismutase dynamics. J Am Chem Soc 142:19660–19667. https://doi.org/10.1021/jacs.0c09242
Boos W, Shuman H (1998) Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation. Microbiol Mol Biol Rev 62:204–229. https://doi.org/10.1128/mmbr.62.1.204-229.1998
Cala-De Paepe D, Stanek J, Jaudzems K, Tars K, Andreas LB, Pintacuda G (2017) Is protein deuteration beneficial for proton detected solid-state NMR at and above 100 kHz magic-angle spinning? Solid State Nucl Magn Reson 87:126–136. https://doi.org/10.1016/j.ssnmr.2017.07.004
Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293. https://doi.org/10.1007/BF00197809
Evenäs J, Tugarinov V, Skrynnikov NR, Goto NK, Muhandiram R, Kay LE (2001) Ligand-induced structural changes to maltodextrin-binding protein as studied by solution NMR spectroscopy. J Mol Biol 309:961–974. https://doi.org/10.1006/jmbi.2001.4695
Gardner KH (1998) Solution NMR studies of a 42 KDa Escherichia coli maltose binding protein/β-cyclodextrin complex: chemical shift assignments and analysis. J Am Chem Soc 120:11738–11748. https://doi.org/10.1021/ja982019w
Madl T, Bermel W, Zangger K (2009) Use of relaxation enhancements in a paramagnetic environment for the structure determination of proteins using NMR spectroscopy. Angew Chemie Int Ed 48:8259–8262. https://doi.org/10.1002/anie.200902561
Mandala VS, Hong M (2019) High-sensitivity protein solid-state NMR spectroscopy. Curr Opin Struct Biol 58:183–190
Martin RW, Zilm KW (2003) Preparation of protein nanocrystals and their characterization by solid state NMR. J Magn Reson 165:162–174. https://doi.org/10.1016/S1090-7807(03)00253-2
Rovó P, Smith CA, Gauto D, De Groot BL, Schanda P, Linser R (2019) Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15 N and 1 H relaxation dispersion techniques. J Am Chem Soc 141:858–869. https://doi.org/10.1021/jacs.8b09258
Schmidt E, Güntert P (2012) A new algorithm for reliable and general NMR resonance assignment. J Am Chem Soc 134:12817–12829. https://doi.org/10.1021/ja305091n
Schmidt HLF, Sperling LJ, Gao YG, Wylie BJ, Boettcher JM, Wilson SR, Rienstra CM (2007) Crystal polymorphism of protein GB1 examined by solid-state NMR spectroscopy and X-ray diffraction. J Phys Chem B 111:14362–14369. https://doi.org/10.1021/jp075531p
Selmke B, Borbat PP, Nickolaus C, Varadarajan R, Freed JH, Trommer WE (2018) Open and closed form of maltose binding protein in its native and molten globule state as studied by electron paramagnetic resonance spectroscopy. Biochemistry 57:5507–5512. https://doi.org/10.1021/acs.biochem.8b00322
Seo MH, Park J, Kim E, Hohng S, Kim HS (2014) Protein conformational dynamics dictate the binding affinity for a ligand. Nat Commun. https://doi.org/10.1038/ncomms4724
Sharff AJ, Rodseth LE, Spurlino JC, Quiocho FA (1992) Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 31:10657–10663. https://doi.org/10.1021/bi00159a003
Sharff AJ, Quiocho FA, Rodseth LE, Quiocho FA (1993) Refined 1.8-Å structure reveals the mode of binding of β-cyclodextrin to the maltodextrin binding protein. Biochemistry 32:10553–10559. https://doi.org/10.1021/bi00091a004
Spurlino JC, Lu GY, Quiocho FA (1991) The 2.3-A resolution structure of the maltose- or maltodextrin-binding protein, a primary receptor of bacterial active transport and chemotaxis. J Biol Chem 266:5202–5219. https://doi.org/10.1016/s0021-9258(19)67774-4
Stanek J, Andreas LB, Jaudzems K, Cala D, Lalli D, Bertarello A, Schubeis T, Akopjana I, Kotelovica S, Tars K, Pica A, Leone S, Picone D, Xu Z-Q, Dixon NE, Martinez D, Berbon M, El Mammeri N, Noubhani A, Saupe S, Habenstein B, Loquet A, Pintacuda G (2016) NMR spectroscopic assignment of backbone and side-chain protons in fully protonated proteins: microcrystals, sedimented assemblies, and amyloid fibrils. Angew Chemie Int Ed 55:15504–15509. https://doi.org/10.1002/anie.201607084
Stanek J, Schubeis T, Paluch P, Güntert P, Andreas LB, Pintacuda G (2020) Automated backbone NMR resonance assignment of large proteins using redundant linking from a single simultaneous acquisition. J Am Chem Soc 142:5793–5799. https://doi.org/10.1021/jacs.0c00251
Takeuchi K, Arthanari H, Shimada I, Wagner G (2015) Nitrogen detected TROSY at high field yields high resolution and sensitivity for protein NMR. J Biomol NMR 63:323–331. https://doi.org/10.1007/s10858-015-9991-y
Tang C, Schwieters CD, Clore GM (2007) Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449:1078–1082. https://doi.org/10.1038/nature06232
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 Struct Funct Genet 59:687–696. https://doi.org/10.1002/prot.20449
Waugh DS (2016) Crystal structures of MBP fusion proteins. Protein Sci 25:559–571
Yang D, Kay LE (1999) Improved 1HN-detected triple resonance TROSY-based experiments. J Biomol NMR 13:3–10. https://doi.org/10.1023/A:1008329230975