Nội dung được dịch bởi AI, chỉ mang tính chất tham khảo
Nhận diện amino acid cho việc chỉ định cộng hưởng tự động của các protein không có cấu trúc cố định
Tóm tắt
Việc chỉ định cộng hưởng là một yêu cầu tiên quyết cho hầu hết mọi nghiên cứu dựa trên NMR về protein. Tuy nhiên, điều này có thể rất thách thức trong một số trường hợp, do tính chất của protein đang được nghiên cứu. Điều này xảy ra đối với các protein không có cấu trúc cố định, ví dụ, mà phổ NMR của chúng gặp khó khăn với sự phân tán hóa học thấp và độ phân giải tổng thể thấp. Đối với những hệ thống này, việc chỉ định theo chuỗi đặc hiệu tốn rất nhiều thời gian, vì vậy triển vọng sử dụng các chiến lược tự động cho việc chỉ định của chúng trở nên rất hấp dẫn. Trong bài báo này, chúng tôi trình bày một phiên bản mới của chương trình chỉ định tự động TSAR dành riêng cho các protein không có cấu trúc cố định. Cụ thể, chúng tôi chứng minh cách mà quy trình tự động có thể được cải thiện bằng cách tích hợp các phương pháp nhận diện amino acid và thông tin về sự dịch chuyển hóa học trong các amino acid đã chọn. Phương pháp này đã được thử nghiệm in silico trên 16 protein không có cấu trúc cố định và thực nghiệm trên α-synuclein, với kết quả đáng kể.
Từ khóa
#chỉ định cộng hưởng #protein không có cấu trúc cố định #NMR #nhận diện amino acid #phân tích tự độngTài liệu tham khảo
Barnwal RP, Rout AK, Atreya HS, Chary KVR (2008) Identification of C-terminal neighbours of amino acid residues without an aliphatic 13Cγ as an aid to NMR assignments in proteins. J Biomol NMR 41:191–197. doi:10.1007/s10858-008-9254-2
Bermel W, Felli IC, Kummerle R, Pierattelli R (2008) 13C direct-detection biomolecular NMR. Concepts Magn Reson A 32A:183–200. doi:10.1002/cmr.a
Bermel W, Bertini I, Felli IC, Pierattelli R (2009) Speeding up 13C direct detection biomolecular NMR spectroscopy. J Am Chem Soc 131:15339–15345. doi:10.1021/ja9058525
Bermel W, Bertini I, Chill J, Felli IC, Haba N, Kumar MVV, Pierattelli R (2012a) Exclusively heteronuclear 13C-detected amino-acid-selective NMR experiments for the study of intrinsically disordered proteins (IDPs). ChemBioChem 13:2425–2432. doi:10.1002/cbic.201200447
Bermel W, Bertini I, Felli IC, Gonnelli L, Koźmiński W, Piai A, Pierattelli R, Stanek J (2012b) Speeding up sequence specific assignment of IDPs. J Biomol NMR 53:293–301. doi:10.1007/s10858-012-9639-0
Bermel W, Felli IC, Gonnelli L, Koźmiński W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A (2013) High-dimensionality 13C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. J Biomol NMR 57:353–361. doi:10.1007/s10858-013-9793-z
Bertini I, Felli IC, Gonnelli L, Pierattelli R, Spyranti Z, Spyroulias GA (2006) Mapping protein-protein interaction by 13C-detected heteronuclear NMR spectroscopy. J Biomol NMR 36:111–122. doi:10.1007/s10858-006-9068-z
Bohlen JM, Bodenhausen G (1993) Experimental aspects of chirp NMR Spectroscopy. J Magn Reson Ser A 102:293–301. doi:10.1006/jmra.1993.1107
Brutscher B, Felli IC, Gil-Caballero S, Hošek T, Kümmerle R, Piai A, Pierattelli R, Sólyom Z (2015) NMR Methods for the study of instrinsically disordered proteins structure, dynamics, and interactions: general overview and practical guidelines. Adv Exp Med Biol 870:49–122. doi:10.1007/978-3-319-20164-1_3
Chakraborty S, Susmitha AL, Hosur RV (2012) Selective lighting up of segments around Gly, Ala and Ser/Thr in proteins. Magn Reson Chem 50:587–591. doi:10.1002/mrc.3843
Coggins BE, Venters RA, Zhou P (2010) Radial sampling for fast NMR: concepts and practices over three decades. Prog Nucl Magn Reson Spectrosc 57:381–419. doi:10.1016/j.pnmrs.2010.07.001
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. doi:10.1007/BF00197809
Dötsch V, Wagner G (1996) Editing for amino-acid type in CBCACONH experiments based on the 13C beta-13C gamma coupling. J Magn Reson B 111:310–313. doi:10.1006/jmrb.1996.0100
Dötsch V, Matsuo H, Wagner G (1996a) Amino-acid-type identification for deuterated proteins with a beta-carbon-edited HNCOCACB experiment. J Magn Reson B 112:95–100. doi:10.1006/jmrb.1996.0117
Dötsch V, Oswald RE, Wagner G (1996b) Selective identification of threonine, valine, and isoleucine sequential connectivities with a TVI-CBCACONH experiment. J Magn Reson B 110:304–308. doi:10.1006/jmrb.1996.0047
Dötsch V, Oswald RE, Wagner G (1996c) Amino-acid-type-selective triple-resonance experiments. J Magn Reson B 110:107–111
Dunker AK, Oldfield CJ, Meng J, Romero P, Yang JY, Chen JW, Vacic V, Obradovic Z, Uversky VN (2008) The unfoldomics decade: an update on intrinsically disordered proteins. BMC Gen 9(Suppl 2):S1. doi:10.1186/1471-2164-9-S2-S1
Dziekański P, Grudziąż K, Jarvoll P, Koźmiński W, Zawadzka-Kazimierczuk A (2015) 13C-detected NMR experiments for automatic resonance assignment of IDPs and multiple-fixing SMFT processing. J Biomol NMR 62:179–190. doi:10.1007/s10858-015-9932-9
Emsley L, Bodenhausen G (1992) Optimization of shaped selective pulses for NMR using a quaternion description of their overall propagators. J Magn Reson 97:135–148. doi:10.1016/0022-2364(92)90242-Y
Felli IC, Pierattelli R (2014) Novel methods based on 13C detection to study intrinsically disordered proteins. J Magn Reson 241:115–125. doi:10.1016/j.jmr.2013.10.020
Feng W, Rios CB, Montelione GT (1996) Phase labeling of C-H and C-C spin-system topologies: application in PFG-HACANH and PFG-HACA(CO)NH triple-resonance experiments for determining backbone resonance assignments in proteins. J Biomol NMR 8:98–104
Feuerstein S, Plevin MJ, Willbold D, Brutscher B (2012) IHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins. J Magn Reson 214:329–334. doi:10.1016/j.jmr.2011.10.019
Freeman R, Kupče E (2012) Concepts in projection-reconstruction. Top Curr Chem 316:1–20. doi:10.1007/128
Gil S, Hošek T, Solyom Z, Kümmerle R, Brutscher B, Pierattelli R, Felli IC (2013) NMR spectroscopic studies of intrinsically disordered proteins at near-physiological conditions. Angew Chem Int Ed Engl 52:11808–11812. doi:10.1002/anie.201304272
Goddard TD, Kneller DG (2002) Sparky 3. University of California, San Francisco
Grzesiek S, Bax A (1992) Correlating backbone amide and side chain resonances in larger proteins by multiple relayed triple resonance NMR. J Am Chem Soc 114:6291–6293. doi:10.1021/ja00042a003
Hiller S, Wider G (2012) Automated projection spectroscopy and its applications. Top Curr Chem 316:21–47. doi:10.1007/128
Holland DJ, Gladden LF (2014) Less is more: how compressed sensing is transforming metrology in chemistry. Angew Chem Int Ed 53:13330–13340. doi:10.1002/anie.201400535
Huang C, Ren G, Zhou H, Wang C (2005) A new method for purification of recombinant human alpha-synuclein in Escherichia coli. Protein Expr Purif 42:173–177. doi:10.1016/j.pep.2005.02.014
Jaipuria G, Lobo NP, Shet D, Atreya HS (2012) High resolution methyl selective 13C-NMR of proteins in solution and solid state. J Biomol NMR 54:33–42. doi:10.1007/s10858-012-9647-0
Kazimierczuk K, Orekhov VY (2011) Accelerated NMR spectroscopy by using compressed sensing. Angew Chem Int Ed Engl 50:5556–5559. doi:10.1002/anie.201100370
Kazimierczuk K, Zawadzka A, Koźmiński W (2008) Optimization of random time domain sampling in multidimensional NMR. J Magn Reson 192:123–130. doi:10.1016/j.jmr.2008.02.003
Kazimierczuk K, Zawadzka A, Koźmiński W (2009) Narrow peaks and high dimensionalities: exploiting the advantages of random sampling. J Magn Reson 197:219–228. doi:10.1016/j.jmr.2009.01.003
Kazimierczuk K, Misiak M, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W (2012) Generalized Fourier Transform for non-uniform sampled data. Top Curr Chem 316:79–124. doi:10.1007/128
Kazimierczuk K, Stanek J, Zawadzka-Kazimierczuk A, Koźmiński W (2013) High-dimensional NMR spectra for structural studies of biomolecules. ChemPhysChem 14:3015–3025. doi:10.1002/cphc.201300277
Lescop E, Brutscher B (2009) Highly automated protein backbone resonance assignment within a few hours: The “BATCH” strategy and software package. J Biomol NMR 44:43–57. doi:10.1007/s10858-009-9314-2
Lescop E, Rasia R, Brutscher B (2008) Hadamard amino-acid-type edited NMR experiment for fast protein resonance assignment. J Am Chem Soc 130:5014–5015. doi:10.1021/ja800914h
Mobli M, Hoch JC (2008) Maximum entropy spectral reconstruction of non-uniformly sampled data. Concepts Magn Reson A Bridg Educ Res 32A:436–448. doi:10.1002/cmr.a.20126
Nováček J, Zawadzka-Kazimierczuk A, Papoušková V, Žídek L, Sanderová H, Krásný L, Koźmiński W, Sklenář V (2011) 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion. J Biomol NMR 50:1–11. doi:10.1007/s10858-011-9496-2
Nováček J, Haba NY, Chill JH, Zídek L, Sklenář V (2012) 4D non-uniformly sampled HCBCACON and 1J(NCα)-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins. J Biomol NMR 53:139–148. doi:10.1007/s10858-012-9631-8
Nováček J, Janda L, Dopitová R, Žídek L, Sklenář V (2013) Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c. J Biomol NMR 56:291–301. doi:10.1007/s10858-013-9761-7
Nowakowski M, Saxena S, Stanek J, Żerko S, Koźmiński W (2015) Applications of high dimensionality experiments to biomolecular NMR. Prog Nucl Magn Reson Spectrosc 90–91:49–73. doi:10.1016/j.pnmrs.2015.07.001
Orekhov VY, Jaravine VA (2011) Analysis of non-uniformly sampled spectra with multi-dimensional decomposition. Prog Nucl Magn Reson Spectrosc 59:271–292. doi:10.1016/j.pnmrs.2011.02.002
Pantoja-Uceda D, Santoro J (2008) Amino acid type identification in NMR spectra of proteins via β- and γ-carbon edited experiments. J Magn Reson 195:187–195. doi:10.1016/j.jmr.2008.09.010
Pantoja-Uceda D, Santoro J (2011) Selective observation of Asp and Glu resonances in 13CO detected experiments. Magn Reson Chem 49:558–561. doi:10.1002/mrc.2780
Pantoja-Uceda D, Santoro J (2012) New amino acid residue type identification experiments valid for protonated and deuterated proteins. J Biomol NMR 54:145–153. doi:10.1007/s10858-012-9665-y
Piai A, Hošek T, Gonnelli L, Zawadzka-Kazimierczuk A, Koźmiński W, Brutscher B, Bermel W, Pierattelli R, Felli IC (2014) “CON-CON” assignment strategy for highly flexible intrinsically disordered proteins. J Biomol NMR 60:209–218. doi:10.1007/s10858-014-9867-6
Rios CB, Feng W, Tashiro M, Shang Z, Montelione GT (1996) Phase labeling of C-H and C-C spin-system topologies: application in constant-time PFG-CBCA(CO)NH experiments for discriminating amino acid spin-system types. J Biomol NMR 8:345–350. doi:10.1007/BF00410332
Schubert M, Smalla M, Schmieder P, Oschkinat H (1999) MUSIC in triple-resonance experiments: amino acid type-selective (1)H–(15)N correlations. J Magn Reson 141:34–43. doi:10.1006/jmre.1999.1881
Schubert M, Ball LJ, Oschkinat H, Schmieder P (2000) Bridging the gap: a set of selective 1H-15N-correlations to link sequential neighbors of prolines. J Biomol NMR 17:331–335. doi:10.1023/A:1008362904205
Schubert M, Oschkinat H, Schmieder P (2001a) MUSIC, selective pulses, and tuned delays: amino acid type-selective 1H–15N correlations, II. J Magn Reson 148:61–72. doi:10.1006/jmre.2000.2222
Schubert M, Oschkinat H, Schmieder P (2001b) MUSIC and aromatic residues: amino acid type-selective 1H–15N correlations, III. J Magn Reson 153:186–192. doi:10.1006/jmre.2001.2447
Schubert M, Oschkinat H, Schmieder P (2001c) Amino acid type-selective backbone 1H–15N-correlations for Arg and Lys. J Biomol NMR 20:379–384
Schubert M, Labudde D, Leitner D, Oschkinat H, Schmieder P (2005) A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments. J Biomol NMR 31:115–128. doi:10.1007/s10858-004-8263-z
Shaka A, Keeler J, Freeman R (1983) Evaluation of a new broadband decoupling sequence: WALTZ-16. J Magn Reson 53:313–340. doi:10.1016/0022-2364(83)90035-5
Shaka A, Barker P, Freeman R (1985) Computer-optimized decoupling scheme for wideband applications and low-level operation. J Magn Reson 64:547–552. doi:10.1016/0022-2364(85)90122-2
Tamiola K, Acar B, Mulder FAA (2010) Sequence-specific random coil chemical shifts of intrinsically disordered proteins. J Am Chem Soc 132:18000–18003. doi:10.1021/ja105656t
Ulrich EL, Akutsu H, Doreleijers JF et al (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408. doi:10.1093/nar/gkm957
Zawadzka-Kazimierczuk A, Koźmiński W, Billeter M (2012) TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra. J Biomol NMR 54:81–95. doi:10.1007/s10858-012-9652-3
