1
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Villard J, Kılıç M, Rothlisberger U. Surrogate Based Genetic Algorithm Method for Efficient Identification of Low-Energy Peptide Structures. J Chem Theory Comput 2023; 19:1080-1097. [PMID: 36692853 PMCID: PMC9933449 DOI: 10.1021/acs.jctc.2c01078] [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] [Indexed: 01/25/2023]
Abstract
Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide (Masson, A.; J. Am. Soc. Mass Spectrom.2015, 26, 1444-1454) and (ii) the doubly protonated cyclic decapeptide gramicidin S (Nagornova, N. S.; J. Am. Chem. Soc.2010, 132, 4040-4041). We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤10 kcal/mol (i), ≤5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra.
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2
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Zviagin A, Kopysov V, Nagornova NS, Boyarkin OV. Tracking local and global structural changes in a protein by cold ion spectroscopy. Phys Chem Chem Phys 2022; 24:8158-8165. [PMID: 35332911 DOI: 10.1039/d2cp00217e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Characterization of native structures of proteins in the gas phase remains challenging due to the unpredictable conformational changes the molecules undergo during desolvation and ionization. We spectroscopically studied cryogenically cooled protonated protein ubiquitin and its microhydrated complexes prepared in the gas phase in a range of charge states under different ionization conditions. The UV spectra appear vibrationally resolved for the unfolded protein, but become redshifted and smooth for the native-like structures of ubiquitin. This spectroscopic change results from the H-bonding of the hydroxyl of Tyr to the amide group of Glu-51 in the compact structures; the minimum length of this bond was estimated to be ∼1.7 Å. IR spectroscopy reflects the global structural change by observing redshifts of free NH/OH-stretch vibrational transitions. Evaporative cooling of microhydrated complexes of ubiquitin keeps the protein chilly during ionization, enabling native-like conformers with up to eight protons to survive in the gas phase.
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Affiliation(s)
- Andrei Zviagin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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3
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Roy TK. Performance of Vibrational Self-Consistent Field Theory for Accurate Potential Energy Surfaces: Fundamentals, Excited States, and Intensities. J Phys Chem A 2022; 126:608-622. [PMID: 35050620 DOI: 10.1021/acs.jpca.1c09989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of vibrational structure calculations beyond harmonic approximation in the framework of the vibrational self-consistent field method with second-order perturbation corrections (VSCF-PT2) is investigated in conjunction with very accurate potential energy surfaces (PESs) given by various coupled-cluster electronic structure theories. The quality of anharmonic calculations depends on the accuracy of the underlying multidimensional PES obtained from its functional form, which is given by the level of electronic structure theory. Two such highest levels of typical coupled-cluster electronic structure methods, CCSD and the ″gold standard″ CCSD(T), along with their variants such as CCD, CR-CCL (completely renormalized CR-CC(2,3) approach), and CCSD(TQ) are tested for the construction of accurate anharmonic potentials without any fitting or ad hoc scaling and using cc-pVTZ basis sets. The accuracy of VSCF-PT2 theory in comparison to experimental values is tested for a series of 16 molecules with 135 fundamental bands, 64 overtones, and combination bands and also for 39 intensities. It is found that CCD and CCSD bind the potential tighter than CCSD(T) and the computed VSCF-PT2 transitions are more blue-shifted showing higher deviation from the experiment. In general, VSCF-PT2 results computed at the CCSD(T) potential offer a good cost/accuracy ratio, with the mean absolute deviation and the mean absolute percentage error with the experiment being ∼16 cm-1 and 1.38, respectively, for fundamentals. Additionally, while the CR-CCL and CCSD(TQ) methods offer similar levels of accuracies as compared to CCSD(T), the former offers a better accuracy/cost ratio than the latter and is a suitable alternative to CCSD(T).
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Samba, Jammu and Kashmir 181143, India
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4
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Suzuki Y, Hirata K, Lisy JM, Ishiuchi SI, Fujii M. Double Ion Trap Laser Spectroscopy of Alkali Metal Ion Complexes with a Partial Peptide of the Selectivity Filter in K + Channels─Temperature Effect and Barrier for Conformational Conversions. J Phys Chem A 2021; 125:9609-9618. [PMID: 34637306 DOI: 10.1021/acs.jpca.1c06440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Potassium ion channels selectively permeate K+, as well as Rb+ and Cs+ to some degree, while excluding Na+ and Li+. Conformations of alkali metal complexes of Ac-Tyr-NHMe, a model peptide of the selectivity filter in a K+ channel, were previously found to correlate with the permeability of alkali metal ions to a K+ channel by cold ion trap infrared spectroscopy. With an additional temperature-controlled ion trap, we examined the conformations of the alkali metal complexes, allowing the ions to collide with a He buffer gas at different temperatures, prior to spectroscopic investigation. The conformational distribution of the K+-peptide complex shows the most significant variation with temperature, which suggests that this complex has more flexibility when complexed with K+ and suggests lower barrier heights than other metal-peptide complexes. The variability of the conformational distribution with temperature for the ions follows the same order of ion permeability of a K+ channel. This work demonstrates that the additional temperature-controlled ion trap is a powerful tool to explore the conformational landscape of flexible molecular systems.
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Affiliation(s)
- Yukina Suzuki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - James M Lisy
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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5
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Saparbaev E, Yamaletdinov R, Boyarkin OV. Identification of Isomeric Lipids by UV Spectroscopy of Noncovalent Complexes with Aromatic Molecules. Anal Chem 2021; 93:12822-12826. [PMID: 34516082 DOI: 10.1021/acs.analchem.1c02866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The tremendous structural and isomeric diversity of lipids enables a wide range of their functions in nature but makes the identification of these biomolecules challenging. We distinguish and quantify isomeric lipids using cold ion UV fragmentation spectroscopy of their noncovalent complexes with aromatic amino acids and dipeptides. On the basis of structural simulations, specific isomer-sensitive aromatic "sensors" have been preselected for lipids of each studied class. Tyrosine appeared to be a good "sensor" to distinguish steroids and prostaglandins, which are rich in functional groups, while diphenylalanine is a better choice for sensing largely hydrophobic phospholipids. With this sensor, the relative concentrations of two isomeric glycerophospholipids mixed in solution have been determined with 3.3% accuracy, which should degrade only to 3.7% for a 14 s express measurement.
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Affiliation(s)
- Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ruslan Yamaletdinov
- Nikolaev Institute of Inorganic Chemistry, Novosibirsk 630090, Russian Federation
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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6
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Roy TK, Gerber RB. Dual Basis Approach for Ab Initio Anharmonic Calculations of Vibrational Spectroscopy: Application to Microsolvated Biomolecules. J Chem Theory Comput 2020; 16:7005-7016. [PMID: 32991804 DOI: 10.1021/acs.jctc.0c00725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dual electronic basis set approach is introduced for more efficient but accurate calculations of the anharmonic vibrational spectra in the framework of the vibrational self-consistent field (VSCF) theory. In this approach, an accurate basis set is used to compute the vibrational spectra at the harmonic level. The results are used to scale the potential surface from a more modest but much more efficient basis set. The scaling is such that at the harmonic level the new, scaled potential agrees with one of the accurate basis sets. The approach is tested in the application of the microsolvated, protected amino acid Ac-Phe-OMe, using the scaled anharmonic hybrid potential in the VSCF and VSCF-PT2 algorithms. The hybrid potential method yields results that are in good accord with the experiment and very close to those obtained in calculations with the high-level, very costly potential from the large basis set. At the same time, the hybrid potential calculations are considerably less expensive. The results of the hybrid calculations are much more accurate than those computed from the potential surface corresponding to the modest basis set. The results are very encouraging for using the hybrid potential method for inexpensive yet sufficiently accurate anharmonic calculations for the spectra of large biomolecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Dist: Samba Jammu-181143, India
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel.,Department of Chemistry, University of California, Irvine, California 92697, United States
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7
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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8
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Mitra H, Roy TK. Comprehensive Benchmark Results for the Accuracy of Basis Sets for Anharmonic Molecular Vibrations. J Phys Chem A 2020; 124:9203-9221. [DOI: 10.1021/acs.jpca.0c06634] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hrishit Mitra
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
| | - Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu, Jammu and Kashmir 181143, India
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9
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Rolland AD, Prell JS. Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:282-291. [PMID: 31983791 PMCID: PMC6979403 DOI: 10.1016/j.trac.2019.04.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon,
Eugene, OR, USA 97403-1252
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10
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Corinti D, Maccelli A, Chiavarino B, Maitre P, Scuderi D, Bodo E, Fornarini S, Crestoni ME. Vibrational signatures of curcumin's chelation in copper(II) complexes: An appraisal by IRMPD spectroscopy. J Chem Phys 2019; 150:165101. [PMID: 31042893 DOI: 10.1063/1.5086666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Curcumin (Cur) is a natural polyphenol with a wide spectrum of biological activities and appealing therapeutic potential. Herein, it has been delivered by electrospray ionization as gaseous protonated species, [Cur + H]+, and as a Cu(ii) complex, [Cu(Cur - H)]+, a promising antioxidant and radical scavenger. The gas phase structures were assayed by infrared multiple photon dissociation (IRMPD) spectroscopy in both the fingerprint (800-2000 cm-1) and hydrogen stretching (3100-3750 cm-1) ranges. Comparison between the experimental features and linear IR spectra of the lowest energy structures computed at the B3LYP/6-311+G(d,p) level reveals that bare [Cu(Cur - H)]+ exists in a fully planar and symmetric arrangement, where the metal interacts with the two oxygens of the syn-enolate functionality of deprotonated Cur and both OCH3 groups are engaged in H-bonding with the ortho OH. The effect of protonation on the energetic and geometric determinants of Cur has been explored as well, revealing that bare [Cur + H]+ may exist as a mixture of two close-lying isomers associated with the most stable binding motifs. The additional proton is bound to either the diketo or the keto-enol configuration of Cur, in a bent or nearly planar arrangement, respectively.
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Affiliation(s)
- Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Alessandro Maccelli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Philippe Maitre
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Debora Scuderi
- Laboratoire de Chimie Physique (UMR8000), CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405, Orsay, France
| | - Enrico Bodo
- Dipartimento di Chimica, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma "La Sapienza," Piazzale Aldo Moro, 5, I-00185 Roma, Italy
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11
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Affiliation(s)
- Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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12
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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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13
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Pereverzev AY, Boyarkin OV. Exploring the relevance of gas-phase structures to biology: cold ion spectroscopy of the decapeptide neurokinin A. Phys Chem Chem Phys 2018; 19:3468-3472. [PMID: 28106178 DOI: 10.1039/c6cp07953a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Linking the intrinsic tertiary structures of biomolecules to their native geometries is a central prerequisite for making gas-phase studies directly relevant to biology. The isolation of molecules in the gas phase eliminates hydrophilic interactions with solvents, to some extent mimicking a hydrophobic environment. Intrinsic structures therefore may resemble native ones for peptides that in vivo reside in a hydrophobic environment (e.g., binding pockets of receptors). In this study, we investigate doubly protonated neurokinin A (NKA) using IR-UV double resonance cold ion spectroscopy and find only five conformers of this decapeptide in the gas phase. In contrast, NMR data show that in aqueous solutions, NKA exhibits high conformational heterogeneity, which reduces to a few well-defined structures in hydrophobic micelles. Do the gas-phase structures of NKA resemble these native structures? The IR spectra reported here allow the validation of future structural calculations that may answer this question.
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Affiliation(s)
- A Y Pereverzev
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
| | - O V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Federale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland.
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14
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Ujma J, Kopysov V, Nagornova NS, Migas LG, Lizio MG, Blanch EW, MacPhee C, Boyarkin OV, Barran PE. Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Maria Giovanna Lizio
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Ewan W. Blanch
- School of Science; RMIT University; 124a La Trobe Street Melbourne VIC 3001 Australia
| | - Cait MacPhee
- The School of Physics and Astronomy; James Maxwell Clark Building; The University of Edinburgh; Edinburgh EH9 3FD UK
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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15
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Ujma J, Kopysov V, Nagornova NS, Migas LG, Lizio MG, Blanch EW, MacPhee C, Boyarkin OV, Barran PE. Initial Steps of Amyloidogenic Peptide Assembly Revealed by Cold-Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 57:213-217. [DOI: 10.1002/anie.201710188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 10/20/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Jakub Ujma
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Natalia S. Nagornova
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Maria Giovanna Lizio
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Ewan W. Blanch
- School of Science; RMIT University; 124a La Trobe Street Melbourne VIC 3001 Australia
| | - Cait MacPhee
- The School of Physics and Astronomy; James Maxwell Clark Building; The University of Edinburgh; Edinburgh EH9 3FD UK
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry; Manchester Institute for Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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16
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Roy TK, Nagornova NS, Boyarkin OV, Gerber RB. A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy. J Phys Chem A 2017; 121:9401-9408. [PMID: 29091429 DOI: 10.1021/acs.jpca.7b10357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry & Chemical Sciences, Central University of Jammu , Jammu, 180011 India
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University , Jerusalem 91904, Israel.,Department of Chemistry, University of California , Irvine, California 92697, United States.,Department of Chemistry, University of Helsinki , P.O. Box 55, 00014 Helsinki, Finland
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17
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017; 56:15639-15643. [DOI: 10.1002/anie.201709437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 10/16/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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18
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Pereverzev AY, Kopysov V, Boyarkin OV. High Susceptibility of Histidine to Charge Solvation Revealed by Cold Ion Spectroscopy. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aleksandr Y. Pereverzev
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire; École Polytechnique Fédérale de Lausanne; 1015 Lausanne Switzerland
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19
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DeBlase AF, Harrilal CP, Lawler JT, Burke NL, McLuckey SA, Zwier TS. Conformation-Specific Infrared and Ultraviolet Spectroscopy of Cold [YAPAA+H]+ and [YGPAA+H]+ Ions: A Stereochemical “Twist” on the β-Hairpin Turn. J Am Chem Soc 2017; 139:5481-5493. [PMID: 28353347 DOI: 10.1021/jacs.7b01315] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P. Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John T. Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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20
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Sahu N, Gadre SR. Vibrational infrared and Raman spectra of polypeptides: Fragments-in-fragments within molecular tailoring approach. J Chem Phys 2017; 144:114113. [PMID: 27004868 DOI: 10.1063/1.4943966] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested out for the estimation of the above molecular properties for three isomers, viz., β-strand, 310- and α-helix of acetyl(alanine)nNH2 (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm(-1) is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine)20 and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.
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Affiliation(s)
- Nityananda Sahu
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
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21
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Stamm A, Maué D, Schaly A, Schlicher S, Bartl J, Kubik S, Gerhards M. Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues. Phys Chem Chem Phys 2017; 19:10718-10726. [DOI: 10.1039/c6cp08696a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Structural analyses of isolated cyclic tetrapeptides with varying amino acid residues were performed by applying combined IR/UV spectroscopy in the molecular beam and DFT calculations. The intrinsic structural properties especially with regard to the influence of different amino acid residues are fundamental for optimizing their binding ability.
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Affiliation(s)
- A. Stamm
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - D. Maué
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
| | - A. Schaly
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Schlicher
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - J. Bartl
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - S. Kubik
- TU Kaiserslautern
- Fachbereich Chemie
- Organische Chemie
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern
- Fachbereich Chemie & Research Center Optimas
- Physikalische Chemie
- D-67663 Kaiserslautern
- Germany
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22
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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23
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Otaki H, Yagi K, Ishiuchi SI, Fujii M, Sugita Y. Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations. J Phys Chem B 2016; 120:10199-10213. [DOI: 10.1021/acs.jpcb.6b06672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Shun-ichi Ishiuchi
- Laboratory
for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Masaaki Fujii
- Laboratory
for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Yuji Sugita
- RIKEN Advanced Institute for Computational Science, 7-1-26 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
- RIKEN Quantitative Biology Center, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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24
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Kopysov V, Makarov A, Boyarkin OV. Nonstatistical UV Fragmentation of Gas-Phase Peptides Reveals Conformers and Their Structural Features. J Phys Chem Lett 2016; 7:1067-1071. [PMID: 26950179 DOI: 10.1021/acs.jpclett.6b00292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Solving the 3D structure of a biomolecule requires recognition of its conformers and measurements of their individual structural identities, which can be compared with calculations. We employ the phenomenon of nonstatistical photofragmentation, detected by a combination of UV cold ion spectroscopy and high-resolution mass spectrometry, to identify the main conformers of gas-phase peptides and to recover individual UV absorption and mass spectra of all of these conformers in a single laser scan. We first validate this approach with a benchmark dipeptide, Tyr-Ala, and then apply it to a decapeptide, gramicidin S. The revealed characteristic structural difference between the conformers of the latter identifies some of the previously calculated structures of gramicidin S as the most likely geometries of its remaining unsolved conformer.
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Affiliation(s)
- Vladimir Kopysov
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific , Hanna-Kunath Str. 11, 28199 Bremen, Germany
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne , Station-6, 1015 Lausanne, Switzerland
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25
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Burke NL, DeBlase AF, Redwine JG, Hopkins JR, McLuckey SA, Zwier TS. Gas-Phase Folding of a Prototypical Protonated Pentapeptide: Spectroscopic Evidence for Formation of a Charge-Stabilized β-Hairpin. J Am Chem Soc 2016; 138:2849-57. [PMID: 26853832 DOI: 10.1021/jacs.6b00093] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - James G. Redwine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John R. Hopkins
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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26
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Dunbar RC, Martens J, Berden G, Oomens J. Complexes of Ni(ii) and Cu(ii) with small peptides: deciding whether to deprotonate. Phys Chem Chem Phys 2016; 18:26923-26932. [DOI: 10.1039/c6cp03974j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared multiple photon dissociation (IRMPD) spectroscopy differentiates two binding modes (iminol versus charge solvated) for Ni(ii) bound to model peptides.
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Affiliation(s)
| | - Jonathan Martens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Giel Berden
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
| | - Jos Oomens
- FELIX Laboratory
- Institute for Molecules and Materials
- Radboud University
- 6525ED Nijmegen
- The Netherlands
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27
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Roy TK, Sharma R, Gerber RB. First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments. Phys Chem Chem Phys 2016; 18:1607-14. [DOI: 10.1039/c5cp05979h] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data.
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Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- Central University of Rajasthan
| | - Rahul Sharma
- Department of Chemistry
- Indian Institute of Technology
- Roorkee
- India
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center
- The Hebrew University of Jerusalem
- Israel
- Department of Chemistry
- University of California
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28
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Sun Y, Vahidi S, Sowole MA, Konermann L. Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:31-40. [PMID: 26369778 DOI: 10.1007/s13361-015-1244-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/27/2015] [Accepted: 07/29/2015] [Indexed: 06/05/2023]
Abstract
The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments. ᅟ
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Affiliation(s)
- Yu Sun
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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29
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Zabuga AV, Kamrath MZ, Rizzo TR. Franck–Condon-like Progressions in Infrared Spectra of Biological Molecules. J Phys Chem A 2015; 119:10494-501. [DOI: 10.1021/acs.jpca.5b08801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
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30
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Sowole MA, Vuong S, Konermann L. Interactions of hemoglobin and myoglobin with their ligands CN(-), CO, and O2 monitored by electrospray ionization-mass spectrometry. Anal Chem 2015; 87:9538-45. [PMID: 26327529 DOI: 10.1021/acs.analchem.5b02506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Electrospray ionization (ESI)-mass spectrometry (MS) can provide information on protein-ligand interactions via detection of the corresponding complexes as gaseous ions. Unfortunately, some systems are prone to dissociation upon transfer into the gas phase. The reversible oxygen binding to hemoglobin (Hb) has been extensively studied in solution using a wide range of biophysical techniques. In addition to O2, ferrous (Fe(II)) Hb can bind CO. High affinity interactions with CN(-) are limited to the ferric (Fe(III)) state. In analogous fashion, CN(-), CO, and O2 bind to myoglobin (Mb). It remains unclear whether any of these ligand-bound forms can be observed by ESI-MS. In this work we demonstrate the successful detection of MbCN, while MbCO and MbO2 do not survive under ESI-MS conditions. Control experiments suggest that an older report of "MbO2" detection by ESI-MS may involve the misassignment of oxidation artifacts formed under corona discharge conditions. The situation is more favorable for ESI-MS studies on Hb. The most intense signal in the HbCN mass distribution corresponds to the expected complex with four cyanide moieties bound. Ligand loss during ESI-MS is around 20%. HbCO is detectable as well, albeit with a more noticeable level of ligand dissociation (∼50%) which produces the 2CO-bound state as the highest intensity ion in the spectrum. In addition, our data suggest that low levels of HbO2 can survive the transition into the gas phase, evident from +64 Da and +128 Da signals that can be assigned to Hb carrying two and four oxygen molecules, respectively. The application of collisional activation induces neutral ligand loss for all three Hb derivatives. It appears that this is the first report on the detection of MbCN, HbCO, and HbO2 in the gas phase. We hope that this work will pave the way towards future spectroscopic investigations of desolvated Mb and Hb, complementing the extensive literature on CN(-), CO, and O2 bound globins in the condensed phase.
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Affiliation(s)
- Modupeola A Sowole
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Stephanie Vuong
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario , London, Ontario N6A 5B7, Canada
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31
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Abstract
It is known that a C-terminal lysine stabilizes helix formation in polyalanine peptides that have seven or more residues. Using a combination of cold ion spectroscopy and DFT calculations, we demonstrate that even a three-residue peptide, Ac-Phe-Ala-LysH(+), adopts a structure in which the lysine side chain forms three hydrogen bonds with backbone carbonyls, reproducing the capping motif of larger polyalanine helices. This is confirmed by comparison with Ac-Phe-(Ala)5-LysH(+), which forms a 310 helix containing the same structural feature. In both molecules, we identified the vibrational bands of the N- and C-terminal amide NH stretches, which lack strong hydrogen bonds with carbonyls and consequently appear in a characteristic region above 3400 cm(-1). A similar pattern is also present in the even longer peptide Ac-Phe-(Ala)10-LysH(+), illustrating the generality of this capping motif. The two longer peptides contain additional, characteristic amide NH stretch bands below 3400 cm(-1), which form the core of the helix.
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Affiliation(s)
- Aleksandra V Zabuga
- 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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32
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Kopysov V, Makarov A, Boyarkin OV. Colors for Molecular Masses: Fusion of Spectroscopy and Mass Spectrometry for Identification of Biomolecules. Anal Chem 2015; 87:4607-11. [DOI: 10.1021/acs.analchem.5b00822] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Vladimir Kopysov
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Alexander Makarov
- Thermo Fisher Scientific, Hanna-Kunath
Strasse 11, 28199 Bremen, Germany
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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33
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Roy TK, Kopysov V, Nagornova NS, Rizzo TR, Boyarkin OV, Gerber RB. Conformational Structures of a Decapeptide Validated by First Principles Calculations and Cold Ion Spectroscopy. Chemphyschem 2015; 16:1374-8. [DOI: 10.1002/cphc.201500085] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/11/2022]
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34
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Voronina L, Rizzo TR. Spectroscopic studies of kinetically trapped conformations in the gas phase: the case of triply protonated bradykinin. Phys Chem Chem Phys 2015; 17:25828-36. [DOI: 10.1039/c5cp01651g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We explore conformational space of triply protonated bradykinin. Three conformational families are mobility-separated and spectroscopically characterized. Kinetically trapped structures are identified via annealing.
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Affiliation(s)
- Liudmila Voronina
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire
- École Polytechnique Fédérale de Lausanne
- EPFL SB ISIC LCPM
- CH-1015 Lausanne
- Switzerland
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35
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Shahangi F, Chermahini AN, Farrokhpour H, Teimouri A. Selective complexation of alkaline earth metal ions with nanotubular cyclopeptides: DFT theoretical study. RSC Adv 2015. [DOI: 10.1039/c4ra08302d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The interaction of alkaline earth metal cations including Be2+, Mg2+, Ca2+, Sr2+ and Ba2+ with cyclic peptides containing 3 or 4 (S) alanine molecules (CyAla3 and CyAla4) was investigated by density functional theory (DFT-CAM-B3LYP and DFT-B3LYP).
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Affiliation(s)
- Fereshte Shahangi
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | | | - Hossein Farrokhpour
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | - Abbas Teimouri
- Chemistry Department
- Payame Noor University
- 19395-4697 Tehran
- Iran
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36
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Zabuga AV, Kamrath MZ, Boyarkin OV, Rizzo TR. Fragmentation mechanism of UV-excited peptides in the gas phase. J Chem Phys 2014; 141:154309. [DOI: 10.1063/1.4897158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- 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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37
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Gregori B, Guidoni L, Chiavarino B, Scuderi D, Nicol E, Frison G, Fornarini S, Crestoni ME. Vibrational Signatures of S-Nitrosoglutathione as Gaseous, Protonated Species. J Phys Chem B 2014; 118:12371-82. [DOI: 10.1021/jp5072742] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Leonardo Guidoni
- Dipartimento
di Scienza Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio 2, Coppito, L’Aquila I-64100, Italy
| | | | - Debora Scuderi
- Laboratoire
de Chimie Physique, UMR8000 CNRS, Faculté des Sciences, Université Paris-Sud, Batiment 350, 91405 Orsay Cedex, France
| | - Edith Nicol
- Laboratoire
de Chimie Moléculaire, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
| | - Gilles Frison
- Laboratoire
de Chimie Moléculaire, Ecole Polytechnique and CNRS, 91128 Palaiseau Cedex, France
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38
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Kopysov V, Nagornova NS, Boyarkin OV. Identification of Tyrosine-Phosphorylated Peptides Using Cold Ion Spectroscopy. J Am Chem Soc 2014; 136:9288-91. [DOI: 10.1021/ja5053544] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vladimir Kopysov
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Natalia S. Nagornova
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire
de Chimie Physique
Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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39
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Kocak A, Sallese Z, Johnston MD, Metz RB. Vibrational Spectroscopy of Co+(CH4)n and Ni+(CH4)n (n = 1–4). J Phys Chem A 2014; 118:3253-65. [DOI: 10.1021/jp500617n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abdulkadir Kocak
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Zachary Sallese
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Michael D. Johnston
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Ricardo B. Metz
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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40
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41
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Dunbar RC. Spectroscopy of Metal-Ion Complexes with Peptide-Related Ligands. Top Curr Chem (Cham) 2014; 364:183-223. [DOI: 10.1007/128_2014_578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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42
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Nagornova NS, Rizzo TR, Boyarkin OV. Exploring the Mechanism of IR-UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins. Angew Chem Int Ed Engl 2013; 52:6002-5. [DOI: 10.1002/anie.201301656] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 11/11/2022]
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43
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Nagornova NS, Rizzo TR, Boyarkin OV. Exploring the Mechanism of IR-UV Double-Resonance for Quantitative Spectroscopy of Protonated Polypeptides and Proteins. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301656] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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44
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Durand S, Rossa M, Hernandez O, Paizs B, Maître P. IR Spectroscopy of b4 Fragment Ions of Protonated Pentapeptides in the X–H (X = C, N, O) Region. J Phys Chem A 2013; 117:2508-16. [DOI: 10.1021/jp400634t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sylvère Durand
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Maximiliano Rossa
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Oscar Hernandez
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
| | - Béla Paizs
- Computational Proteomics Group, German Cancer Research Center, Im Neuenheimer Feld
580, 69120 Heidelberg, Germany
- School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW,
U.K
| | - Philippe Maître
- Laboratoire de Chimie Physique,
Université Paris Sud, UMR8000 CNRS, Faculté des Sciences,
Bât. 350, 91405 Orsay Cedex, France
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45
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Frankevich V, Barylyuk K, Chingin K, Nieckarz R, Zenobi R. Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein. Chemphyschem 2013; 14:929-35. [DOI: 10.1002/cphc.201200959] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 01/22/2013] [Indexed: 01/19/2023]
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46
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Wolk AB, Garand E, Jones IM, Hamilton AD, Johnson MA. Quantifying Intrinsic Ion-Driven Conformational Changes in Diphenylacetylene Supramolecular Switches with Cryogenic Ion Vibrational Spectroscopy. J Phys Chem A 2013; 117:5962-9. [DOI: 10.1021/jp3111925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Arron B. Wolk
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, P.O. Box 208107, New
Haven, Connecticut 06520, United States
| | - Etienne Garand
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Ian M. Jones
- Department of Chemistry
and Biochemistry, The University of Texas at Austin, 1 University Station A5300, Austin, Texas
78712, United States
| | - Andrew D. Hamilton
- Department of Chemistry, University of Oxford, 12 Mansfield Road,
Oxford OX1 3TA, Great Britain
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Department of Chemistry, Yale University, P.O. Box 208107, New
Haven, Connecticut 06520, United States
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47
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Sohn WY, Ishiuchi SI, Miyazaki M, Kang J, Lee S, Min A, Choi MY, Kang H, Fujii M. Conformationally resolved spectra of acetaminophen by UV-UV hole burning and IR dip spectroscopy in the gas phase. Phys Chem Chem Phys 2013. [PMID: 23207427 DOI: 10.1039/c2cp43552g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electronic and vibrational spectra of acetaminophen were measured by using UV-UV hole burning (HB) and IR dip spectroscopy. HB spectra show the coexistence of 4 different species, which include two new ones. Low-frequency transitions in the spectra are reproduced by a one-dimensional periodic potential with a free-rotor basis set for the methyl group. From the analysis, we concluded that acetaminophen has two conformers and each conformer gives two independent transitions starting from the most stable 0a(1) and the hot 1e internal rotational levels. It is also found that the HB spectrum of the trans-conformer in the previous report is that from the 1e excited level, while the HB spectrum of the cis-conformer is contaminated by the transitions of the trans-conformer. Potential curves of the methyl rotational motion are determined both in S(0) and S(1).
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Affiliation(s)
- Woon Yong Sohn
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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48
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Papadopoulos G, Svendsen A, Boyarkin OV, Rizzo TR. Conformational distribution of bradykinin [bk + 2 H]2+ revealed by cold ion spectroscopy coupled with FAIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1173-81. [PMID: 22528205 DOI: 10.1007/s13361-012-0384-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Revised: 03/22/2012] [Accepted: 03/23/2012] [Indexed: 05/25/2023]
Abstract
We employ cold ion spectroscopy (CIS) in conjunction with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to study the peptide bradykinin in its doubly protonated charge state ([bk + 2 H](2+)). Using FAIMS, we partially separate the electrosprayed [bk + 2 H](2+) ions into two conformational families and selectively introduce one of them at a time into a cold ion trap mass spectrometer, where we probe them by UV photofragment spectroscopy. Although the two conformational families have distinct electronic spectra, some cross-conformer contamination can be observed under certain conditions. We demonstrate that this contamination comes from isomerization of ions energized during and/or after their separation and not from incomplete separation of the initially electrosprayed conformations in the FAIMS stage. By varying the injection voltage of the ions into our mass spectrometer, we can intentionally induce isomerization to produce what seems to be a gas phase equilibrium distribution of conformers. This distribution is different from the one produced initially by electrospray, indicating that some of the conformers are kinetically trapped and may be related to conformers that are more favored in solution.
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Affiliation(s)
- Georgios Papadopoulos
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
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49
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Wassermann TN, Boyarkin OV, Paizs B, Rizzo TR. Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1029-1045. [PMID: 22460621 DOI: 10.1007/s13361-012-0368-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/17/2012] [Accepted: 02/23/2012] [Indexed: 05/31/2023]
Abstract
We have applied conformer-selective infrared-ultraviolet (IR-UV) double-resonance photofragment spectroscopy at low temperatures in an ion trap mass spectrometer for the spectroscopic characterization of peptide fragment ions. We investigate b- and a-type ions formed by collision-induced dissociation from protonated leucine-enkephalin. The vibrational analysis and assignment are supported by nitrogen-15 isotopic substitution of individual amino acid residues and assisted by density functional theory calculations. Under such conditions, b-type ions of different size are found to appear exclusively as linear oxazolone structures with protonation on the N-terminus, while a rearrangement reaction is confirmed for the a (4) ion in which the side chain of the C-terminal phenylalanine residue is transferred to the N-terminal side of the molecule. The vibrational spectra that we present here provide a particularly stringent test for theoretical approaches.
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Affiliation(s)
- Tobias N Wassermann
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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50
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Rosu F, Gabelica V, De Pauw E, Antoine R, Broyer M, Dugourd P. UV Spectroscopy of DNA Duplex and Quadruplex Structures in the Gas Phase. J Phys Chem A 2012; 116:5383-91. [DOI: 10.1021/jp302468x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frédéric Rosu
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Valérie Gabelica
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Edwin De Pauw
- Département de Chimie, Université de Liège, Building B6c, 3, allée de la chimie, 4000 Liège, Belgium
| | - Rodolphe Antoine
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Michel Broyer
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
| | - Philippe Dugourd
- CNRS and Université Lyon 1, UMR5579, Boulevard du 11 novembre 1918, 69622 Villeurbanne, France
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