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Artykuły w czasopismach na temat „Rapid resonance assignment of proteins”

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Data publikacji: 6 września 2023

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1

Fredriksson, Jonas, Wolfgang Bermel, and Martin Billeter. "Complete protein assignment from sets of spectra recorded overnight." Journal of Biomolecular NMR 73, no. 1-2 (2019): 59–70. http://dx.doi.org/10.1007/s10858-019-00226-8.

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Abstract A flexible and scalable approach for protein NMR is introduced that builds on rapid data collection via projection spectroscopy and analysis of the spectral input data via joint decomposition. Input data may originate from various types of spectra, depending on the ultimate goal: these may result from experiments based on triple-resonance pulse sequences, or on TOCSY or NOESY sequences, or mixtures thereof. Flexible refers to the free choice of spectra for the joint decompositions depending on the purpose: assignments, structure, dynamics, interactions. Scalable means that the approac

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2

Rout, Ashok K., Ravi P. Barnwal, Geetika Agarwal, and Kandala V. R. Chary. "Root-mean-square-deviation-based rapid backbone resonance assignments in proteins." Magnetic Resonance in Chemistry 48, no. 10 (2010): 793–97. http://dx.doi.org/10.1002/mrc.2664.

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3

Sukumaran, Sujeesh, Shahid A. Malik, Shankararama Sharma R., Kousik Chandra, and Hanudatta S. Atreya. "Rapid NMR assignments of intrinsically disordered proteins using two-dimensional13C-detection based experiments." Chemical Communications 55, no. 54 (2019): 7820–23. http://dx.doi.org/10.1039/c9cc03530c.

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4

Chatterjee, Amarnath, Neel S. Bhavesh, Sanjay C. Panchal, and Ramakrishna V. Hosur. "A novel protocol based on HN(C)N for rapid resonance assignment in (15N, 13C) labeled proteins: implications to structural genomics." Biochemical and Biophysical Research Communications 293, no. 1 (2002): 427–32. http://dx.doi.org/10.1016/s0006-291x(02)00240-1.

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5

Kostic, Milka, Susan Sondej Pochapsky, and Thomas C. Pochapsky. "Rapid Recycle13C‘,15N and13C,13C‘ Heteronuclear and Homonuclear Multiple Quantum Coherence Detection for Resonance Assignments in Paramagnetic Proteins: Example of Ni2+-Containing Acireductone Dioxygenase." Journal of the American Chemical Society 124, no. 31 (2002): 9054–55. http://dx.doi.org/10.1021/ja0268480.

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Vendrell, J., F. X. Avilés, M. Vilanova, C. H. Turner, and C. Crane-Robinson. "1H-n.m.r. studies of the isolated activation segment from pig procarboxypeptidase A." Biochemical Journal 267, no. 1 (1990): 213–20. http://dx.doi.org/10.1042/bj2670213.

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The isolated activation segment (asA) from pig pancreatic procarboxypeptidase A was studied by 1H-n.m.r. spectroscopy over a wide range of solution conditions. Isolated asA shows many characteristics of compactly folded globular proteins, such as the observation of perturbed positions for resonances from methyl groups, alpha-carbon atoms, histidine residues and the tyrosine residue. The single tyrosine residue (Tyr-70) exhibits a very high pKa, and both histidine and tyrosine residues show slow chemical modification (deuteration and iodination). In contrast, asA shows rapid NH exchange. Analys

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7

Kumar, Dinesh, and Ramakrishna V. Hosur. "hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone (1 HN , 15 N and 13 C′) resonances in 15 N/13 C-labeled proteins." Magnetic Resonance in Chemistry 49, no. 9 (2011): 575–83. http://dx.doi.org/10.1002/mrc.2787.

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8

Fiorito, Francesco, Sebastian Hiller, Gerhard Wider, and Kurt Wüthrich. "Automated Resonance Assignment of Proteins: 6 DAPSY-NMR." Journal of Biomolecular NMR 35, no. 1 (2006): 27–37. http://dx.doi.org/10.1007/s10858-006-0030-x.

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9

Higman, Victoria A. "Solid-state MAS NMR resonance assignment methods for proteins." Progress in Nuclear Magnetic Resonance Spectroscopy 106-107 (June 2018): 37–65. http://dx.doi.org/10.1016/j.pnmrs.2018.04.002.

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10

Crippen, Gordon M., Aikaterini Rousaki, Matthew Revington, Yongbo Zhang, and Erik R. P. Zuiderweg. "SAGA: rapid automatic mainchain NMR assignment for large proteins." Journal of Biomolecular NMR 46, no. 4 (2010): 281–98. http://dx.doi.org/10.1007/s10858-010-9403-2.

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11

Fox, Daniel A., та Linda Columbus. "Solution NMR resonance assignment strategies for β-barrel membrane proteins". Protein Science 22, № 8 (2013): 1133–40. http://dx.doi.org/10.1002/pro.2291.

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12

Trbovic, Nikola, Christian Klammt, Alexander Koglin, Frank Löhr, Frank Bernhard, and Volker Dötsch. "Efficient Strategy for the Rapid Backbone Assignment of Membrane Proteins." Journal of the American Chemical Society 127, no. 39 (2005): 13504–5. http://dx.doi.org/10.1021/ja0540270.

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13

ALIPANAHI, BABAK, XIN GAO, EMRE KARAKOC, et al. "ERROR TOLERANT NMR BACKBONE RESONANCE ASSIGNMENT AND AUTOMATED STRUCTURE GENERATION." Journal of Bioinformatics and Computational Biology 09, no. 01 (2011): 15–41. http://dx.doi.org/10.1142/s0219720011005276.

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Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable the subsequent automatic structure determination steps. We have designed an integer linear programming (ILP) based assignment system (IPASS) that has enabled fully automatic protein structure determination for four test proteins. IPASS employs probabilistic spin system typing based on chemical shifts and secondary structure predictions. Further

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14

Pannetier, Nicolas, Klaartje Houben, Laurence Blanchard, and Dominique Marion. "Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins." Journal of Magnetic Resonance 186, no. 1 (2007): 142–49. http://dx.doi.org/10.1016/j.jmr.2007.01.013.

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15

Leopold, M. F., Jeffrey L. Urbauer, and A. Joshua Wand. "Resonance assignment strategies for the analysis of nmr spectra of proteins." Molecular Biotechnology 2, no. 1 (1994): 61–93. http://dx.doi.org/10.1007/bf02789290.

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16

Piai, Alessandro, Leonardo Gonnelli, Isabella C. Felli, et al. "Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins." Journal of Biomolecular NMR 64, no. 3 (2016): 239–53. http://dx.doi.org/10.1007/s10858-016-0024-2.

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17

Li, Kuo-Bin, and B. C. Sanctuary. "Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR. 2. Side Chain and Sequence-Specific Assignment." Journal of Chemical Information and Computer Sciences 37, no. 3 (1997): 467–77. http://dx.doi.org/10.1021/ci960372k.

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18

Knox, Robert W., George J. Lu, Stanley J. Opella, and Alexander A. Nevzorov. "A Resonance Assignment Method for Oriented-Sample Solid-State NMR of Proteins." Journal of the American Chemical Society 132, no. 24 (2010): 8255–57. http://dx.doi.org/10.1021/ja102932n.

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19

Gossert, Alvar D., Sebastian Hiller, and César Fernández. "Automated NMR Resonance Assignment of Large Proteins for Protein−Ligand Interaction Studies." Journal of the American Chemical Society 133, no. 2 (2011): 210–13. http://dx.doi.org/10.1021/ja108383x.

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20

Wei, Qingtao, Jiajing Chen, Juan Mi, Jiahai Zhang, Ke Ruan та Jihui Wu. "NMR Backbone Assignment of Large Proteins by Using13Cα-Only Triple-Resonance Experiments". Chemistry - A European Journal 22, № 28 (2016): 9556–64. http://dx.doi.org/10.1002/chem.201601871.

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21

Karjalainen, Mikael, Helena Tossavainen, Maarit Hellman та Perttu Permi. "HACANCOi: a new Hα-detected experiment for backbone resonance assignment of intrinsically disordered proteins". Journal of Biomolecular NMR 74, № 12 (2020): 741–52. http://dx.doi.org/10.1007/s10858-020-00347-5.

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AbstractUnidirectional coherence transfer is highly efficient in intrinsically disordered proteins (IDPs). Their elevated ps-ns timescale dynamics ensures long transverse (T2) relaxation times allowing sophisticated coherence transfer pathway selection in comparison to folded proteins. 1Hα-detection ensures non-susceptibility to chemical exchange with the solvent and enables chemical shift assignment of consecutive proline residues, typically abundant in IDPs. However, many IDPs undergo a disorder-to-order transition upon interaction with their target protein, which leads to the loss of the fa

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22

Barbet-Massin, Emeline, Andrew J. Pell, Joren S. Retel, et al. "Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning." Journal of the American Chemical Society 136, no. 35 (2014): 12489–97. http://dx.doi.org/10.1021/ja507382j.

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23

Morris, Howard R., and Piero Pucci. "A new method for rapid assignment of S-S bridges in proteins." Biochemical and Biophysical Research Communications 126, no. 3 (1985): 1122–28. http://dx.doi.org/10.1016/0006-291x(85)90302-x.

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24

Lin, Guohui, Dong Xu, Zhi-Zhong Chen, Tao Jiang, Jianjun Wen, and Ying Xu. "Computational Assignment of Protein Backbone NMR Peaks by Efficient Bounding and Filtering." Journal of Bioinformatics and Computational Biology 01, no. 02 (2003): 387–409. http://dx.doi.org/10.1142/s0219720003000083.

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NMR resonance assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents a new computational method based on the combinat

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25

Hiller, Sebastian, Christian Wasmer, Gerhard Wider, and Kurt Wüthrich. "Sequence-Specific Resonance Assignment of Soluble Nonglobular Proteins by 7D APSY-NMR Spectroscopy." Journal of the American Chemical Society 129, no. 35 (2007): 10823–28. http://dx.doi.org/10.1021/ja072564+.

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26

Cutting, Brian, André Strauss, Gabriele Fendrich, Paul W. Manley, and Wolfgang Jahnke. "NMR resonance assignment of selectively labeled proteins by the use of paramagnetic ligands." Journal of Biomolecular NMR 30, no. 2 (2004): 205–10. http://dx.doi.org/10.1023/b:jnmr.0000048947.28598.ea.

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27

Schubert, Mario, Michael Kolbe, Brigitte Kessler, Dieter Oesterhelt, and Peter Schmieder. "Heteronuclear Multidimensional NMR Spectroscopy of Solubilized Membrane Proteins: Resonance Assignment of Native Bacteriorhodopsin." ChemBioChem 3, no. 10 (2002): 1019–23. http://dx.doi.org/10.1002/1439-7633(20021004)3:10<1019::aid-cbic1019>3.0.co;2-c.

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28

Solyom, Zsofia, Melanie Schwarten, Leonhard Geist, Robert Konrat, Dieter Willbold, and Bernhard Brutscher. "BEST-TROSY experiments for time-efficient sequential resonance assignment of large disordered proteins." Journal of Biomolecular NMR 55, no. 4 (2013): 311–21. http://dx.doi.org/10.1007/s10858-013-9715-0.

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29

Schmidt, Elena, and Peter Güntert. "Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins." Journal of Biomolecular NMR 57, no. 2 (2013): 193–204. http://dx.doi.org/10.1007/s10858-013-9779-x.

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30

Shcherbakov, Alexander A., Matthias Roos, Byungsu Kwon, and Mei Hong. "Two-dimensional 19F–13C correlation NMR for 19F resonance assignment of fluorinated proteins." Journal of Biomolecular NMR 74, no. 2-3 (2020): 193–204. http://dx.doi.org/10.1007/s10858-020-00306-0.

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31

Kumar, Dinesh, Subhradip Paul, and Ramakrishna V. Hosur. "BEST-HNN and 2D-(HN)NH experiments for rapid backbone assignment in proteins." Journal of Magnetic Resonance 204, no. 1 (2010): 111–17. http://dx.doi.org/10.1016/j.jmr.2010.02.013.

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32

Averseng, Olivier, Agnès Hagège, Frédéric Taran, and Claude Vidaud. "Surface Plasmon Resonance for Rapid Screening of Uranyl Affine Proteins." Analytical Chemistry 82, no. 23 (2010): 9797–802. http://dx.doi.org/10.1021/ac102578y.

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33

LI, K. B., and B. C. SANCTUARY. "ChemInform Abstract: Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR. Part 2. Side Chain and Sequence-Specific Assignment." ChemInform 28, no. 37 (2010): no. http://dx.doi.org/10.1002/chin.199737284.

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34

Romero, Javier A., Paulina Putko, Mateusz Urbańczyk, Krzysztof Kazimierczuk, and Anna Zawadzka-Kazimierczuk. "Linear discriminant analysis reveals hidden patterns in NMR chemical shifts of intrinsically disordered proteins." PLOS Computational Biology 18, no. 10 (2022): e1010258. http://dx.doi.org/10.1371/journal.pcbi.1010258.

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NMR spectroscopy is key in the study of intrinsically disordered proteins (IDPs). Yet, even the first step in such an analysis—the assignment of observed resonances to particular nuclei—is often problematic due to low peak dispersion in the spectra of IDPs. We show that the assignment process can be aided by finding “hidden” chemical shift patterns specific to the amino acid residue types. We find such patterns in the training data from the Biological Magnetic Resonance Bank using linear discriminant analysis, and then use them to classify spin systems in an α-synuclein sample prepared by us.

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35

Song, Sunho, Sanford A. Asher, Samuel Krimm, and Jagdeesh Bandekar. "Assignment of a new conformation-sensitive UV resonance Raman band in peptides and proteins." Journal of the American Chemical Society 110, no. 25 (1988): 8547–48. http://dx.doi.org/10.1021/ja00233a042.

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36

Salzmann, M., K. Pervushin, G. Wider, H. Senn, and K. Wuthrich. "TROSY in triple-resonance experiments: New perspectives for sequential NMR assignment of large proteins." Proceedings of the National Academy of Sciences 95, no. 23 (1998): 13585–90. http://dx.doi.org/10.1073/pnas.95.23.13585.

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37

Feuerstein, Sophie, Michael J. Plevin, Dieter Willbold, and Bernhard Brutscher. "iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins." Journal of Magnetic Resonance 214 (January 2012): 329–34. http://dx.doi.org/10.1016/j.jmr.2011.10.019.

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38

Williams, Robert V., Monique J. Rogals, Alexander Eletsky, et al. "AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins." Journal of Magnetic Resonance 345 (December 2022): 107336. http://dx.doi.org/10.1016/j.jmr.2022.107336.

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39

Löhr, Frank, and Heinz Rüterjans. "A new triple-resonance experiment for the sequential assignment of backbone resonances in proteins." Journal of Biomolecular NMR 6, no. 2 (1995): 189–97. http://dx.doi.org/10.1007/bf00211783.

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40

Medvedeva, Svetlana, Jean-Pierre Simorre, Bernhard Brutscher, Françoise Guerlesquin, and Dominique Marion. "Extensive1H NMR resonance assignment of proteins using natural abundance gradient-enhanced13C−1H correlation spectroscopy." FEBS Letters 333, no. 3 (1993): 251–56. http://dx.doi.org/10.1016/0014-5793(93)80664-g.

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41

Löhr, Frank, and Heinz Rüterjans. "Novel Pulse Sequences for the Resonance Assignment of Aromatic Side Chains in13C-Labeled Proteins." Journal of Magnetic Resonance, Series B 112, no. 3 (1996): 259–68. http://dx.doi.org/10.1006/jmrb.1996.0140.

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42

Plevin, Michael J., Olivier Hamelin, Jérôme Boisbouvier, and Pierre Gans. "A simple biosynthetic method for stereospecific resonance assignment of prochiral methyl groups in proteins." Journal of Biomolecular NMR 49, no. 2 (2011): 61–67. http://dx.doi.org/10.1007/s10858-010-9463-3.

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43

Iuga, Adriana, Michael Spoerner, Christian Ader, Eike Brunner, and Hans Robert Kalbitzer. "Rapid assignment of solution 31P NMR spectra of large proteins by solid-state spectroscopy." Biochemical and Biophysical Research Communications 346, no. 1 (2006): 301–5. http://dx.doi.org/10.1016/j.bbrc.2006.05.116.

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44

Boyko, Kristina V., Erin A. Rosenkranz, Derrick M. Smith, et al. "Sortase-mediated segmental labeling: A method for segmental assignment of intrinsically disordered regions in proteins." PLOS ONE 16, no. 10 (2021): e0258531. http://dx.doi.org/10.1371/journal.pone.0258531.

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A significant number of proteins possess sizable intrinsically disordered regions (IDRs). Due to the dynamic nature of IDRs, NMR spectroscopy is often the tool of choice for characterizing these segments. However, the application of NMR to IDRs is often hindered by their instability, spectral overlap and resonance assignment difficulties. Notably, these challenges increase considerably with the size of the IDR. In response to these issues, here we report the use of sortase-mediated ligation (SML) for segmental isotopic labeling of IDR-containing samples. Specifically, we have developed a ligat

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45

Jang, Richard, Xin Gao, and Ming Li. "Towards Fully Automated Structure-Based NMR Resonance Assignment of15N-Labeled Proteins From Automatically Picked Peaks." Journal of Computational Biology 18, no. 3 (2011): 347–63. http://dx.doi.org/10.1089/cmb.2010.0251.

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Zawadzka-Kazimierczuk, Anna, Krzysztof Kazimierczuk, and Wiktor Koźmiński. "A set of 4D NMR experiments of enhanced resolution for easy resonance assignment in proteins." Journal of Magnetic Resonance 202, no. 1 (2010): 109–16. http://dx.doi.org/10.1016/j.jmr.2009.10.006.

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47

Wen, Jie, Jihui Wu, and Pei Zhou. "Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins." Journal of Magnetic Resonance 209, no. 1 (2011): 94–100. http://dx.doi.org/10.1016/j.jmr.2010.12.012.

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48

Boucher, Wayne, Ernest D. Laue, Sharon Campbell-Burk, and Peter J. Domaille. "Four-dimensional heteronuclear triple resonance NMR methods for the assignment of backbone nuclei in proteins." Journal of the American Chemical Society 114, no. 6 (1992): 2262–64. http://dx.doi.org/10.1021/ja00032a053.

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Stratmann, Dirk, Carine van Heijenoort, and Eric Guittet. "NOEnet–Use of NOE networks for NMR resonance assignment of proteins with known 3D structure." Bioinformatics 25, no. 4 (2008): 474–81. http://dx.doi.org/10.1093/bioinformatics/btn638.

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50

McIntosh, Lawrence P., and Frederick W. Dahlquist. "Biosynthetic Incorporation of15N and13C for Assignment and Interpretation of Nuclear Magnetic Resonance Spectra of Proteins." Quarterly Reviews of Biophysics 23, no. 1 (1990): 1–38. http://dx.doi.org/10.1017/s0033583500005400.

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The use of isotopic substitution is a time-honoured method for simplifying the nuclear magnetic resonance spectra of biological macromolecules. For example, the biosynthetic incorporation of a heteronucleus such as15N or13C into a specific amino acid residue in a protein followed by direct observation of the15N or13C NMR spectrum could provide a means to specifically observe a given amino acid type in that protein. By observation of the chemical shift or relaxation properties as a function of pH, ligand concentration, etc. a number of important conclusions concerning the pKavalues of specific

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