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Wu R, Metternich JB, Kamenik AS, Tiwari P, Harrison JA, Kessen D, Akay H, Benzenberg LR, Chan TWD, Riniker S, Zenobi R. Determining the gas-phase structures of α-helical peptides from shape, microsolvation, and intramolecular distance data. Nat Commun 2023; 14:2913. [PMID: 37217470 PMCID: PMC10203302 DOI: 10.1038/s41467-023-38463-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Mass spectrometry is a powerful technique for the structural and functional characterization of biomolecules. However, it remains challenging to accurately gauge the gas-phase structure of biomolecular ions and assess to what extent native-like structures are maintained. Here we propose a synergistic approach which utilizes Förster resonance energy transfer and two types of ion mobility spectrometry (i.e., traveling wave and differential) to provide multiple constraints (i.e., shape and intramolecular distance) for structure-refinement of gas-phase ions. We add microsolvation calculations to assess the interaction sites and energies between the biomolecular ions and gaseous additives. This combined strategy is employed to distinguish conformers and understand the gas-phase structures of two isomeric α-helical peptides that might differ in helicity. Our work allows more stringent structural characterization of biologically relevant molecules (e.g., peptide drugs) and large biomolecular ions than using only a single structural methodology in the gas phase.
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Affiliation(s)
- Ri Wu
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Jonas B Metternich
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Anna S Kamenik
- Laboratorium für Physikalische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Prince Tiwari
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
- Laboratory of Atmospheric Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen PSI, Switzerland
| | - Julian A Harrison
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Dennis Kessen
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
- University of Münster, MEET Battery Research Center, Corrensstrasse 46, 48149, Münster, Germany
| | - Hasan Akay
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - Lukas R Benzenberg
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland.
| | - Renato Zenobi
- Laboratorium für Organische Chemie, D-CHAB, ETH Zürich, 8093, Zurich, Switzerland.
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2
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Tikhonov DS, Scutelnic V, Sharapa DI, Krotova AA, Dmitrieva AV, Obenchain DA, Schnell M. Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations. Struct Chem 2022. [DOI: 10.1007/s11224-022-02053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractHere, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$
+
ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$
2
H
+
and (Imidazole)$$_{3}\mathrm{H}^{+}$$
3
H
+
the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.
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Wu R, Metternich JB, Tiwari P, Benzenberg LR, Harrison JA, Liu Q, Zenobi R. Structural Studies of a Stapled Peptide with Native Ion Mobility-Mass Spectrometry and Transition Metal Ion Förster Resonance Energy Transfer in the Gas Phase. J Am Chem Soc 2022; 144:14441-14445. [PMID: 35943275 DOI: 10.1021/jacs.2c02776] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Native mass spectrometry has emerged as an important tool for gas-phase structural biology. However, the conformations that a biomolecular ion adopts in the gas phase can differ from those found in solution. Herein, we report a synergistic, native ion mobility-mass spectrometry (IM-MS) and transition metal ion Förster resonance energy transfer (tmFRET)-based approach to probe the gas-phase ion structures of a nonstapled peptide (nsp; Ac-CAARAAHAAAHARARA-NH2) and a stapled peptide (sp; Ac-CXARAXHAAAHARARA-NH2). The stapled peptide contains a single hydrocarbon chain connecting the peptide backbone in the i and i + 4 positions via a Grubbs ring-closure metathesis. Fluorescence lifetime measurements indicated that the Cu-bound complexes of carboxyrhodamine 6g (crh6g)-labeled stapled peptide (sp-crh6g) had a shorter donor-acceptor distance (rDA) than the labeled nonstapled peptide (nsp-crh6g). Experimental collision cross-section (CCS) values were then determined by native IM-MS, which could separate the conformations of Cu-bound complexes of nsp-crh6g and sp-crh6g. Finally, the experimental CCS (i.e., shape) and rDA (i.e., distance) values were used as constraints for computational studies, which unambiguously revealed how a staple reduces the elongation of the peptide ions in the gas phase. This study demonstrates the superiority of combining native IM-MS, tmFRET, and computational studies to investigate the structure of biomolecular ions.
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Affiliation(s)
- Ri Wu
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jonas B Metternich
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Prince Tiwari
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Lukas R Benzenberg
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Julian A Harrison
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Qinlei Liu
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Laboratorium für Organische Chemie, Department of Chemistry and Applied Biosciences, ETH Zürich, CH-8093 Zürich, Switzerland
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Single-Disulfide Conopeptide Czon1107, an Allosteric Antagonist of the Human α3β4 Nicotinic Acetylcholine Receptor. Mar Drugs 2022; 20:md20080497. [PMID: 36005500 PMCID: PMC9409646 DOI: 10.3390/md20080497] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Conopeptides are peptides in the venom of marine cone snails that are used for capturing prey or as a defense against predators. A new cysteine-poor conopeptide, Czon1107, has exhibited non-competitive inhibition with an undefined allosteric mechanism in the human (h) α3β4 nicotinic acetylcholine receptors (nAChRs). In this study, the binding mode of Czon1107 to hα3β4 nAChR was investigated using molecular dynamics simulations coupled with mutagenesis studies of the peptide and electrophysiology studies on heterologous hα3β4 nAChRs. Overall, this study clarifies the structure–activity relationship of Czon1107 and hα3β4 nAChR and provides an important experimental and theoretical basis for the development of new peptide drugs.
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5
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Liu L, Dong X, Liu Y, Österlund N, Gräslund A, Carloni P, Li J. Role of hydrophobic residues for the gaseous formation of helical motifs. Chem Commun (Camb) 2019; 55:5147-5150. [PMID: 30977489 DOI: 10.1039/c9cc01898k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid-β (1-40) dimer (2Aβ). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving 19FFAED23, consistent with infrared spectroscopy data on an Aβ segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains "shield" helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.
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Affiliation(s)
- Lin Liu
- College of Chemistry, Fuzhou University, 350002 Fuzhou, China.
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Martins JC, Kuprov I, Sinnaeve D, Linclau B. Synthesis and Conformational Properties of 3,4-Difluoro-l-prolines. J Org Chem 2019; 84:3100-3120. [PMID: 30777755 DOI: 10.1021/acs.joc.8b02920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fluorinated proline derivatives have found diverse applications in areas ranging from medicinal chemistry over structural biochemistry to organocatalysis. Depending on the stereochemistry of monofluorination at the proline 3- or 4-position, different effects on the conformational properties of proline (ring pucker, cis/ trans isomerization) are introduced. With fluorination at both 3- and 4-positions, matching or mismatching effects can occur depending on the relative stereochemistry. Here we report, in full, the syntheses and conformational properties of three out of the four possible 3,4-difluoro-l-proline diastereoisomers. The yet unreported conformational properties are described for (3 S,4 S)- and (3 R,4 R)-difluoro-l-proline, which are shown to bias ring pucker and cis/ trans ratios on the same order of magnitude as their respective monofluorinated progenitors, although with significantly faster amide cis/ trans isomerization rates. The reported analogues thus expand the scope of available fluorinated proline analogues as tools to tailor proline's distinct conformational and dynamical properties, allowing for the interrogation of its role in, for instance, protein stability or folding.
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Affiliation(s)
- Gert-Jan Hofman
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.,Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Mark E Light
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Bruno Kieffer
- Biomolecular NMR , University of Strasbourg , IGBMC, CNRS UMR 7104, INSERM U1258, 1 rue Laurent Fries/BP 10142 , Illkirch Cedex 67404 , France
| | - Jose C Martins
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Bruno Linclau
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
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7
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Fuller DR, Conant CR, El-Baba TJ, Brown CJ, Woodall DW, Russell DH, Clemmer DE. Conformationally Regulated Peptide Bond Cleavage in Bradykinin. J Am Chem Soc 2018; 140:9357-9360. [PMID: 30028131 DOI: 10.1021/jacs.8b04751] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion mobility and mass spectrometry techniques are used to investigate the stabilities of different conformations of bradykinin (BK, Arg1-Pro2-Pro3-Gly4-Phe5-Ser6-Pro7-Phe8-Arg9). At elevated solution temperatures, we observe a slow protonation reaction, i.e., [BK+2H]2++H+ → [BK+3H]3+, that is regulated by trans → cis isomerization of Arg1-Pro2, resulting in the Arg1- cis-Pro2- cis-Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 (all- cis) configuration. Once formed, the all- cis [BK+3H]3+ spontaneously cleaves the bond between Pro2-Pro3 with perfect specificity, a bond that is biologically resistant to cleavage by any human enzyme. Temperature-dependent kinetics studies reveal details about the intrinsic peptide processing mechanism. We propose that nonenzymatic cleavage at Pro2-Pro3 occurs through multiple intermediates and is regulated by trans → cis isomerization of Arg1-Pro2. From this mechanism, we can extract transition state thermochemistry: Δ G‡ = 94.8 ± 0.2 kJ·mol-1, Δ H‡ = 79.8 ± 0.2 kJ·mol-1, and Δ S‡ = -50.4 ± 1.7 J·mol-1·K-1 for the trans → cis protonation event; and, Δ G‡ = 94.1 ± 9.2 kJ·mol-1, Δ H‡ = 107.3 ± 9.2 kJ·mol-1, and Δ S‡ = 44.4 ± 5.1 J·mol-1·K-1 for bond cleavage. Biological resistance to the most favored intrinsic processing pathway prevents formation of Pro3-Gly4-Phe5-Ser6- cis-Pro7-Phe8-Arg9 that is approximately an order of magnitude more antigenic than BK.
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Affiliation(s)
- Daniel R Fuller
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Christopher R Conant
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Christopher J Brown
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Daniel W Woodall
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - David H Russell
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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8
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Kamrath MZ, Rizzo TR. Combining Ion Mobility and Cryogenic Spectroscopy for Structural and Analytical Studies of Biomolecular Ions. Acc Chem Res 2018; 51:1487-1495. [PMID: 29746100 DOI: 10.1021/acs.accounts.8b00133] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion mobility spectrometry (IMS) has become a valuable tool in biophysical and bioanalytical chemistry because of its ability to separate and characterize the structure of gas-phase biomolecular ions on the basis of their collisional cross section (CCS). Its importance has grown with the realization that in many cases, biomolecular ions retain important structural characteristics when produced in the gas phase by electrospray ionization (ESI). While a CCS can help distinguish between structures of radically different types, one cannot expect a single number to differentiate similar conformations of a complex molecule. Molecular spectroscopy has also played an increasingly important role for structural characterization of biomolecular ions. Spectroscopic measurements, particularly when performed at cryogenic temperatures, can be extremely sensitive to small changes in a molecule's conformation and provide tight constraints for calculations of biomolecular structures. However, spectra of complex molecules can be heavily congested due to the presence of multiple stable conformations, each of which can have a distinct spectrum. This congestion can inhibit spectral analysis and complicate the extraction of structural information. Even when a single conformation is present, the conformational search process needed to match a measured spectrum with a computed structure can be overwhelming for peptides of more than a few amino acids, for example. We have recently combined ion mobility spectrometry and cryogenic ion spectroscopy (CIS) to characterize the structures of gas-phase biomolecular ions. In this Account, we illustrate how the coupling of IMS and CIS is by nature synergistic. On the one hand, IMS can be used as a conformational filter to reduce spectral congestion that arises from heterogeneous samples, facilitating structural analysis. On the other hand, highly resolved, cryogenic spectra can serve as a selective detector for IMS that can increase the effective resolution and hence the maximum number of distinct species that can be detected. Taken together, spectra and CCS measurements on the same system facilitates structural analysis and strengthens the conclusions that can be drawn from each type of data. After describing different approaches to combining these two techniques in such a way as to simplify the data obtained from each one separately, we present two examples that illustrate the type of insight gained from using spectra and CCS data together for characterizing gas-phase biomolecular ions. In one example, the CCS is used as a constraint for quantum chemical structure calculations of kinetically trapped species, where a lowest-energy criterion is not applicable. In a second example, we use both the CCS and a cryogenic infrared spectrum as a means to distinguish isomeric glycans.
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Affiliation(s)
- Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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9
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Kida M, Kubo M, Ujihira T, Ebata T, Abe M, Inokuchi Y. Selective Probing of Potassium Ion in Solution by Intramolecular Excimer Fluorescence of Dibenzo-Crown Ethers. Chemphyschem 2018. [DOI: 10.1002/cphc.201800163] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Motoki Kida
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Mayuko Kubo
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Tomoyuki Ujihira
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Yoshiya Inokuchi
- Department of Chemistry, Graduate School of Science; Hiroshima University; Higashi-Hiroshima, Hiroshima 739-8526 Japan
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