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Fu W, Chi H, Dai X, Zhu H, Mesias VSD, Liu W, Huang J. Efficient optical plasmonic tweezer-controlled single-molecule SERS characterization of pH-dependent amylin species in aqueous milieus. Nat Commun 2023; 14:6996. [PMID: 37914718 PMCID: PMC10620188 DOI: 10.1038/s41467-023-42812-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
It is challenging to characterize single or a few biomolecules in physiological milieus without excluding the influences of surrounding environment. Here we utilize optical plasmonic trapping to construct a dynamic nanocavity, which reduces the diffraction-limited detection volume and provides reproducible electromagnetic field enhancements to achieve high-throughput single-molecule surface-enhanced Raman spectroscopy (SERS) characterizations in aqueous environments. Specifically, we study human Islet Amyloid Polypeptide (amylin, hIAPP) under different physiological pH conditions by combining spectroscopic experiments and molecular dynamics (MD) simulations. Based on a statistically significant amount of time-dependent SERS spectra, two types of low-populated transient species of hIAPP containing either turn or β-sheet structure among its predominant helix-coil monomers are characterized during the early-stage incubation at neutral condition, which play a crucial role in driving irreversible amyloid fibril developments even after a subsequent adjustment of pH to continue the prolonged incubation at acidic condition. Our results might provide profound mechanistic insight into the pH-regulated amyloidogenesis and introduce an alternative approach for investigating complex biological processes at the single-molecule level.
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Affiliation(s)
- Wenhao Fu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Huanyu Chi
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Xin Dai
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK, Hong Kong Science Park, Hong Kong, China
| | - Hongni Zhu
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Vince St Dollente Mesias
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Wei Liu
- State Key Laboratory of Synthetic Chemistry, Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
| | - Jinqing Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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2
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Pezzotti G, Boschetto F, Ohgitani E, Fujita Y, Shin‐Ya M, Adachi T, Yamamoto T, Kanamura N, Marin E, Zhu W, Nishimura I, Mazda O. Raman Molecular Fingerprints of SARS-CoV-2 British Variant and the Concept of Raman Barcode. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103287. [PMID: 34877818 PMCID: PMC8787433 DOI: 10.1002/advs.202103287] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/04/2021] [Indexed: 06/12/2023]
Abstract
The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub-types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK-521), and found bold vibrational differences. These included: i) fractions of sulfur-containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
- Department of Orthopedic SurgeryTokyo Medical University6‐7‐1 Nishi‐Shinjuku, Shinjuku‐kuTokyo160‐0023Japan
- The Center for Advanced Medical Engineering and InformaticsOsaka University2‐2 Yamadaoka, SuitaOsaka565‐0854Japan
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University2‐3‐10 Kanda‐Surugadai, Chiyoda‐kuTokyo101‐0062Japan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Francesco Boschetto
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Eriko Ohgitani
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Yuki Fujita
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
| | - Masaharu Shin‐Ya
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
| | - Tetsuya Adachi
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Toshiro Yamamoto
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Narisato Kanamura
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Elia Marin
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
- Department of Dental MedicineGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐kuKyoto602‐8566Japan
| | - Wenliang Zhu
- Ceramic Physics LaboratoryKyoto Institute of TechnologySakyo‐ku, MatsugasakiKyoto606‐8585Japan
| | - Ichiro Nishimura
- Division of Advanced ProsthodonticsThe Jane and Jerry Weintraub Center for Reconstructive BiotechnologyUCLA School of DentistryLos AngelesCA90095USA
| | - Osam Mazda
- Department of ImmunologyGraduate School of Medical ScienceKyoto Prefectural University of MedicineKamigyo‐ku, 465 Kajii‐choKyoto602‐8566Japan
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3
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Macha P, Mayes ML, Visayas BRB, Soni V, Sammeta VR, Vasudev MC. Influence of dityrosine nanotubes on the expression of dopamine and differentiation in neural cells. J Mater Chem B 2021; 9:3900-3911. [PMID: 33928965 DOI: 10.1039/d0tb02680h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study, we report the synthesis of self-assembled dityrosine nanotubes as a biologically functional scaffold and their interactions with neural cells. Quantum chemical methods were used to determine the forces involved in the self-assembly process. The physicochemical properties of the nanostructures relevant to their potential as bioactive scaffolds were characterized. The morphology, secondary structure, crystallinity, mechanical properties, and thermal characteristics of YY nanotubes were analyzed. The influence of these nanotubes as scaffolds for neural cells was studied in vitro to understand their effects on cell proliferation, morphology, and gene expression. The scanning electron microscopy and fluorescence confocal microscopy demonstrated the feasibility of nanotube scaffolds for enhanced adhesion to rat and human neural cells (PC12 and SH-SY5Y). Preliminary ELISA and qPCR analyses demonstrate the upregulation of dopamine synthesis and genes involved in dopamine expression and differentiation. The expression levels of DβH, AADC, VMAT2 and MAOA in SH-SY5Y cells cultured on the nanotube scaffolds for 7 days were elevated in comparison to the control cells.
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Affiliation(s)
- Prathyushakrishna Macha
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA.
| | - Maricris L Mayes
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Benjoe Rey B Visayas
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Vikas Soni
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA. and Department of Mechanical Engineering, George Washington University, DC 20052, USA
| | | | - Milana C Vasudev
- Department of Bioengineering, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA.
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4
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Hamedani Y, Macha P, Evangelista EL, Sammeta VR, Chalivendra V, Rasapalli S, Vasudev MC. Electrospinning of tyrosine‐based oligopeptides: Self‐assembly or forced assembly? J Biomed Mater Res A 2019; 108:829-838. [DOI: 10.1002/jbm.a.36861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 01/14/2023]
Affiliation(s)
- Yasaman Hamedani
- Department of Bioengineering University of Massachusetts Dartmouth Dartmouth Massachusetts
- Biomedical Engineering and Biotechnology Program University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Prathyushakrishna Macha
- Department of Bioengineering University of Massachusetts Dartmouth Dartmouth Massachusetts
- Biomedical Engineering and Biotechnology Program University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Elvira L. Evangelista
- Department of Bioengineering University of Massachusetts Dartmouth Dartmouth Massachusetts
- Biomedical Engineering and Biotechnology Program University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Vamshikrishna R. Sammeta
- Department of Chemistry and Biochemistry University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Vijaya Chalivendra
- Department of Mechanical Engineering University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Sivappa Rasapalli
- Department of Chemistry and Biochemistry University of Massachusetts Dartmouth Dartmouth Massachusetts
| | - Milana C. Vasudev
- Department of Bioengineering University of Massachusetts Dartmouth Dartmouth Massachusetts
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5
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Macha P, Perreault L, Hamedani Y, Mayes ML, Vasudev MC. Molecular Mechanisms of Tryptophan–Tyrosine Nanostructures Formation and their Influence on PC-12 Cells. ACS APPLIED BIO MATERIALS 2018; 1:1266-1275. [DOI: 10.1021/acsabm.8b00121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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6
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Belyanchikov MA, Gorelik VS, Gorshunov BP, Pyatyshev AY. Laser spectroscopy and dynamics of crystal lattices of chirally pure and racemic phases of amino acids. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517020079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Sereda V, Lednev IK. Two Mechanisms of Tip Enhancement of Raman Scattering by Protein Aggregates. APPLIED SPECTROSCOPY 2017; 71:118-128. [PMID: 27407009 DOI: 10.1177/0003702816651890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for probing the surface of biological species with nanometer spatial resolution. Here, we report the TER spectra of an individual insulin fibril, the protein cast film and a short peptide (LVEALYL) microcrystal mimicking the fibril core. Two different types of TER spectra were acquired depending on the "roughness" of the probed surface at the molecular level. A fully reproducible, low-intensity, normal Raman-type spectrum was characteristic of the top flat surface of the microcrystal while highly variable, higher intensity TER spectra were obtained for the edges of the microcrystal, cast film, and fibril. As a result, two tip enhancement mechanisms of Raman scattering, long- and short-range, were proposed by analogy with the physical and chemical enhancement mechanisms, respectively, known for surface-enhanced Raman spectroscopy.
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8
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Tah B, Dutta D, Pal P, Talapatra GB, Mishra S. QM/MM simulation of the amide-I band in the Raman spectrum of insulin. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1170220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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9
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Sereda V, Sawaya MR, Lednev IK. Structural Organization of Insulin Fibrils Based on Polarized Raman Spectroscopy: Evaluation of Existing Models. J Am Chem Soc 2015; 137:11312-20. [DOI: 10.1021/jacs.5b07535] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Valentin Sereda
- Department
of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Michael R. Sawaya
- UCLA−DOE Institute, 611 Charles
E. Young Drive, Los Angeles, California 90095-1570, United States
| | - Igor K. Lednev
- Department
of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, New York 12222, United States
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10
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11
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Degtyar E, Mlynarczyk B, Fratzl P, Harrington MJ. Recombinant engineering of reversible cross-links into a resilient biopolymer. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.03.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Yao G, Zhang J, Huang Q. Conformational and vibrational analyses of meta-tyrosine: An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:111-123. [PMID: 26125991 DOI: 10.1016/j.saa.2015.06.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
M-tyrosine is one kind of positional isomer of tyrosine which is widely applied in agrichemical, medicinal chemistry, and food science. However, the structural and vibrational features of m-tyrosine have not been reported or systematically investigated. In this work, potential energy surface (PES) calculations were used for searching and determining the stable zwitterionic conformers of m-tyrosine, and the Raman spectra of m-tyrosine and deuterated m-tyrosine were measured and interpreted based on theoretical computation. For the spectral simulation, several DFT-based quantum chemistry (QC) methods were employed, and the M06-2X functional with SMD solvent model was found to be best in reproducing the Raman spectra and geometrical property. As such, this study has not only presented a detailed study of m-tyrosine's vibrational property which is lack in the literature, but also may shed some light on the optimal choice of QC methods for calculation of conformations and vibrational properties of zwitterionic amino acids.
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Affiliation(s)
- Guohua Yao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Jingjing Zhang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Qing Huang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China; University of Science & Technology of China, Hefei, Anhui 230026, PR China.
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13
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Sereda V, Lednev IK. Polarized Raman Spectroscopy of Aligned Insulin Fibrils. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2014; 45:665-671. [PMID: 25316956 PMCID: PMC4194063 DOI: 10.1002/jrs.4523] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Amyloid fibrils are associated with many neurodegenerative diseases. The application of conventional techniques of structural biology, X-ray crystallography and solution NMR, for fibril characterization is limited because of the non-crystalline and insoluble nature of the fibrils. Here, polarized Raman spectroscopy was used to determine the orientation of selected chemical groups in aligned insulin fibrils, specifically of peptide carbonyls. The methodology is solely based on the measurement of the change in Raman scattered intensity as a function of the angle between the incident laser polarization and the aligned fibrils. The order parameters 〈 P2 〉 and 〈 P4 〉 of the orientation distribution function were obtained, and the most probable distribution of C=O group orientation was calculated. The results indicate that the peptides' carbonyl groups are oriented at an angle of 13±5° from the fibril axis, which is in consistent with previously reported qualitative descriptions of an almost parallel orientation of the C=O groups relative to the main fibril axis.
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Affiliation(s)
- Valentin Sereda
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Igor K. Lednev
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
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14
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Profantová B, Profant V, Zíma V, Kopecký V, Bednárová L, Zentz C, Baumruk V, Turpin PY, Štěpánek J. Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study. J Phys Chem B 2013; 117:16086-95. [DOI: 10.1021/jp4099864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barbora Profantová
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
- Laboratoire
Jean Perrin, FRE 3231, Université Pierre et Marie Curie, place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Václav Profant
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Vlastimil Zíma
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Vladimír Kopecký
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Lucie Bednárová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Christian Zentz
- ER12, Université Pierre et Marie Curie, Place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Vladimír Baumruk
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
| | - Pierre-Yves Turpin
- Laboratoire
Jean Perrin, FRE 3231, Université Pierre et Marie Curie, place Jussieu 4, 75252 Paris CEDEX 5, France
| | - Josef Štěpánek
- Institute
of Physics, Faculty of Mathematics and Physics, Charles University in Prague, Ke Karlovu 5, 121 16 Prague 2, Czech Republic
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15
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Rodríguez-Pérez JC, Hamley IW, Squires AM. Determination of orientations of aromatic groups in self-assembled peptide fibrils by polarised Raman spectroscopy. Phys Chem Chem Phys 2013; 15:13940-50. [PMID: 23852406 DOI: 10.1039/c3cp52595c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this paper we describe a novel combination of Raman spectroscopy, isotope editing and X-ray scattering as a powerful approach to give detailed structural information on aromatic side chains in peptide fibrils. The orientation of the tyrosine residues in fibrils of the peptide YTIAALLSPYS with respect to the fibril axis has been determined from a combination of polarised Raman spectroscopy and X-ray diffraction measurements. The Raman intensity of selected tyrosine bands collected at different polarisation geometries is related to the values and orientation of the Raman tensor for those specific vibrations. Using published Raman tensor values we solved the relevant expressions for both of the two tyrosine residues present in this peptide. Ring deuteration in one of the two tyrosine side chains allowed for the calculation to be performed individually for both, by virtue of the isotopic shift that eliminates band overlapping. Sample disorder was taken into account by obtaining the distribution of orientations of the samples from X-ray diffraction experiments. The results provide previously unavailable details about the molecular conformation of this peptide, and demonstrate the value of this approach for the study of amyloid fibrils.
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16
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Li L, Hutter T, Steiner U, Mahajan S. Single molecule SERS and detection of biomolecules with a single gold nanoparticle on a mirror junction. Analyst 2013; 138:4574-8. [PMID: 23748709 DOI: 10.1039/c3an00447c] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Using the bianalyte method we unambiguously demonstrate that a single gold nanosphere on a metal film junction, in the so-called nanoparticle on a mirror configuration, is capable of single molecule detection with surface-enhanced Raman spectroscopy (SERS). Also this configuration serves as a convenient and highly sensitive SERS sensor for detection of biomolecules. Such simple nano-junction based systems are ideal for chemical and biomedical analysis.
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Affiliation(s)
- Li Li
- Institute for Life Sciences, Highfield Campus, University of Southampton, SO17 1BJ, UK
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17
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Lekprasert B, Korolkov V, Falamas A, Chis V, Roberts CJ, Tendler SJB, Notingher I. Investigations of the Supramolecular Structure of Individual Diphenylalanine Nano- and Microtubes by Polarized Raman Microspectroscopy. Biomacromolecules 2012; 13:2181-7. [DOI: 10.1021/bm3005929] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - Vasile Chis
- Faculty of Physics, Babes Bolyai University, Cluj-Napoca, Romania
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18
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Lamshöft M, Ivanova B. Protonation and coordination ability of small peptides – theoretical and experimental approaches for elucidation. J COORD CHEM 2011. [DOI: 10.1080/00958972.2011.598926] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Marc Lamshöft
- a Institute of Environmental Research of the Faculty of Chemistry, Dortmund University of Technology , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Bojidarka Ivanova
- a Institute of Environmental Research of the Faculty of Chemistry, Dortmund University of Technology , Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
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19
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Hamley IW, Castelletto V, Moulton CM, Rodríguez-Pérez J, Squires AM, Eralp T, Held G, Hicks MR, Rodger A. Alignment of a Model Amyloid Peptide Fragment in Bulk and at a Solid Surface. J Phys Chem B 2010; 114:8244-54. [DOI: 10.1021/jp101374e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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20
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Desamero RZB, Kang J, Dol C, Chinwong J, Walters K, Sivarajah T, Profit AA. Spectroscopic characterization of the SH2- and active site-directed peptide sequences of a bivalent Src kinase inhibitor. APPLIED SPECTROSCOPY 2009; 63:767-774. [PMID: 19589214 DOI: 10.1366/000370209788701125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The spectral properties of the SH2 and active site-directed sequences of the bivalent Src kinase inhibitor Ac-EELL(F5)Phe-(GABA)3-pYEEIE-amide (1) have been determined. Ac-pYEEIE-amide (2) and AcEELL(F5)Phe-amide (3), as well as the amino acids phosphotyrosine (pTyr) and pentafluorophenylalanine (F5)Phe, have been characterized by electronic absorption, fluorescence, and vibrational spectroscopy. Specific and unique marker bands that originate from the phosphate group of pTyr and the fluorinated aromatic ring of (F5)Phe have been identified, with the latter showing some solvent dependence. Peptide 2 was found to have excitation and emission wavelengths emanating from pTyr at 268 and 295 nm, respectively, whereas peptide 3 displayed excitation and emission peaks attributable to (F5)Phe at 274 and 315 nm, respectively. Fourier transform infrared (FT-IR) analysis of the amino acid pTyr identified distinct marker bands at approximately 930, 1090, and 1330 cm(-1) that could be attributed to the phosphate group. These markers were also observed in the IR spectrum of peptide 2. Likewise, peptide 3 displayed a characteristic C-F stretching mode at 961 cm(-1) due to the presence of (F5)Phe, including two C-F reporting ring modes at 1509 and 1527 cm(-1). Identifying and monitoring spectroscopic changes in these marker bands may afford a means to observe the molecular interactions that occur when peptides 1-3 bind to the Src kinase.
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Affiliation(s)
- Ruel Z B Desamero
- The Graduate Center, The City University of New York, 94-20 Guy R. Brewer Boulevard, Jamaica, New York 11451, USA.
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Tsuboi M, Benevides JM, Thomas GJ. Raman tensors and their application in structural studies of biological systems. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2009; 85:83-97. [PMID: 19282645 PMCID: PMC3524303 DOI: 10.2183/pjab.85.83] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Accepted: 01/13/2009] [Indexed: 05/27/2023]
Abstract
The Raman scattering of a molecule is generated by interactions of its electrons with incident light. The electric vector of the Raman scattered light is related to the electric vector of the incident light through a characteristic Raman tensor. A unique Raman tensor exists for each Raman-active molecular vibrational mode. In the case of biologically important macromolecules Raman tensors have been determined for a few hundred vibrational Raman bands. These include proteins and their amino acid constituents, as well as nucleic acids (DNA and RNA) and their nucleotide constituents. In this review Raman tensors for 39 representative vibrational Raman bands of biological molecules are considered. We present details of the Raman tensor determinations and discuss their application in structural studies of filamentous bacteriophages (fd, Pf1, Pf3 and PH75), fowl feather rachis and eyespots of the protists, Chlamydomonas and Euglena.
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Ivanova BB. Aromatic dipeptides and their salts--solid-state linear-dichroic infrared (IR-LD) spectral analysis and ab initio calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 70:324-331. [PMID: 18029224 DOI: 10.1016/j.saa.2007.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 09/12/2007] [Indexed: 05/25/2023]
Abstract
Stereo-structural analysis and IR-bands assignment of the aromatic dipeptides L-tryrosyl-L-phenylalanine (Tyr-Phe), L-phenylalanyl-L-tyrosine (Phe-Tyr) and their hydrochloride salts have been carried out by means of IR-LD spectroscopy of oriented as nematic liquid crystal suspension solid samples. The experimental data are compared with known crystallographic ones and theoretical predicted geometries at RHF/ and UHF/6-31G**.
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Affiliation(s)
- Bojidarka B Ivanova
- Sofia University St. Kl. Ohridski, Faculty of Chemistry, 1164 Sofia, Bulgaria.
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23
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Kolev T, Koleva BB, Spiteller M. Copper(II) complexes with hydroxyl-containing dipeptides glycyl- L -serine and L -seryl- L -tyrosine. J COORD CHEM 2008. [DOI: 10.1080/00958970701787687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Tsonko Kolev
- a Institut für Umweltforschung, Universität Dortmund , Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Bojidarka B. Koleva
- b Lehrstuhl für Analytische Chemie, Ruhr-Universität Bochum, Universitätsstraße 150 , 44780 Bochum, Germany
| | - Michael Spiteller
- a Institut für Umweltforschung, Universität Dortmund , Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
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24
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Tfayli A, Piot O, Draux F, Pitre F, Manfait M. Molecular characterization of reconstructed skin model by Raman microspectroscopy: comparison with excised human skin. Biopolymers 2007; 87:261-74. [PMID: 17763468 DOI: 10.1002/bip.20832] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human skin is directly exposed to different exogenous agents. Many research works have studied the diffusion, interactions, absorption mechanisms, and/or toxicity of these agents toward different cutaneous structures. With the use of living animals for such tests being more and more rejected; and the number of human volunteers being limited; different types of skin models are used. In the last few years, reconstructed epidermis from cell cultures has been frequently employed, and recent changes in the European chemical policy have approved and encouraged the use of these reconstructed models for skin-related research works and assessments. Among the techniques used actually to study the skin, Raman microspectroscopy is a rising and powerful nondestructive technique that detects characteristic molecular vibrations. In this study, we created a spectral database to index the vibration peaks and bands of a well-known reconstructed epidermis model, the Episkin. The comparison with a native epidermis signal enabled us to put in evidence several spectral differences associated with molecular and structural differences between the skin and the reconstructed model, both maintained in living conditions. In addition to that, we have showed the feasibility of tracking the penetration of a pharmaceutical molecule through the Episkin model. (
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Affiliation(s)
- Ali Tfayli
- MeDIAN Unit, CNRS UMR 6142, Faculty of Pharmacy, University of Reims Champagne-Ardenne, France
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25
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Yokote Y, Kubo Y, Takahashi R, Ikeda T, Akahane K, Tsuboi M. Structural Details of a Fowl Feather Elucidated by Using Polarized Raman Microspectroscopy. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007. [DOI: 10.1246/bcsj.80.1148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Tfayli A, Piot O, Pitre F, Manfait M. Follow-up of drug permeation through excised human skin with confocal Raman microspectroscopy. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:1049-58. [PMID: 17565493 DOI: 10.1007/s00249-007-0191-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 05/09/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Skin is a multilayered organ which covers and protects the surface of human body by providing a barrier function against exogenous agents. Meanwhile, the efficacy of several topically applicated drugs is directly related to their penetration through the skin barrier. Several techniques are commonly used to evaluate the rate, the speed and the depth of penetration of these drugs, but few of them can provide real-time results. Therefore, the use of nondestructive and structurally informative techniques permits a real breakthrough in the investigations on skin penetration at a microscopic scale. Confocal Raman microspectroscopy is a nondestructive and rapid technique which allows information to be obtained from deep layers under the skin surface, giving the possibility of a real-time tracking of the drug in the skin layers. The specific Raman signature of the drug enables its identification in the skin. In this study, we try to follow the penetration of Metronidazole, a drug produced by Galderma as a therapeutic agent for Rosacea treatment, through the skin. The first step was the spectral characterization of Metronidazole in the skin. Then micro-axial profiles were conducted to follow the penetration of the drug in the superficial layers, on excised human skin specimens. For more accurate information, transverse sections were cut from the skin and spectral images were conducted, giving information down to several millimeters deep. Moreover, the collected spectra permit us to follow the structural modifications, induced by the Metronidazole on the skin, by studying the changes in the spectral signature of the skin constituents.
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Affiliation(s)
- Ali Tfayli
- MeDIAN Unit, CNRS UMR 6142, Faculty of Pharmacy, University of Reims Champagne, Ardenne, France
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27
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Koleva B, Kolev T, Spiteller M. Mononuclear Au(III)-complexes with tryptophan-containing dipeptides: Synthesis, spectroscopic and structural elucidation. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2006.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Ivanova BB. IR-LD spectroscopic characterization of L-Tryptophan containing dipeptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 64:931-8. [PMID: 16488186 DOI: 10.1016/j.saa.2005.08.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2005] [Revised: 08/30/2005] [Accepted: 08/31/2005] [Indexed: 05/06/2023]
Abstract
IR-spectroscopic and stereo-structural analysis of aromatic l-Tryptophan containing dipeptides l-Tryptophan-l-Tryptophan (Trp-Trp), l-Tyrosine-l-Tryptophan (Tyr-Trp) and cyclo(Trp-Trp) have been carried out by means of solid-state linear-dichroic infrared (IR-LD) spectroscopy of oriented as suspension in nematic liquid crystal solids. The experimental data have been compared with analogous ones of the simple amino acids l-Tyrosnine (l-Tyr) and l-Tryptophan (l-Trp). In cyclo(Trp-Trp), the IR-spectral changes towards the IR-ones of acyclic Trp-Trp have been determined. A theoretical analysis of Tyr-Trp at Hartree-Fock level of theory and 6-31G** basis set is also applied.
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Affiliation(s)
- Bojidarka B Ivanova
- Sofia University "St. Kl. Ohridski", Faculty of Chemistry, 1164 Sofia, Bulgaria.
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29
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Wolpert M, Hellwig P. Infrared spectra and molar absorption coefficients of the 20 alpha amino acids in aqueous solutions in the spectral range from 1800 to 500 cm(-1). SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 64:987-1001. [PMID: 16458063 DOI: 10.1016/j.saa.2005.08.025] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 08/15/2005] [Accepted: 08/31/2005] [Indexed: 05/06/2023]
Abstract
In this work, we present the absorption spectra and molar coefficients of all 20 amino acids in aqueous solutions down to 500 cm(-1). The spectral region between 1200 and 500 cm(-1) was yet disregarded for protein infrared spectroscopy, mainly due to the strong H(2)O absorption. Absorption spectra were obtained mainly for physiological relevant pH region. Intense bands for aromatic amino acids, histidine and such with OH group could clearly be identified throughout the given spectral region. For sulfur-containing amino acids cysteine and methionine some strong bands besides the weak carbon-sulfur stretching vibration was shown. Effects of aqueous solution environment, pH, protonation states were discussed, together with previously reported data from theoretical approaches. With this complete set of spectral information application to proteins in the whole mid infrared region could be described precise and the potential of the lower spectral region to study typical cofactor ligands like histidine, shown.
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Affiliation(s)
- Martina Wolpert
- Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt/Main, Germany
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30
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Tsuboi M, Benevides JM, Bondre P, Thomas GJ. Structural details of the thermophilic filamentous bacteriophage PH75 determined by polarized Raman microspectroscopy. Biochemistry 2005; 44:4861-9. [PMID: 15779912 DOI: 10.1021/bi0479306] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The filamentous virus PH75, which infects the thermophile Thermus thermophilus, consists of a closed DNA strand of 6500 nucleotides encapsidated by 2700 copies of a 46-residue coat subunit (pVIII). The PH75 virion is similar in composition to filamentous viruses infecting mesophilic bacteria but is distinguished by in vivo assembly at 70 degrees C and thermostability to at least 90 degrees C. Structural details of the PH75 assembly are not known, although a fiber X-ray diffraction based model suggests that capsid subunits are highly alpha-helical and organized with the same symmetry (class II) as in the mesophilic filamentous phages Pf1 and Pf3 [Pederson et al. (2001) J. Mol. Biol. 309, 401-421]. This is distinct from the symmetry (class I) of phages fd and M13. We have employed polarized Raman microspectroscopy to obtain further details of PH75 architecture. The spectra are interpreted in combination with known Raman tensors for modes of the pVIII main chain (amide I) and Trp and Tyr side chains to reveal the following structural features of PH75: (i) The average pVIII peptide group is oriented with greater displacement from the virion axis than peptide groups of fd, Pf1, or Pf3. The data correspond to an average helix tilt angle of 25 degrees in PH75 vs 16 degrees in fd, Pf1, and Pf3. (ii) The indolyl ring of Trp 37 in PH75 projects nearly equatorially from the subunit alpha-helix axis, in contrast to the more axial orientations for Trp 26 of fd and Trp 38 of Pf3. (iii) The phenolic rings of Tyr 15 and Tyr 39 project along the subunit helix axis, and one phenoxyl engages in hydrogen-bonding interaction that has no counterpart in either fd or Pf1 tyrosines. Also, in contrast to fd, Pf1, and Pf3, the packaged DNA genome of PH75 exhibits no Raman anisotropy, suggesting that DNA bases are not oriented unidirectionally within the nucleocapsid assembly. The structural findings are discussed in relation to intrasubunit and intersubunit interactions that may confer hyperthermostability to the PH75 virion. A refined molecular model is proposed for the PH75 capsid subunit.
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Affiliation(s)
- Masamichi Tsuboi
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110, USA
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31
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Zhang D, Ortiz C, Xie Y, Davisson VJ, Ben-Amotz D. Detection of the site of phosphorylation in a peptide using Raman spectroscopy and partial least squares discriminant analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2005; 61:471-475. [PMID: 15582814 DOI: 10.1016/j.saa.2004.04.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Accepted: 04/20/2004] [Indexed: 05/24/2023]
Abstract
Normal (non-enhanced) Raman spectroscopy is used to determine the site of phosphorylation on a 13-residue peptide whose sequence derives from the cellular protein pp60(c-src) (protein tyrosine kinase). Raman spectra of serine, threonine and tyrosine amino acids and their phosphorylated derivatives are used to aid in the interpretation of peptide spectra. The purity of the synthetic peptides are confirmed by mass spectroscopy. Peptide Raman measurements are performed using the recently reported drop-coating deposition Raman (DCDR) method, followed by Savistky-Golay second derivative (SGSD) pre-processing and multivariate spectral classification using partial least squares (PLS) discriminant analysis. Leave-one-out training/testing results are displayed using a PLS psuedo-probability score plot and shown to facilitate error-free spectral determination of the site of phosphorylation.
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Affiliation(s)
- Dongmao Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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32
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Overman SA, Kristensen DM, Bondre P, Hewitt B, Thomas GJ. Effects of Virion and Salt Concentrations on the Raman Signatures of Filamentous Phages fd, Pf1, Pf3, and PH75. Biochemistry 2004; 43:13129-36. [PMID: 15476406 DOI: 10.1021/bi0485023] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Filamentous phages consist of a single-stranded DNA genome encapsidated by several thousand copies of a small alpha-helical coat protein subunit plus several copies of four minor proteins at the filament ends. The filamentous phages are important as cloning vectors, vehicles for peptide display, and substrates for macromolecular alignment. Effective use of a filamentous phage in such applications requires an understanding of experimental factors that may influence the propensity of viral filaments to laterally aggregate in solution. Because the Raman spectrum of a filamentous phage is strongly dependent on the relative orientation of the virion with respect to the polarization direction of the electromagnetic radiation employed to excite the spectrum, we have applied Raman spectroscopy to investigate lateral aggregation of phages fd, Pf1, Pf3, and PH75 in solution. The results show that lateral aggregation of the virions and anisotropic orientation of the aggregates are both disfavored by high concentrations of salt (>200 mM NaCl) in solutions containing a relatively low virion concentration (<10 mg/mL). Conversely, the formation of lateral aggregates and their anisotropic orientation are strongly favored by a low salt concentration (<0.1 mM NaCl), irrespective of the virion concentration over a wide range. The use of Raman polarization effects to distinguish isotropic and anisotropic solutions of filamentous phages is consistent with previously reported Raman analyses of virion structures in both solutions and fibers. The Raman data are supported by electron micrographs of negatively stained specimens of phage fd, which permit an independent assessment of salt effects on lateral aggregation. The present results also identify new Raman bands that serve as potential markers of subunit side-chain orientations in filamentous virus assemblies.
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Affiliation(s)
- Stacy A Overman
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, 5100 Rockhill Road, Kansas City, Missouri 64110, USA
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33
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Xie Y, Zhang D, Jarori GK, Davisson VJ, Ben-Amotz D. The Raman detection of peptide tyrosine phosphorylation. Anal Biochem 2004; 332:116-21. [PMID: 15301956 DOI: 10.1016/j.ab.2004.05.052] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Indexed: 10/26/2022]
Abstract
Drop-coating-deposition-Raman (DCDR) is used to detect spectral changes induced by phosphorylation of tyrosine amino acid residues in peptides. Four peptides are investigated, with sequences derived from the human protein-tyrosine kinase, p60c-src, with Y-216, Y-419, and Y-530 phosphorylation sites. Although the spectra of the four peptides are quite different, tyrosine phosphorylation is found to invariably induce the collapse of a doublet at 820-850cm(-1) and the attenuation of a peak around 1205cm(-1). Moreover, amide III band shifts suggest that tyrosine phosphorylation may promote beta sheet formation, particularly in peptides that lack phenylalanine residues. The degree of tyrosine phosphorylation in peptide mixtures is determined using DCDR combined with partial least squares multivariate calibration with a 2% root mean standard error of prediction.
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Affiliation(s)
- Yong Xie
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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34
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Tsuboi M, Kubo Y, Ikeda T, Overman SA, Osman O, Thomas GJ. Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy. Biochemistry 2003; 42:940-50. [PMID: 12549913 DOI: 10.1021/bi020566v] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Pseudomonas bacteriophage Pf1 is a long ( approximately 2000 nm) and thin ( approximately 6.5 nm) filament consisting of a covalently closed, single-stranded DNA genome of 7349 nucleotides coated by 7350 copies of a 46-residue alpha-helical subunit. The coat subunits are arranged as a superhelix of C(1)()S(5.4)() symmetry (class II). Polarized Raman and polarized FTIR spectroscopy of oriented Pf1 fibers show that the packaged single-stranded DNA genome is ordered specifically with respect to the capsid superhelix. Bases are nonrandomly arranged along the capsid interior, deoxynucleosides are uniformly in the C2'-endo/anti conformation, and the average DNA phosphodioxy group (PO(2)(-)) is oriented so that the line connecting the oxygen atoms (O.O) forms an angle of 71 degrees +/- 5 degrees with the virion axis. Raman and infrared amide band polarizations show that the subunit alpha-helix axis is inclined at an average angle of 16 degrees +/- 4 degrees with respect to the virion axis. The alpha-helical symmetry of the capsid subunit is remarkably rigorous, resulting in splitting of Raman-active helix vibrational modes at 351, 445 and 1026 cm(-)(1) into apparent A-type and E(2)()-type symmetry pairs. The subunit tyrosines (Tyr 25 and Tyr 40) are oriented with phenoxyl rings packed relatively close to parallel to the virion axis. The Tyr 25 and Tyr 40 orientations of Pf1 are surprisingly close to those observed for Tyr 21 and Tyr 24 of the Ff virion (C(5)()S(2)() symmetry, class I), suggesting a preferred tyrosyl side chain conformation in packed alpha-helical subunits, irrespective of capsid symmetry. The polarized Raman spectra also provide information on the orientations of subunit alanine, valine, leucine and isoleucine side chains of the Pf1 virion.
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Affiliation(s)
- Masamichi Tsuboi
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110
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35
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Tsuboi M, Ushizawa K, Nakamura K, Benevides JM, Overman SA, Thomas GJ. Orientations of Tyr 21 and Tyr 24 in the capsid of filamentous virus Ff determined by polarized Raman spectroscopy. Biochemistry 2001; 40:1238-47. [PMID: 11170449 DOI: 10.1021/bi001936n] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The capsid of filamentous virus Ff is assembled from approximately 2750 copies of a 50-residue alpha-helical subunit, the two tyrosines of which (Tyr 21 and Tyr 24) are located within a hydrophobic sequence that constitutes the subunit interface. We have determined the side chain orientations of Tyr 21 and Tyr 24 by polarized Raman microspectroscopy of oriented Ff fibers, utilizing a novel experimental approach that combines site-specific mutation and residue-specific deuteration of capsid subunits. The polarized Raman signature of Tyr 21 was obtained by incorporating C(delta 1),C(delta 2),C(epsilon 1),C(epsilon 2)-tetradeuteriotyrosine at position 21 in an Ff mutant in which Tyr 24 is replaced with methionine. Similarly, the polarized Raman signature of Tyr 24 was obtained by incorporating C(delta 1),C(delta 2),C(epsilon 1),C(epsilon 2)-tetradeuteriotyrosine at position 24 in the analogous Tyr 21 --> Met mutant. Polarizations of the corresponding C-D stretching bands in the 2200-2400 cm(-1) interval of the Raman spectrum were measured and interpreted using tensors transferred from a polarized Raman analysis of L-tyrosine-2,3,5,6-d(4) single crystals. Polarized Raman analysis was extended to the bands of Ff near 642 and 855 cm(-1), which originate from vibrational modes of the tyrosine phenolic ring. The results indicate the following: (i) For both Tyr 21 and Tyr 24, the phenolic 2-fold axis (C(1)-C(4) line) is inclined at 41 +/- 5 degrees from the virion axis and the normal to the plane of the phenolic ring is inclined at 71 +/- 5 degrees from the virion axis; (ii) the mutation of Tyr 24, but not the mutation of Tyr 21, perturbs Raman markers of the subunit tryptophan (Trp 26), suggesting interdependence of Tyr 24 and Trp 26 orientations in native Ff; and (iii) polarization anisotropies observed for Raman markers of Ff DNA bases are unperturbed by mutation of either Tyr 21 or Tyr 24, indicating that nonrandom base orientations of packaged Ff DNA are independent of the mutation of either Tyr 21 or Tyr 24. A molecular model consistent with these findings is proposed.
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Affiliation(s)
- M Tsuboi
- Division of Cell Biology and Biophysics, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, USA
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36
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Bjerneld EJ, Johansson P, Käll M. Single Molecule Vibrational Fine-structure of Tyrosine Adsorbed on Ag Nano-Crystals. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/1438-5171(200009)1:3<239::aid-simo239>3.0.co;2-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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