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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. Relationships between conformational and vibrational features of tryptophan characteristic Raman markers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 316:124377. [PMID: 38701580 DOI: 10.1016/j.saa.2024.124377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Tryptophan (Trp) residue provides characteristic vibrational markers to the middle wavenumber spectral region of the Raman spectra recorded from peptides and proteins. In this report, we were particularly interested in eight Trp Raman markers, referred to as Wi (i = 1,…,8). All responsible for pronounced Raman lines, these markers originate from indole moiety, a bicyclic conjugated segment involved in the Trp structure. Numerous investigations have previously attempted to relate the variations observed in the spectral features of these markers to the environmental changes of Trp residues. To emphasize the most important points we can mention (i) the variations in the Raman profile of W4 (∼1360 cm-1) and W5 (∼1340 cm-1), frequently observed as a doublet with variable intensity ratio. These two markers were thought to result from a Fermi-resonance effect between certain planar and nonplanar modes; (ii) the changes observed in the wavenumbers and relative intensities of W4, W7 (∼880 cm-1) and W8 (∼760 cm-1) were supposed to be related to the accessibility of Trp to surrounding water molecules; and (iii) the wavenumber fluctuations of W3 (∼1550 cm-1), taken as a Trp side chain orientational marker. However, some ambiguities still exist regarding the interpretation of these markers, needing further clarification. Herein, upon a joint experimental and theoretical analysis based on a multiconformational approach, attention was paid to the relationships between structural and vibrational features of three indole-containing compounds with increasing structural complexity, i.e., skatole (3-methylindole), tryptophan, and tripeptide Gly-Trp-Gly. This study clearly shows that the existing assignments given to certain Trp Raman markers should be reconsidered, especially those based on the Fermi-resonance origin of W4-W5 (∼1360-1340 cm-1) doublet, as well as the purely environmental dependence of W7 and W8 markers.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148. 74 rue Marcel Cachin. 93017 Bobigny Cédex France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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Sofińska K, Seweryn S, Skirlińska-Nosek K, Barbasz J, Lipiec E. Tip-enhanced Raman spectroscopy reveals the structural rearrangements of tau protein aggregates at the growth phase. NANOSCALE 2024; 16:5294-5301. [PMID: 38372161 DOI: 10.1039/d3nr06365h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Tau protein aggregates inside neurons in the course of Alzheimer's disease (AD). Because of the enormous number of people suffering from AD, this disease has become one of the world's major health and social problems. The presence of tau lesions clearly correlates with cognitive impairments in AD patients, thus, tau is the target of potential treatments for AD, next to amyloid-β. The exact mechanism of tau aggregation has not been understood in detail so far; especially little is known about the structural rearrangements of tau aggregates at the growth phase. The research into tau conformation at each step of the aggregation pathway will contribute to the design of effective therapeutic approaches. To follow the secondary structure of individual tau aggregates at the growth phase, we applied tip-enhanced Raman spectroscopy (TERS). The nanospectroscopic approach enabled us to follow the structure of individual aggregates occurring in the subsequent phases of tau aggregation. We applied multivariate data analysis to extract the spectral differences for tau aggregates at different aggregation phases. Moreover, atomic force microscopy (AFM) allowed the tracking of the morphological alterations for species occurring with the progression of tau aggregation.
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Affiliation(s)
- Kamila Sofińska
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
| | - Sara Seweryn
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Katarzyna Skirlińska-Nosek
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Krakow, Poland
| | - Jakub Barbasz
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Ewelina Lipiec
- Jagiellonian University, Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Łojasiewicza 11, 30-348 Krakow, Poland.
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Hernández B, Coïc YM, Kruglik SG, Sanchez-Cortes S, Ghomi M. The relationship between the tyrosine residue 850-830 cm -1 Raman doublet intensity ratio and the aromatic side chain χ 1 torsion angle. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123681. [PMID: 38039641 DOI: 10.1016/j.saa.2023.123681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Tyrosine (Tyr) residue in a peptide chain is characterized by the presence of seven Raman markers, referred to as Yi (i = 1, …, 7), distributed over the middle wavenumber spectral region. Particularly, the changes observed in the relative intensity of Y5 and Y6 markers, appearing as a side by side doublet at ca. 850-830 cm-1, has received a great attention. Primarily assigned to a Fermi-resonance effect between phenol ring planar and nonplanar modes, former density functional theory calculations led us to affiliate the Y5-Y6 doublet to two distinct fundamental modes. Furthermore, despite the previous assumptions, it was evidenced that the reversal of the doublet intensity ratio cannot be solely explained by hydrogen bonding on the phenol hydroxyl group involved in Tyr. Herein, upon analyzing the observed and theoretical data collected from the cationic species of the tripeptide Gly-Tyr-Gly, the crucial effect of the aromatic side chain orientation, especially that of the χ1 torsion angle defined around the CαCβ bond, on the Tyr doublet intensity ratio has been evidenced.
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Affiliation(s)
- Belén Hernández
- LVTS, INSERM U1148, 74 rue Marcel Cachin, 93017 Bobigny Cédex, France
| | - Yves-Marie Coïc
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Unité de Chimie des Biomolécules, F-75015 Paris, France
| | - Sergei G Kruglik
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Jean-Perrin, 4 Place Jussieu, 75005 Paris, France
| | | | - Mahmoud Ghomi
- Instituto de Estructura de la Materia, IEM-CSIC, Serrano 121, 28006 Madrid, Spain.
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Hudecová J, Kapitán J, Dračínský M, Michal P, Profant V, Bouř P. Structure of Zinc and Nickel Histidine Complexes in Solution Revealed by Molecular Dynamics and Raman Optical Activity. Chemistry 2022; 28:e202202045. [DOI: 10.1002/chem.202202045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Josef Kapitán
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
| | - Pavel Michal
- Department of Optics Palacký University 17. listopadu 12 771 46 Olomouc Czech Republic
| | - Václav Profant
- Faculty of Mathematics and Physics Charles University Ke Karlovu 5 121 16 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16000 Prague Czech Republic
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Amino acid side chain contribution to protein FTIR spectra: impact on secondary structure evaluation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:641-651. [PMID: 33558954 PMCID: PMC8189991 DOI: 10.1007/s00249-021-01507-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 01/25/2023]
Abstract
Prediction of protein secondary structure from FTIR spectra usually relies on the absorbance in the amide I–amide II region of the spectrum. It assumes that the absorbance in this spectral region, i.e., roughly 1700–1500 cm−1 is solely arising from amide contributions. Yet, it is accepted that, on the average, about 20% of the absorbance is due to amino acid side chains. The present paper evaluates the contribution of amino acid side chains in this spectral region and the potential to improve secondary structure prediction after correcting for their contribution. We show that the β-sheet content prediction is improved upon subtraction of amino acid side chain contributions in the amide I–amide II spectral range. Improvement is relatively important, for instance, the error of prediction of β-sheet content decreases from 5.42 to 4.97% when evaluated by ascending stepwise regression. Other methods tested such as partial least square regression and support vector machine have also improved accuracy for β-sheet content evaluation. The other structures such as α-helix do not significantly benefit from side chain contribution subtraction, in some cases prediction is even degraded. We show that co-linearity between secondary structure content and amino acid composition is not a main limitation for improving secondary structure prediction. We also show that, even though based on different criteria, secondary structures defined by DSSP and XTLSSTR both arrive at the same conclusion: only the β-sheet structure clearly benefits from side chain subtraction. It must be concluded that side chain contribution subtraction benefit for the evaluation of other secondary structure contents is limited by the very rough description of side chain absorbance which does not take into account the variations related to their environment. The study was performed on a large protein set. To deal with the large number of proteins present, we worked on protein microarrays deposited on BaF2 slides and FTIR spectra were acquired with an imaging system.
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Ota C, Suzuki H, Tanaka SI, Takano K. Spectroscopic Signature of the Steric Strains in an Escherichia coli RNase HI Cavity-Filling Destabilized Mutant Protein. J Phys Chem B 2019; 124:91-100. [DOI: 10.1021/acs.jpcb.9b09852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hikari Suzuki
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shun-ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto 606-8522, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto 606-8522, Japan
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Fujihara J, Nishimoto N, Yasuda T, Takeshita H. Discrimination Between Infant and Adult Bloodstains Using Micro-Raman Spectroscopy: A Preliminary Study. J Forensic Sci 2018; 64:698-701. [PMID: 30170335 DOI: 10.1111/1556-4029.13904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/30/2018] [Accepted: 08/17/2018] [Indexed: 11/29/2022]
Abstract
In the present study, we used micro-Raman spectroscopy with high-resolution analysis to discriminate between bloodstains from infants and bloodstains from adults. Raman peaks were detected at 674, 754, 976, 1002, 1105, 1127, 1176, 1248, 1340, 1368, 1390, 1560, and 1611 cm-1 ; these peaks were derived from hemoglobin, albumin, and glucose. However, a peak was obtained at 1105 cm-1 , which was assigned to histidine; this peak was observed only for bloodstains from adults. Human adult hemoglobin (HbA) is composed of an α2 β2 tetramer structure, whereas human fetal hemoglobin (HbF) is composed of an α2 γ2 . Therefore, the lack of a Raman peak at 1105 cm-1 in bloodstains from infants indicates the possibility of two histidine substitutions (His116Ile and His143Ser) in the γ chain of HbF. This study discriminates between bloodstains from infants and bloodstains from adults using micro-Raman spectroscopy, with beneficial implications in forensic science.
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Affiliation(s)
- Junko Fujihara
- Department of Legal Medicine, Shimane University School of Medicine, 89-1 Enya, Izumo, Shimane 693-8501, Japan
| | - Naoki Nishimoto
- Shimane Institute for Industrial Technology, 1 Hokuryo, Matsue, Japan
| | - Toshihiro Yasuda
- Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui 910-1193, Japan
| | - Haruo Takeshita
- Department of Legal Medicine, Shimane University School of Medicine, 89-1 Enya, Izumo, Shimane 693-8501, Japan
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9
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Pazderka T, Kopecký V. Drop coating deposition Raman spectroscopy of proteinogenic amino acids compared with their solution and crystalline state. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 185:207-216. [PMID: 28577510 DOI: 10.1016/j.saa.2017.05.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/03/2017] [Accepted: 05/20/2017] [Indexed: 06/07/2023]
Abstract
The Raman spectra of 20 proteinogenic amino acids were recorded in the solution, glass phase (as drop coating deposition Raman (DCDR) samples) and crystalline forms in the wide spectral range of 200-3200cm-1. The most apparent spectral differences between the Raman spectra of the crystalline forms, glass phases and aqueous solutions of amino acids were briefly discussed and described in the frame of published works. The possible density dependencies of spectral bands were noted. In some cases, a strong influence of the sample density, as well as of the organization of the water envelope, was observed. The most apparent changes were observed for Ser and Thr. Nevertheless, for the majority of amino acids, the DCDR sample form is an intermediate between the solution and crystalline forms. In contrast, aromatic amino acids have only a small sensitivity to the form of the sample. Our reference set of Raman spectra is useful for revealing discrepancies between the SERS and solid/solution spectra of amino acids. We also found that some previously published Raman spectra of polycrystalline samples resemble glassy state rather than crystalline spectra. Therefore, this reference set of spectra will find application in every branch of Raman spectroscopy where the spectra of biomolecules are collected from coatings.
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Affiliation(s)
- Tomáš Pazderka
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Vladimír Kopecký
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic.
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Hernández B, Pflüger F, Dauchez M, Ghomi M. Privileged hydration sites in aromatic side chains: effect on conformational equilibrium. Phys Chem Chem Phys 2017; 19:28684-28695. [DOI: 10.1039/c7cp04685e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The most energetically favourable hydration sites of aromatic (Phe, Tyr, Trp and His) side chains revealed by DFT-based theoretical calculations.
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Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
- Sorbonne Paris Cité
| | - Fernando Pflüger
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny cedex
| | - Manuel Dauchez
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)
- UMR 7369
- 51687 Reims Cedex 2
- France
- Sorbonne Paris Cité
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11
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Yamada D, Yamamoto J, Zhang Y, Iwata T, Hitomi K, Getzoff ED, Iwai S, Kandori H. Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase. Biochemistry 2016; 55:715-23. [PMID: 26719910 DOI: 10.1021/acs.biochem.5b01111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Yu Zhang
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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Hernández B, López-Tobar E, Sanchez-Cortes S, Coïc YM, Baron B, Chenal A, Kruglik SG, Pflüger F, Cohen R, Ghomi M. From bulk to plasmonic nanoparticle surfaces: the behavior of two potent therapeutic peptides, octreotide and pasireotide. Phys Chem Chem Phys 2016; 18:24437-50. [DOI: 10.1039/c6cp04421b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural dynamics of two potent somatostatin analogues in an aqueous environment and their binding sites on plasmonic nanoparticles were described.
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Affiliation(s)
- Belén Hernández
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | | | | | - Yves-Marie Coïc
- Institut Pasteur
- Unité de Chimie des Biomolécules
- UMR 3523
- 75724 Paris Cedex 15
- France
| | - Bruno Baron
- Institut Pasteur
- Plate-Forme de Biophysique de Macromolécules et de leurs Interactions
- 75724 Paris Cedex 15
- France
| | - Alexandre Chenal
- Institut Pasteur
- Unité Biochimie des Interactions Macromoléculaires
- UMR CNRS 3528
- 75724 Paris Cedex 15
- France
| | - Sergei G. Kruglik
- Sorbonne Universités
- UPMC Univ. Paris 06
- UMR 8237
- Laboratoire Jean Perrin
- 75005 Paris
| | - Fernando Pflüger
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
| | - Régis Cohen
- Service d’Endocrinologie
- Centre Hospitalier de Saint-Denis
- 93200 Saint-Denis
- France
| | - Mahmoud Ghomi
- Sorbonne Paris Cité
- Université Paris 13
- Groupe de Biophysique Moléculaire
- UFR Santé-Médecine-Biologie Humaine
- 93017 Bobigny Cedex
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
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Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
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14
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Bermúdez C, Mata S, Cabezas C, Alonso JL. Tautomerism in Neutral Histidine. Angew Chem Int Ed Engl 2014; 53:11015-8. [DOI: 10.1002/anie.201405347] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Indexed: 11/10/2022]
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15
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16
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Protonation–deprotonation of the glycine backbone as followed by Raman scattering and multiconformational analysis. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Hoffman KW, Romei MG, Londergan CH. A New Raman Spectroscopic Probe of Both the Protonation State and Noncovalent Interactions of Histidine Residues. J Phys Chem A 2013; 117:5987-96. [DOI: 10.1021/jp311815k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Kevin W. Hoffman
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
| | - Matthew G. Romei
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United
States
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18
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Wächtler M, Bräutigam M, Popp J, Dietzek B. Mechanism of protonation induced changes in Raman spectra of a trisheteroleptic ruthenium complex revealed by DFT calculations. RSC Adv 2013. [DOI: 10.1039/c3ra00157a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
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20
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Balakrishnan G, Jarzecki AA, Wu Q, Kozlowski PM, Wang D, Spiro TG. Mode recognition in UV resonance Raman spectra of imidazole: histidine monitoring in proteins. J Phys Chem B 2012; 116:9387-95. [PMID: 22779777 DOI: 10.1021/jp305083t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The imidazole side-chains of histidine residues perform key roles in proteins, and spectroscopic markers are of great interest. The imidazole Raman spectrum is subject to resonance enhancement at UV wavelengths, and a number of UVRR markers of structure have been investigated. We report a systematic experimental and computational study of imidazole UVRR spectra, which elucidates the band pattern, and the effects of protonation and deprotonation, of H/D exchange, of metal complexation, and of addition of a methyl substituent, modeling histidine itself. A consistent assignment scheme is proposed, which permits tracking of the bands through these chemical variations. The intensities are dominated by normal mode contributions from stretching of the strongest ring bonds, C(2)N and C(4)C(5), consistent with enhancement via resonance with a dominant imidazole π-π* transition.
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Ghosh A, Tucker MJ, Hochstrasser RM. Identification of arginine residues in peptides by 2D-IR echo spectroscopy. J Phys Chem A 2011; 115:9731-8. [PMID: 21539337 PMCID: PMC3162110 DOI: 10.1021/jp201794n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The CN stretching vibrations of the guanidyl group in the arginine dipeptide side chain are examined by two-dimensional infrared spectroscopy. In D(2)O, the spectra display two distinct diagonal peaks. These nearly degenerate modes undergo ultrafast energy transfer. The energy-transfer rate was determined directly from the 2D-IR spectra to be 1/2.1 ps(-1). The cross peaks in 2D-IR arising from the energy transfer provide a definitive identification of arginine in larger proteins. An example of arginine in the transmembrane protein M2, found in influenza viruses, is given.
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Affiliation(s)
- Ayanjeet Ghosh
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Robin M. Hochstrasser
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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22
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Hernández B, Pflüger F, Adenier A, Nsangou M, Kruglik SG, Ghomi M. Energy maps, side chain conformational flexibility, and vibrational features of polar amino acidsL-serine andL-threonine in aqueous environment. J Chem Phys 2011; 135:055101. [DOI: 10.1063/1.3617415] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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23
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Zhu G, Zhu X, Fan Q, Wan X. Raman spectra of amino acids and their aqueous solutions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:1187-95. [PMID: 21242101 DOI: 10.1016/j.saa.2010.12.079] [Citation(s) in RCA: 259] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 12/24/2010] [Accepted: 12/25/2010] [Indexed: 05/14/2023]
Abstract
Amino acids are the basic "building blocks" that combine to form proteins and play an important physiological role in all life-forms. Amino acids can be used as models for the examination of the importance of intermolecular bonding in life processes. Raman spectra serve to obtain information regarding molecular conformation, giving valuable insights into the topology of more complex molecules (peptides and proteins). In this paper, amino acids and their aqueous solution have been studied by Raman spectroscopy. Comparisons of certain values for these frequencies in amino acids and their aqueous solutions are given. Spectra of solids when compared to those of the solute in solution are invariably much more complex and almost always sharper. We present a collection of Raman spectra of 18 kinds of amino acids (L-alanine, L-arginine, L-aspartic acid, cystine, L-glutamic acid, L-glycine, L-histidine, L-isoluecine, L-leucine, L-lysine, L-phenylalanine, L-methionone, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, L-valine) and their aqueous solutions that can serve as references for the interpretation of Raman spectra of proteins and biological materials.
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Affiliation(s)
- Guangyong Zhu
- Department of Chemical Engineering, Shanghai University, Shanghai, PR China
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24
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Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Side chain flexibility and protonation states of sulfur atom containing amino acids. Phys Chem Chem Phys 2011; 13:17284-94. [DOI: 10.1039/c1cp21054h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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25
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Hernández B, Pflüger F, Adenier A, Kruglik SG, Ghomi M. Vibrational Analysis of Amino Acids and Short Peptides in Hydrated Media. VIII. Amino Acids with Aromatic Side Chains: l-Phenylalanine, l-Tyrosine, and l-Tryptophan. J Phys Chem B 2010; 114:15319-30. [DOI: 10.1021/jp106786j] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Belén Hernández
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Fernando Pflüger
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Alain Adenier
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Sergei G. Kruglik
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
| | - Mahmoud Ghomi
- Groupe de Biophysique Moléculaire, UFR SMBH, Université Paris 13, 74 rue Marcel Cachin, 93017 Bobigny cedex, France; Laboratoire ITODYS, UMR 7086, Université Paris Diderot, Bâtiment Lavoisier, 15, rue Jean-Antoine de Baïf, 75205 Paris cedex 13, France; and Laboratoire Acides Nucléiques et Biophotonique (FRE 3207), Université Pierre et Marie Curie Paris 06, 75252 Paris, France
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