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Raum HN, Modig K, Akke M, Weininger U. Proton Transfer Kinetics in Histidine Side Chains Determined by pH-Dependent Multi-Nuclear NMR Relaxation. J Am Chem Soc 2024; 146:22284-22294. [PMID: 39103163 PMCID: PMC11328173 DOI: 10.1021/jacs.4c04647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Histidine is a key amino-acid residue in proteins with unique properties engendered by its imidazole side chain that can exist in three different states: two different neutral tautomeric forms and a protonated, positively charged one with a pKa value close to physiological pH. Commonly, two or all three states coexist and interchange rapidly, enabling histidine to act as both donor and acceptor of hydrogen bonds, coordinate metal ions, and engage in acid/base catalysis. Understanding the exchange dynamics among the three states is critical for assessing histidine's mechanistic role in catalysis, where the rate of proton exchange and interconversion among tautomers might be rate limiting for turnover. Here, we determine the exchange kinetics of histidine residues with pKa values representative of the accessible range from 5 to 9 by measuring pH-dependent 15N, 13C, and 1H transverse relaxation rate constants for 5 nuclei in each imidazole. Proton exchange between the imidazole and the solvent is mediated by hydronium ions at acidic and neutral pH, whereas hydroxide mediated exchange becomes the dominant mechanism at basic pH. Proton transfer is very fast and reaches the diffusion limit for pKa values near neutral pH. We identify a direct pathway between the two tautomeric forms, likely mediated by a bridging water molecule or, in the case of high pH, hydroxide ion. For histidines with pKa 7, we determine all rate constants (lifetimes) involving protonation over the entire pH range. Our approach should enable critical insights into enzymatic acid/base catalyzed reactions involving histidines in proteins.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Halle (Saale) D-06120, Germany
| | - Kristofer Modig
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, Lund SE-22100, Sweden
| | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, Lund SE-22100, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Halle (Saale) D-06120, Germany
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2
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Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. J Struct Biol X 2022; 7:100079. [PMID: 36578472 PMCID: PMC9791609 DOI: 10.1016/j.yjsbx.2022.100079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein's hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10-20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.
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3
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Pazicky S, Werle ALA, Lei J, Löw C, Weininger U. Impact of distant peptide substrate residues on enzymatic activity of SlyD. Cell Mol Life Sci 2022; 79:138. [PMID: 35184231 PMCID: PMC8858294 DOI: 10.1007/s00018-022-04179-4] [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: 10/29/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022]
Abstract
Peptidyl-prolyl isomerases (PPIases) catalyze intrinsically slow and often rate-limiting isomerization of prolyl-peptide bonds in unfolded or partially folded proteins, thereby speeding up the folding process and preventing misfolding. They often possess binding and chaperone domains in addition to the domain carrying the isomerization activity. Although generally, their substrates display no identity in their amino acid sequence upstream and downstream of the proline with 20 possibilities for each residue, PPIases are efficient enzymes. SlyD is a highly efficient PPIase consisting of an isomerase domain and an additional chaperone domain. The binding of peptide substrates to SlyD and its enzymatic activity depend to some extend on the proline-proximal residues, however, the impact of proline-distant residues has not been investigated so far. Here, we introduce a label-free NMR-based method to measure SlyD activity on different peptide substrates and analysed the data in the context of obtained binding affinities and several co-crystal structures. We show that especially charged and aromatic residues up to eight positions downstream and three positions upstream of the proline and outside the canonical region of similar conformations affect the activity and binding, although they rarely display distinct conformations in our crystal structures. We hypothesize that these positions primarily influence the association reaction. In the absence of the chaperone domain the isomerase activity strongly correlates with substrate affinity, whereas additional factors play a role in its presence. The mutual orientation of isomerase and chaperone domains depends on the presence of substrates in both binding sites, implying allosteric regulation of enzymatic activity.
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4
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Patel D, Dabhi AM, Dmello C, Seervi M, Sneha KM, Agrawal P, Sahani MH, Kanojia D. FKBP1A upregulation correlates with poor prognosis and increased metastatic potential of HNSCC. Cell Biol Int 2021; 46:443-453. [PMID: 34882900 DOI: 10.1002/cbin.11741] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy globally. The etiology of HNSCC is multifactorial, including cellular stress induced by a tobacco smoking, tobacco chewing excess alcohol consumption, and human papillomavirus infection. The induction of stress includes autophagy as one of the response pathways in maintaining homeostatic equilibrium. We evaluated the expression of autophagy-related genes in HNSCC tissues from RNA sequencing datasets and identified 19 genes correlated with poor prognosis and 18 genes correlated with improved prognosis of HNSCC patients. Further analysis of independent gene expression datasets revealed that ATG12, HSP90AB1, and FKBP1A are overexpressed in HNSCC and correlate with poor prognosis, whereas the overexpression of ANXA1, FOS, and ULK3 correlates with improved prognosis. Using independent datasets, we also found that ATG12, HSP90AB1, and FKBP1A expression increased with an increase in the T-stage of HNSCC. Among all the datasets analyzed, FKBP1A was overexpressed in HNSCC and was strongly associated with lymph node metastasis in multiple in silico datasets. In conclusion, our analysis indicates dynamic alterations in autophagy genes during HNSCC and warrants further investigation, specifically on FKBP1A and its role in tumor progression and metastasis.
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Affiliation(s)
- Dhruti Patel
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Aarsh M Dabhi
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Crismita Dmello
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - K M Sneha
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Pavan Agrawal
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Mayurbhai H Sahani
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, The Maharaja Sayajirao University of Baroda, Vadodara, India
| | - Deepak Kanojia
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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5
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Dreydoppel M, Lichtenecker RJ, Akke M, Weininger U. 1H R 1ρ relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2021; 75:383-392. [PMID: 34510298 PMCID: PMC8642340 DOI: 10.1007/s10858-021-00382-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamic, since they are often key residues in enzyme active sites and protein binding sites. Dynamic processes on microsecond to millisecond timescales can be studied by relaxation dispersion experiments that attenuate conformational exchange contributions to the transverse relaxation rate by varying the refocusing frequency of applied radio-frequency fields implemented as either CPMG pulse trains or continuous spin-lock periods. Here we present an aromatic 1H R1ρ relaxation dispersion experiment enabling studies of two to three times faster exchange processes than achievable by existing experiments for aromatic side chains. We show that site-specific isotope labeling schemes generating isolated 1H-13C spin pairs with vicinal 2H-12C moieties are necessary to avoid anomalous relaxation dispersion profiles caused by Hartmann-Hahn matching due to the 3JHH couplings and limited chemical shift differences among 1H spins in phenylalanine, tyrosine and the six-ring moiety of tryptophan. This labeling pattern is sufficient in that remote protons do not cause additional complications. We validated the approach by measuring ring-flip kinetics in the small protein GB1. The determined rate constants, kflip, agree well with previous results from 13C R1ρ relaxation dispersion experiments, and yield 1H chemical shift differences between the two sides of the ring in good agreement with values measured under slow-exchange conditions. The aromatic1H R1ρ relaxation dispersion experiment in combination with the site-selective 1H-13C/2H-12C labeling scheme enable measurement of exchange rates up to kex = 2kflip = 80,000 s-1, and serve as a useful complement to previously developed 13C-based methods.
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Affiliation(s)
- Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | | | - Mikael Akke
- Division of Biophysical Chemistry, Center for Molecular Protein Science, Department of Chemistry, Lund University, P.O. Box 124, 22100, Lund, Sweden
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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6
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Karunanithy G, Shukla VK, Hansen DF. Methodological advancements for characterising protein side chains by NMR spectroscopy. Curr Opin Struct Biol 2021; 70:61-69. [PMID: 33989947 DOI: 10.1016/j.sbi.2021.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/18/2022]
Abstract
The surface of proteins is covered by side chains of polar amino acids that are imperative for modulating protein functionality through the formation of noncovalent intermolecular interactions. However, despite their tremendous importance, the unique structures of protein side chains require tailored approaches for investigation by nuclear magnetic resonance spectroscopy and so have traditionally been understudied compared with the protein backbone. Here, we review substantial recent methodological advancements within nuclear magnetic resonance spectroscopy to address this issue. Specifically, we consider advancements that provide new insight into methyl-bearing side chains, show the potential of using non-natural amino acids and reveal the actions of charged side chains. Combined, the new methods promise unprecedented characterisations of side chains that will further elucidate protein function.
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Affiliation(s)
- Gogulan Karunanithy
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - Vaibhav Kumar Shukla
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom
| | - D Flemming Hansen
- Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, WC1E 6BT, United Kingdom.
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7
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Marques BS, Stetz MA, Jorge C, Valentine KG, Wand AJ, Nucci NV. Protein conformational entropy is not slaved to water. Sci Rep 2020; 10:17587. [PMID: 33067552 PMCID: PMC7567893 DOI: 10.1038/s41598-020-74382-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The "solvent slaving" model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.
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Affiliation(s)
- Bryan S Marques
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew A Stetz
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine Jorge
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen G Valentine
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77845-2128, USA.
| | - Nathaniel V Nucci
- Department of Physics and Astronomy and Department of Molecular and Cellular Biosciences, Rowan University, 201 Mullica Hill Road, Glassboro, NJ, 08028, USA.
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Raum HN, Schörghuber J, Dreydoppel M, Lichtenecker RJ, Weininger U. Site-selective 1H/ 2H labeling enables artifact-free 1H CPMG relaxation dispersion experiments in aromatic side chains. JOURNAL OF BIOMOLECULAR NMR 2019; 73:633-639. [PMID: 31506857 PMCID: PMC6859156 DOI: 10.1007/s10858-019-00275-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Aromatic side chains are often key residues in enzyme active sites and protein binding sites, making them attractive probes of protein dynamics on the millisecond timescale. Such dynamic processes can be studied by aromatic 13C or 1H CPMG relaxation dispersion experiments. Aromatic 1H CPMG relaxation dispersion experiments in phenylalanine, tyrosine and the six-ring moiety of tryptophan, however, are affected by 3J 1H-1H couplings which are causing anomalous relaxation dispersion profiles. Here we show that this problem can be addressed by site-selective 1H/2H labeling of the aromatic side chains and that artifact-free relaxation dispersion profiles can be acquired. The method has been further validated by measuring folding-unfolding kinetics of the small protein GB1. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. Furthermore, the CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained directly from the spectra. In summary, site-selective 1H/2H labeling enables artifact-free aromatic 1H CPMG relaxation dispersion experiments in phenylalanine and the six-ring moiety of tryptophan, thereby extending the available methods for studying millisecond dynamics in aromatic protein side chains.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, 1090, Vienna, Austria
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany
| | | | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle, Germany.
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9
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Raum HN, Weininger U. Experimental pK a Value Determination of All Ionizable Groups of a Hyperstable Protein. Chembiochem 2019; 20:922-930. [PMID: 30511779 PMCID: PMC6619245 DOI: 10.1002/cbic.201800628] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Indexed: 11/18/2022]
Abstract
Electrostatic interactions significantly contribute to the stability and function of proteins. The stabilizing or destabilizing effect of local charge is reflected in the perturbation of the pKa value of an ionizable group from the intrinsic pKa value. Herein, the charge network of a hyperstable dimeric protein (ribbon-helix-helix (rhh) protein from plasmid pRN1 from Sulfolobus islandicus) is studied through experimental determination of the pKa values of all ionizable groups. Transitions were monitored by multiple NMR signals per ionizable group between pH 0 and 12.5, prior to a global analysis, which accounted for the effects of neighboring residues. It is found that for several residues involved in salt bridges (four Asp and one Lys) the pKa values are shifted in favor of the charged state. Furthermore, the pKa values of residues C40 and Y47, both located in the hydrophobic dimer interface, are shifted beyond 13.7. The necessary energy for such a shift is about two-thirds of the total stability of the protein, which confirms the importance of the hydrophobic core to the overall stability of the rhh protein.
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Affiliation(s)
- Heiner N. Raum
- Institute of PhysicsBiophysicsMartin-Luther-University Halle-Wittenberg06120Halle/SaaleGermany
| | - Ulrich Weininger
- Institute of PhysicsBiophysicsMartin-Luther-University Halle-Wittenberg06120Halle/SaaleGermany
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Raum HN, Dreydoppel M, Weininger U. Conformational exchange of aromatic side chains by 1H CPMG relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2018; 72:105-114. [PMID: 30229369 PMCID: PMC6209042 DOI: 10.1007/s10858-018-0210-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Aromatic side chains are attractive probes of protein dynamics on the millisecond time scale, because they are often key residues in enzyme active sites and protein binding sites. Further they allow to study specific processes, like histidine tautomerization and ring flips. Till now such processes have been studied by aromatic 13C CPMG relaxation dispersion experiments. Here we investigate the possibility of aromatic 1H CPMG relaxation dispersion experiments as a complementary method. Artifact-free dispersions are possible on uniformly 1H and 13C labeled samples for histidine δ2 and ε1, as well as for tryptophan δ1. The method has been validated by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined rate constants and populations agree well with previous results from 13C CPMG relaxation dispersion experiments. The CPMG-derived chemical shift differences between the folded and unfolded states are in good agreement with those obtained directly from the spectra. In contrast, the 1H relaxation dispersion profiles in phenylalanine, tyrosine and the six-ring moiety of tryptophan, display anomalous behavior caused by 3J 1H-1H couplings and, if present, strong 13C-13C couplings. Therefore they require site-selective 1H/2H and, in case of strong couplings, 13C/12C labeling. In summary, aromatic 1H CPMG relaxation dispersion experiments work on certain positions (His δ2, His ε1 and Trp δ1) in uniformly labeled samples, while other positions require site-selective isotope labeling.
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Affiliation(s)
- Heiner N Raum
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Matthias Dreydoppel
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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Weininger U. Optimal Isotope Labeling of Aromatic Amino Acid Side Chains for NMR Studies of Protein Dynamics. Methods Enzymol 2018; 614:67-86. [PMID: 30611433 DOI: 10.1016/bs.mie.2018.08.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aromatic side chains in proteins are often directly evolved in stabilizing the hydrophobic core, protein binding, or enzymatic activity. They are also responsible for specific local dynamic processes, such as histidine tautomerization or ring flips. Despite their importance, they are often not targeted directly by NMR spectroscopy, because of spectroscopic complications and challenges. This chapter addresses state-of-the-art site-selective 13C-labeling methods for aromatic side chains, and describes how they solve several of the spectroscopic issues. A special emphasis is put on thereby enabled protein dynamics experiments of aromatic side chains.
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Affiliation(s)
- Ulrich Weininger
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, Halle, Germany.
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12
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Weininger U. Site-selective 13C labeling of histidine and tryptophan using ribose. JOURNAL OF BIOMOLECULAR NMR 2017; 69:23-30. [PMID: 28856561 PMCID: PMC5626788 DOI: 10.1007/s10858-017-0130-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Experimental studies on protein dynamics at atomic resolution by NMR-spectroscopy in solution require isolated 1H-X spin pairs. This is the default scenario in standard 1H-15N backbone experiments. Side chain dynamic experiments, which allow to study specific local processes like proton-transfer, or tautomerization, require isolated 1H-13C sites which must be produced by site-selective 13C labeling. In the most general way this is achieved by using site-selectively 13C-enriched glucose as the carbon source in bacterial expression systems. Here we systematically investigate the use of site-selectively 13C-enriched ribose as a suitable precursor for 13C labeled histidines and tryptophans. The 13C incorporation in nearly all sites of all 20 amino acids was quantified and compared to glucose based labeling. In general the ribose approach results in more selective labeling. 1-13C ribose exclusively labels His δ2 and Trp δ1 in aromatic side chains and helps to resolve possible overlap problems. The incorporation yield is however only 37% in total and 72% compared to yields of 2-13C glucose. A combined approach of 1-13C ribose and 2-13C glucose maximizes 13C incorporation to 75% in total and 150% compared to 2-13C glucose only. Further histidine positions β, α and CO become significantly labeled at around 50% in total by 3-, 4- or 5-13C ribose. Interestingly backbone CO of Gly, Ala, Cys, Ser, Val, Phe and Tyr are labeled at 40-50% in total with 3-13C ribose, compared to 5% and below for 1-13C and 2-13C glucose. Using ribose instead of glucose as a source for site-selective 13C labeling enables a very selective labeling of certain positions and thereby expanding the toolbox for customized isotope labeling of amino-acids.
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Affiliation(s)
- Ulrich Weininger
- Department of Biophysical Chemistry, Center for Molecular Protein Science, Lund University, P. O. Box 124, 22100, Lund, Sweden.
- Institute of Physics, Biophysics, Martin-Luther-University Halle-Wittenberg, 06120, Halle (Saale), Germany.
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13
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Schörghuber J, Geist L, Platzer G, Konrat R, Lichtenecker RJ. Highly Selective Stable Isotope Labeling of Histidine Residues by Using a Novel Precursor in E. coli-Based Overexpression Systems. Chembiochem 2017; 18:1487-1491. [PMID: 28489326 DOI: 10.1002/cbic.201700192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 12/14/2022]
Abstract
The importance of NMR spectroscopy in unraveling the structural and dynamic properties of proteins is ever-expanding owing to progress in experimental techniques, hardware development, and novel labeling approaches. Multiple sophisticated methods of aliphatic residue labeling can be found in the literature, whereas the selective incorporation of NMR active isotopes into other amino acids still holds the potential for improvement. In order to close this methodological gap, we present a novel metabolic precursor for cell-based protein overexpression to assemble 13 C/2 H isotope patterns in the peptide backbone, as well as in side chain positions of a mechanistically distinguished histidine residue.
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Affiliation(s)
- Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
| | - Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Gerald Platzer
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural Biology, and Biotechnology/Department of Structural and Computational Biology, University of Vienna, 1090, Vienna, Austria
| | - Roman J Lichtenecker
- Institute of Organic Chemistry, University of Vienna, Währingerstrasse 38, 1090, Vienna, Austria
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