101
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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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102
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Li S, Combs JD, Alharbi OE, Kong J, Wang C, Leblanc RM. The (13)C amide I band is still sensitive to conformation change when the regular amide I band cannot be distinguished at the typical position in H2O. Chem Commun (Camb) 2015; 51:12537-9. [PMID: 26153570 DOI: 10.1039/c5cc02263k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The attenuated total reflection technique was utilized to obtain FTIR spectra of (13)C-labeled peptides with a sequence of (AAAAK)4AAAAY in H2O. The regular amide I band was not at the typical position as reported in globular proteins, whereas the (13)C amide I band was still sensitive to conformation change.
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Affiliation(s)
- Shanghao Li
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA.
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103
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Bueno J, Long D, Kauffman JF, Arzhantsev S. Deep-Ultraviolet Resonance Raman (DUVRR) Spectroscopy of Therapeutic Monoclonal Antibodies Subjected to Thermal Stress. Anal Chem 2015; 87:7880-6. [PMID: 26132464 DOI: 10.1021/acs.analchem.5b01606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The structural assessment of Rituximab, an IgG1 mAb, was investigated with deep-ultraviolet resonance Raman (DUVRR) spectroscopy. DUVRR spectroscopy was used to monitor the changes to the secondary structure of Rituximab under thermal stress. DUVRR spectra showed obvious changes from 22 to 72 °C. Specifically, changes in the amide I vibrational mode were assigned to an increase in unordered structure (random coil). Structural changes in samples heated to 72 °C were related to loss in drug potency via a complement dependent cytotoxicity (CDC) bioassay. The DUVRR spectroscopic method shows promise as a tool for the quality assessment of mAb drug products and would represent an improvement over current methodology in terms of analysis time and sample preparation. To determine the scope of the method, protein pharmaceuticals of different molecular weights (ranging from 4 to 143 kDa) and secondary structure (β-sheet, α-helix and unordered structure) were analyzed. The model illustrated the method's sensitivity for the analysis of protein drug products of different secondary structure. Results show promise for DUVRR spectroscopy as a rapid screening tool of a variety of formulated protein pharmaceuticals.
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Affiliation(s)
- Justin Bueno
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, Food and Drug Administration, 645 S. Newstead Avenue, St Louis, Missouri 63110, United States
| | - Dianna Long
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, Food and Drug Administration, 645 S. Newstead Avenue, St Louis, Missouri 63110, United States
| | - John F Kauffman
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, Food and Drug Administration, 645 S. Newstead Avenue, St Louis, Missouri 63110, United States
| | - Sergey Arzhantsev
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, Food and Drug Administration, 645 S. Newstead Avenue, St Louis, Missouri 63110, United States
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104
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Chen J, Yao M, Pagba CV, Zheng Y, Fei L, Feng Z, Barry BA. Directly probing redox-linked quinones in photosystem II membrane fragments via UV resonance Raman scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:558-64. [DOI: 10.1016/j.bbabio.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 02/19/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
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105
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Punihaole D, Jakubek RS, Dahlburg EM, Hong Z, Myshakina NS, Geib S, Asher SA. UV resonance Raman investigation of the aqueous solvation dependence of primary amide vibrations. J Phys Chem B 2015; 119:3931-9. [PMID: 25667957 PMCID: PMC5065019 DOI: 10.1021/jp511356u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the normal mode composition and the aqueous solvation dependence of the primary amide vibrations of propanamide. Infrared, normal Raman, and UV resonance Raman (UVRR) spectroscopy were applied in conjunction with density functional theory (DFT) to assign the vibrations of crystalline propanamide. We examined the aqueous solvation dependence of the primary amide UVRR bands by measuring spectra in different acetonitrile/water mixtures. As previously observed in the UVRR spectra of N-methylacetamide, all of the resonance enhanced primary amide bands, except for the Amide I (AmI), show increased UVRR cross sections as the solvent becomes water-rich. These spectral trends are rationalized by a model wherein the hydrogen bonding and the high dielectric constant of water stabilizes the ground state dipolar (-)O-C═NH2(+) resonance structure over the neutral O═C-NH2 resonance structure. Thus, vibrations with large C-N stretching show increased UVRR cross sections because the C-N displacement between the electronic ground and excited state increases along the C-N bond. In contrast, vibrations dominated by C═O stretching, such as the AmI, show a decreased displacement between the electronic ground and excited state, which result in a decreased UVRR cross section upon aqueous solvation. The UVRR primary amide vibrations can be used as sensitive spectroscopic markers to study the local dielectric constant and hydrogen bonding environments of the primary amide side chains of glutamine (Gln) and asparagine (Asn).
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Affiliation(s)
- David Punihaole
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ryan S. Jakubek
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Elizabeth M. Dahlburg
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Nataliya S. Myshakina
- Science Department, Chatham University, Pittsburgh, Pennsylvania 15232, United States
| | - Steven Geib
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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106
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Galinato MGI, Bowman SEJ, Kleingardner JG, Martin S, Zhao J, Sturhahn W, Alp EE, Bren KL, Lehnert N. Effects of protein structure on iron-polypeptide vibrational dynamic coupling in cytochrome c. Biochemistry 2015; 54:1064-76. [PMID: 25531247 PMCID: PMC4318584 DOI: 10.1021/bi501430z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cytochrome c (Cyt c) has a heme covalently bound to the polypeptide via a Cys-X-X-Cys-His (CXXCH) linker that is located in the interface region for protein-protein interactions. To determine whether the polypeptide matrix influences iron vibrational dynamics, nuclear resonance vibrational spectroscopy (NRVS) measurements were performed on (57)Fe-labeled ferric Hydrogenobacter thermophilus cytochrome c-552, and variants M13V, M13V/K22M, and A7F, which have structural modifications that alter the composition or environment of the CXXCH pentapeptide loop. Simulations of the NRVS data indicate that the 150-325 cm(-1) region is dominated by NHis-Fe-SMet axial ligand and polypeptide motions, while the 325-400 cm(-1) region shows dominant contributions from ν(Fe-NPyr) (Pyr = pyrrole) and other heme-based modes. Diagnostic spectral signatures that directly relate to structural features of the heme active site are identified using a quantum chemistry-centered normal coordinate analysis (QCC-NCA). In particular, spectral features that directly correlate with CXXCH loop stiffness, the strength of the Fe-His interaction, and the degree of heme distortion are identified. Cumulative results from our investigation suggest that compared to the wild type (wt), variants M13V and M13V/K22M have a more rigid CXXCH pentapeptide segment, a stronger Fe-NHis interaction, and a more ruffled heme. Conversely, the A7F variant has a more planar heme and a weaker Fe-NHis bond. These results are correlated to the observed changes in reduction potential between wt protein and the variants studied here. Implications of these results for Cyt c biogenesis and electron transfer are also discussed.
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Affiliation(s)
- Mary Grace I Galinato
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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107
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Rosario-Alomar MF, Quiñones-Ruiz T, Kurouski D, Sereda V, Ferreira EB, Jesús-Kim LD, Hernández-Rivera S, Zagorevski DV, López-Garriga J, Lednev IK. Hydrogen sulfide inhibits amyloid formation. J Phys Chem B 2015; 119:1265-74. [PMID: 25545790 PMCID: PMC4315425 DOI: 10.1021/jp508471v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Amyloid
fibrils are large aggregates of misfolded proteins, which
are often associated with various neurodegenerative diseases such
as Alzheimer’s, Parkinson’s, Huntington’s, and
vascular dementia. The amount of hydrogen sulfide (H2S)
is known to be significantly reduced in the brain tissue of people
diagnosed with Alzheimer’s disease relative to that of healthy
individuals. These findings prompted us to investigate the effects
of H2S on the formation of amyloids in vitro using a model fibrillogenic protein hen egg white lysozyme (HEWL).
HEWL forms typical β-sheet rich fibrils during the course of
70 min at low pH and high temperatures. The addition of H2S completely inhibits the formation of β-sheet and amyloid
fibrils, as revealed by deep UV resonance Raman (DUVRR) spectroscopy
and ThT fluorescence. Nonresonance Raman spectroscopy shows that disulfide
bonds undergo significant rearrangements in the presence of H2S. Raman bands corresponding to disulfide (RSSR) vibrational
modes in the 550–500 cm–1 spectral range
decrease in intensity and are accompanied by the appearance of a new
490 cm–1 band assigned to the trisulfide group (RSSSR)
based on the comparison with model compounds. The formation of RSSSR
was proven further using a reaction with TCEP reduction agent and
LC-MS analysis of the products. Intrinsic tryptophan fluorescence
study shows a strong denaturation of HEWL containing trisulfide bonds.
The presented evidence indicates that H2S causes the formation
of trisulfide bridges, which destabilizes HEWL structure, preventing
protein fibrillation. As a result, small spherical aggregates of unordered
protein form, which exhibit no cytotoxicity by contrast with HEWL
fibrils.
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Affiliation(s)
- Manuel F Rosario-Alomar
- Department of Chemistry and ‡Department of Biology, University of Puerto Rico at Mayagüez , Mayagüez, Puerto Rico 00693
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108
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Dworkowski FSN, Hough MA, Pompidor G, Fuchs MR. Challenges and solutions for the analysis of in situ, in crystallo micro-spectrophotometric data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:27-35. [PMID: 25615857 PMCID: PMC4304683 DOI: 10.1107/s1399004714015107] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
Combining macromolecular crystallography with in crystallo micro-spectrophotometry yields valuable complementary information on the sample, including the redox states of metal cofactors, the identification of bound ligands and the onset and strength of undesired photochemistry, also known as radiation damage. However, the analysis and processing of the resulting data differs significantly from the approaches used for solution spectrophotometric data. The varying size and shape of the sample, together with the suboptimal sample environment, the lack of proper reference signals and the general influence of the X-ray beam on the sample have to be considered and carefully corrected for. In the present article, how to characterize and treat these sample-dependent artefacts in a reproducible manner is discussed and the SLS-APE in situ, in crystallo optical spectroscopy data-analysis toolbox is demonstrated.
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Affiliation(s)
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Guillaume Pompidor
- European Molecular Biology Laboratory Hamburg, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | - Martin R. Fuchs
- Photon Sciences, Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973, USA
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109
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Hong Z, Asher SA. Dependence of Raman and resonance Raman intensities on sample self-absorption. APPLIED SPECTROSCOPY 2015; 69:75-83. [PMID: 25506729 DOI: 10.1366/14-07531] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Resonance Raman cross sections are generally larger than normal or preresonance Raman cross sections. Thus, higher Raman intensities are expected for resonance excitation, especially for backscattering measurements. However, self absorption decreases the observed Raman intensities. In the work here we examine the effect of self absorption on the observed preresonance and resonance Raman intensities. For the simplest case where a single electronic transition dominates the Raman scattering, and where the resonance enhancement scales with the square of the molar absorptivity of the absorption band, theory predicts that for close to resonance excitation the observed Raman intensities monotonically increase as resonance is approached. In the case that an impurity absorbs, the observed Raman intensities may decrease as excitation moves close to resonance for particular conditions of impurity absorption band widths and frequency offsets. Impurity absorption also causes decreases in observed Raman intensities for the more slowly increasing preresonance excitation.
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Affiliation(s)
- Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 USA
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110
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D’Hondt M, Bracke N, Taevernier L, Gevaert B, Verbeke F, Wynendaele E, De Spiegeleer B. Related impurities in peptide medicines. J Pharm Biomed Anal 2014; 101:2-30. [DOI: 10.1016/j.jpba.2014.06.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/05/2014] [Accepted: 06/08/2014] [Indexed: 12/16/2022]
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111
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Advanced experimental methods toward understanding biophysicochemical interactions of interfacial biomolecules by using sum frequency generation vibrational spectroscopy. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5233-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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112
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Parchaňský V, Kapitán J, Bouř P. Inspecting chiral molecules by Raman optical activity spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra10416a] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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113
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Ramachandran G, Milán-Garcés EA, Udgaonkar JB, Puranik M. Resonance Raman spectroscopic measurements delineate the structural changes that occur during tau fibril formation. Biochemistry 2014; 53:6550-65. [PMID: 25284680 DOI: 10.1021/bi500528x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The aggregation of the microtubule-associated protein, tau, into amyloid fibrils is a hallmark of neurodegenerative diseases such as the tauopathies and Alzheimer's disease. Since monomeric tau is an intrinsically disordered protein and the polymeric fibrils possess an ordered cross-β core, the aggregation process is known to involve substantial conformational conversion besides growth. The aggregation mechanism of tau in the presence of inducers such as heparin, deciphered using probes such as thioflavin T/S fluorescence, light scattering, and electron microscopy assays, has been shown to conform to ligand-induced nucleation-dependent polymerization. These probes do not, however, distinguish between the processes of conformational conversion and fibril growth. In this study, UV resonance Raman spectroscopy is employed to look directly at signatures of changes in secondary structure and side-chain packing during fibril formation by the four repeat functional domain of tau in the presence of the inducer heparin, at pH 7 and at 37 °C. Changes in the positions and intensities of the amide Raman bands are shown to occur in two distinct stages during the fibril formation process. The first stage of UVRR spectral changes corresponds to the transformation of monomer into early fibrillar aggregates. The second stage corresponds to the transformation of these early fibrillar aggregates into the final, ordered, mature fibrils and during this stage; the processes of conformational conversion and the consolidation of the fibril core occur simultaneously. Delineation of these secondary structural changes accompanying the formation of tau fibrils holds significance for the understanding of generic and tau-specific principles of amyloid assembly.
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Affiliation(s)
- Gayathri Ramachandran
- National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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114
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Hong Z, Damodaran K, Asher SA. Sodium dodecyl sulfate monomers induce XAO peptide polyproline II to α-helix transition. J Phys Chem B 2014; 118:10565-75. [PMID: 25121643 PMCID: PMC4161145 DOI: 10.1021/jp504133m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
XAO peptide (Ac–X2A7O2–NH2; X: diaminobutyric
acid side chain, −CH2CH2NH3+; O: ornithine side chain,
−CH2CH2CH2NH3+) in aqueous solution shows a predominantly polyproline II
(PPII) conformation without any detectable α-helix-like conformations.
Here we demonstrate by using circular dichroism (CD), ultraviolet
resonance Raman (UVRR) and nuclear magnetic resonance (NMR) spectroscopy
that sodium dodecyl sulfate (SDS) monomers bind to XAO and induce
formation of α-helix-like conformations. The stoichiometry and
the association constants of SDS and XAO were determined from the
XAO–SDS diffusion coefficients measured by pulsed field gradient
NMR. We developed a model for the formation of XAO–SDS aggregate
α-helix-like conformations. Using UVRR spectroscopy, we calculated
the Ramachandran ψ angle distributions of aggregated XAO peptides.
We resolved α-, π- and 310- helical conformations
and a turn conformation. XAO nucleates SDS aggregation at SDS concentrations
below the SDS critical micelle concentration. The XAO4–SDS16 aggregates have four SDS molecules bound to each XAO to
neutralize the four side chain cationic charges. We propose that the
SDS alkyl chains partition into a hydrophobic core to minimize the
hydrophobic area exposed to water. Neutralization of the flanking
XAO charges enables α-helix formation. Four XAO–SDS4 aggregates form a complex with an SDS alkyl chain-dominated
hydrophobic core and a more hydrophilic shell where one face of the
α-helix peptide contacts the water environment.
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Affiliation(s)
- Zhenmin Hong
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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115
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Towards label-free and site-specific probing of the local pH in proteins: pH-dependent deep UV Raman spectra of histidine and tyrosine. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.03.053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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116
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Surface characterization of insulin protofilaments and fibril polymorphs using tip-enhanced Raman spectroscopy (TERS). Biophys J 2014; 106:263-71. [PMID: 24411258 DOI: 10.1016/j.bpj.2013.10.040] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/19/2013] [Accepted: 10/28/2013] [Indexed: 11/22/2022] Open
Abstract
Amyloid fibrils are β-sheet-rich protein aggregates that are strongly associated with a variety of neurodegenerative maladies, such as Alzheimer's and Parkinson's diseases. Even if the secondary structure of such fibrils is well characterized, a thorough understanding of their surface organization still remains elusive. Tip-enhanced Raman spectroscopy (TERS) is one of a few techniques that allow the direct characterization of the amino acid composition and the protein secondary structure of the amyloid fibril surface. Herein, we investigated the surfaces of two insulin fibril polymorphs with flat (flat) and left-twisted (twisted) morphology. It was found that the two differ substantially in both amino acid composition and protein secondary structure. For example, the amounts of Tyr, Pro, and His differ, as does the number of carboxyl groups on the respective surfaces, whereas the amounts of Phe and of positively charged amino and imino groups remain similar. In addition, the surface of protofilaments, the precursors of the mature flat and twisted fibrils, was investigated using TERS. The results show substantial differences with respect to the mature fibrils. A correlation of amino acid frequencies and protein secondary structures on the surface of protofilaments and on flat and twisted fibrils allowed us to propose a hypothetical mechanism for the propagation to specific fibril polymorphs. This knowledge can shed a light on the toxicity of amyloids and define the key factors responsible for fibril polymorphism. Finally, this work demonstrates the potential of TERS for the surface characterization of amyloid fibril polymorphs.
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117
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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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118
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Noda I. Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.025] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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119
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Jones EM, Balakrishnan G, Squier TC, Spiro TG. Distinguishing unfolding and functional conformational transitions of calmodulin using ultraviolet resonance Raman spectroscopy. Protein Sci 2014; 23:1094-101. [PMID: 24895328 DOI: 10.1002/pro.2495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 01/09/2023]
Abstract
Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well-known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this article, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca(2+) binding. This spectral difference is entirely due to differences in tertiary contacts at the interdomain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry, University of Washington, Seattle, Washington, 98195-1700
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120
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Cai Z, Zhang JT, Xue F, Hong Z, Punihaole D, Asher SA. 2D Photonic Crystal Protein Hydrogel Coulometer for Sensing Serum Albumin Ligand Binding. Anal Chem 2014; 86:4840-7. [DOI: 10.1021/ac404134t] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Zhongyu Cai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Jian-Tao Zhang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Fei Xue
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - David Punihaole
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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121
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Xiong J, Roach CA, Oshokoya OO, Schroell RP, Yakubu RA, Eagleburger MK, Cooley JW, Jiji RD. Role of bilayer characteristics on the structural fate of aβ(1-40) and aβ(25-40). Biochemistry 2014; 53:3004-11. [PMID: 24702518 DOI: 10.1021/bi4016296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The β-amyloid (Aβ) peptide is derived from the transmembrane (TM) helix of the amyloid precursor protein (APP) and has been shown to interact with membrane surfaces. To understand better the role of peptide-membrane interactions in cell death and ultimately in Alzheimer's disease, a better understanding of how membrane characteristics affect the binding, solvation, and secondary structure of Aβ is needed. Employing a combination of circular dichroism and deep-UV resonance Raman spectroscopies, Aβ(25-40) was found to fold spontaneously upon association with anionic lipid bilayers. The hydrophobic portion of the disease-related Aβ(1-40) peptide, Aβ(25-40), has often been used as a model for how its legacy TM region may behave structurally in aqueous solvents and during membrane encounters. The structure of the membrane-associated Aβ(25-40) peptide was found to depend on both the hydrophobic thickness of the bilayer and the duration of incubation. Similarly, the disease-related Aβ(1-40) peptide also spontaneously associates with anionic liposomes, where it initially adopts mixtures of disordered and helical structures. The partially disordered helical structures then convert to β-sheet structures over longer time frames. β-Sheet structure is formed prior to helical unwinding, implying a model in which β-sheet structure, formed initially from disordered regions, prompts the unwinding and destabilization of membrane-stabilized helical structure. A model is proposed to describe the mechanism of escape of Aβ(1-40) from the membrane surfaces following its formation by cleavage of APP within the membrane.
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Affiliation(s)
- Jian Xiong
- Department of Chemistry, University of Missouri , Columbia, Missouri 65211, United States
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122
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Jin S, Fan F, Guo M, Zhang Y, Feng Z, Li C. Note: deep ultraviolet Raman spectrograph with the laser excitation line down to 177.3 nm and its application. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:046105. [PMID: 24784683 DOI: 10.1063/1.4870444] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Deep UV Raman spectrograph with the laser excitation line down to 177.3 nm was developed in this laboratory. An ellipsoidal mirror and a dispersed-subtractive triple monochromator were used to collect and disperse Raman light, respectively. The triple monochromator was arranged in a triangular configuration with only six mirrors used. 177.3 nm laser excited Raman spectrum with cut-off wavenumber down to 200 cm(-1) and spectral resolution of 8.0 cm(-1) can be obtained under the condition of high purity N2 purging. With the C-C σ bond in Teflon selectively excited by the 177.3 nm laser, resonance Raman spectrum of Teflon with good quality was recorded on the home-built instrument and the σ-σ(*) transition of C-C bond was studied. The result demonstrates that deep UV Raman spectrograph is powerful for studying the systems with electronic transition located in the deep UV region.
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Affiliation(s)
- Shaoqing Jin
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fengtao Fan
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Meiling Guo
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ying Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhaochi Feng
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Can Li
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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123
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Kurouski D, Lu X, Popova L, Wan W, Shanmugasundaram M, Stubbs G, Dukor RK, Lednev IK, Nafie LA. Is supramolecular filament chirality the underlying cause of major morphology differences in amyloid fibrils? J Am Chem Soc 2014; 136:2302-12. [PMID: 24484302 PMCID: PMC3968177 DOI: 10.1021/ja407583r] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
The unique enhanced
sensitivity of vibrational circular dichroism
(VCD) to the formation and development of amyloid fibrils in solution
is extended to four additional fibril-forming proteins or peptides
where it is shown that the sign of the fibril VCD pattern correlates
with the sense of supramolecular filament chirality and, without exception,
to the dominant fibril morphology as observed in AFM or SEM images.
Previously for insulin, it has been demonstrated that the sign of
the VCD band pattern from filament chirality can be controlled by
adjusting the pH of the incubating solution, above pH 2 for “normal”
left-hand-helical filaments and below pH 2 for “reversed”
right-hand-helical filaments. From AFM or SEM images, left-helical
filaments form multifilament braids of left-twisted fibrils while
the right-helical filaments form parallel filament rows of fibrils
with a flat tape-like morphology, the two major classes of fibril
morphology that from deep UV resonance Raman scattering exhibit the
same cross-β-core secondary structure. Here we investigate whether
fibril supramolecular chirality is the underlying cause of the major
morphology differences in all amyloid fibrils by showing that the
morphology (twisted versus flat) of fibrils of lysozyme, apo-α-lactalbumin,
HET-s (218–289) prion, and a short polypeptide fragment of
transthyretin, TTR (105–115), directly correlates to their
supramolecular chirality as revealed by VCD. The result is strong
evidence that the chiral supramolecular organization of filaments
is the principal underlying cause of the morphological heterogeneity
of amyloid fibrils. Because fibril morphology is linked to cell toxicity,
the chirality of amyloid aggregates should be explored in the widely
used in vitro models of amyloid-associated diseases.
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Affiliation(s)
- Dmitry Kurouski
- Department of Chemistry, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
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124
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Ye S, Li H, Yang W, Luo Y. Accurate Determination of Interfacial Protein Secondary Structure by Combining Interfacial-Sensitive Amide I and Amide III Spectral Signals. J Am Chem Soc 2014; 136:1206-9. [DOI: 10.1021/ja411081t] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Hongchun Li
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Weilai Yang
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yi Luo
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, and Synergetic Innovation Center of Quantum Information & Quantum Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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125
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Kurouski D, Sorci M, Postiglione T, Belfort G, Lednev IK. Detection and structural characterization of insulin prefibrilar oligomers using surface enhanced Raman spectroscopy. Biotechnol Prog 2014; 30:488-95. [PMID: 24376182 DOI: 10.1002/btpr.1852] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 12/01/2013] [Indexed: 12/31/2022]
Abstract
In vitro fibril formation typically exhibits a lag phase followed by a rapid elongation phase. Soluble prefibrilar oligomers form as multiple assembly states occur during the lag phase and, after forming a nucleus, rapidly propagate into amyloid aggregates and fibrils. The structure and morphology of amyloid fibrils have been extensively characterized over the last decades, while little is known about the structural organization of the prefibrilar oligomers or their multiple assembly states. The main difficulty in structural characterization of prefibrilar aggregates is their low concentration (pmolar) and their continual reactive conversion. Herein we overcome these difficulties by utilizing Surface-Enhanced Raman Spectroscopy (SERS) with a model amyloid peptide, insulin. SERS is a powerful analytic tool that is able to provide detection of small molecules down to a single-molecule level. Using SERS we found that during the 3 lag phase before the onset of insulin fibril formation, the amount of insulin oligomers increased more than twice after the first hour of incubation under fibrillation conditions (pH 1.6, 65°C) and then slowly decreased with time. The latter finding is kinetically linked to the conversion of the prefibrilar oligomers into fibril species. This study provides valuable new information about the time-dependent structural organization of insulin oligomers and demonstrates the power and potential of SERS for detection and structural characterization of biological specimens present at low concentrations.
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Affiliation(s)
- Dmitry Kurouski
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222
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126
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Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [DOI: 10.1007/978-3-642-28554-7_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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127
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Hufziger KT, Bykov SV, Asher SA. Raman hyperspectral imaging spectrometer utilizing crystalline colloidal array photonic crystal diffraction. APPLIED SPECTROSCOPY 2014; 68:1219-1223. [PMID: 25333852 DOI: 10.1366/14-07599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We fabricated a novel hyperspectral Raman imaging spectrometer that, for the first time, uses a photonic-crystal wavelength-selecting device to select a narrow-wavelength spectral interval. The photonic crystal consists of an array of highly charged, monodisperse polystyrene particles that self-assemble into a face-centered cubic crystal. The photonic crystal Bragg-diffracts a narrow spectral interval that can be tuned by altering the incident angle of collimated Raman scattered light. Our prototype spectrometer diffracts a ~200 cm(-1) interval of the 488 nm excited visible Raman spectrum of Teflon. This enabled us to select a close-lying triplet of Teflon Raman bands. We imaged the Teflon surface by focusing this narrow region onto a charge-coupled device to create a Raman image of the sample surface that spectrally details the chemical composition.
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Affiliation(s)
- Kyle T Hufziger
- University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Chevron Science Center, Room 701, Pittsburgh, PA 15260 USA
| | - Sergei V Bykov
- University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Chevron Science Center, Room 701, Pittsburgh, PA 15260 USA
| | - Sanford A Asher
- University of Pittsburgh, Department of Chemistry, 219 Parkman Avenue, Chevron Science Center, Room 701, Pittsburgh, PA 15260 USA
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128
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Egidi F, Bloino J, Cappelli C, Barone V. A robust and effective time-independent route to the calculation of Resonance Raman spectra of large molecules in condensed phases with the inclusion of Duschinsky, Herzberg-Teller, anharmonic, and environmental effects. J Chem Theory Comput 2013; 10:346-363. [PMID: 26550003 DOI: 10.1021/ct400932e] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present an effective time-independent implementation to model vibrational resonance Raman (RR) spectra of medium-large molecular systems with the inclusion of Franck-Condon (FC) and Herzberg-Teller (HT) effects and a full account of the possible differences between the harmonic potential energy surfaces of the ground and resonant electronic states. Thanks to a number of algorithmic improvements and very effective parallelization, the full computations of fundamentals, overtones, and combination bands can be routinely performed for large systems possibly involving more than two electronic states. In order to improve the accuracy of the results, an effective inclusion of the leading anharmonic effects is also possible, together with environmental contributions under different solvation regimes. Reduced-dimensionality approaches can further enlarge the range of applications of this new tool. Applications to imidazole, pyrene, and chlorophyll a1 in solution are reported, as well as comparisons with available experimental data.
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Affiliation(s)
- Franco Egidi
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Julien Bloino
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy ; Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organometallici, UOS di Pisa, Via G. Moruzzi 1, 56124 Pisa, Italy
| | - Chiara Cappelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, 56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
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129
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Kurouski D, Postiglione T, Deckert-Gaudig T, Deckert V, Lednev IK. Amide I vibrational mode suppression in surface (SERS) and tip (TERS) enhanced Raman spectra of protein specimens. Analyst 2013; 138:1665-73. [PMID: 23330149 DOI: 10.1039/c2an36478f] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Surface- and tip-enhanced Raman spectroscopy (SERS and TERS) are modern spectroscopic techniques, which are becoming widely used and show a great potential for the structural characterisation of biological systems. Strong enhancement of the Raman signal through localised surface plasmon resonance enables chemical detection at the single-molecule scale. Enhanced Raman spectra collected from biological specimens, such as peptides, proteins or microorganisms, were often observed to lack the amide I band, which is commonly used as a marker for the interpretation of the secondary protein structure. The cause of this phenomenon was unclear for many decades. In this work, we investigated this phenomenon for native insulin and insulin fibrils using both TERS and SERS and compared these spectra to the spectra of well-defined homo peptides. The results indicate that the appearance of the amide I Raman band does not correlate with the protein aggregation state, but is instead determined by the size of the amino acid side chain. For short model peptides, the absence of the amide I band in TERS and SERS spectra correlates with the presence of a bulky side chain. Homo-glycine and -alanine, which are peptides with small side chain groups (H and CH(3), respectively), exhibited an intense amide I band in almost 100% of the acquired spectra. Peptides with bulky side chains, such as tyrosine and tryptophan, exhibited the amide I band in 70% and 31% of the acquired spectra, respectively.
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Affiliation(s)
- Dmitry Kurouski
- University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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130
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Lanza G, Chiacchio MA. Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides. Chemphyschem 2013; 14:3284-93. [DOI: 10.1002/cphc.201300445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
| | - Maria A. Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
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131
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Bykov SV, Sharma B, Asher SA. High-throughput, high-resolution Echelle deep-UV Raman spectrometer. APPLIED SPECTROSCOPY 2013; 67:873-883. [PMID: 23876726 DOI: 10.1366/12-06960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We constructed an ultrahigh-throughput, high-resolution ultraviolet (UV) Raman spectrograph that utilizes a high-efficiency filter-stage monochromator and a high-dispersion Echelle spectrograph. The spectrograph utilizes a total of six mirrors and two gratings, with an overall efficiency at 229 nm of ~18%. The limiting resolution of our spectrometer is 0.6 cm⁻¹ full width half-maximum (FWHM), as measured for 229 nm Rayleigh scattering. Use of a 1 mm-wide entrance slit gives rise to an approximately 10 cm⁻¹ FWHM resolution at 229 nm. The ultrahigh spectrograph throughput enables ultrahigh signal-to-noise ratio, deep UV Raman spectra that allow us to monitor <1% changes in peptide bond composition. The throughput is measured to be 35-fold greater than conventional deep UV Raman spectrometers.
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Affiliation(s)
- Sergei V Bykov
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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132
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Brown MC, Mutter A, Koder RL, JiJi RD, Cooley JW. Observation of persistent α-helical content and discrete types of backbone disorder during a molten globule to ordered peptide transition via deep-UV resonance Raman spectroscopy. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2013; 44:957-962. [PMID: 27795611 PMCID: PMC5082991 DOI: 10.1002/jrs.4316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The molten globule state can aide in the folding of a protein to a functional structure and is loosely defined as an increase in structural disorder with conservation of the ensemble secondary structure content. Simultaneous observation of persistent secondary structure content with increased disorder has remained experimentally problematic. As a consequence, modeling how the molten globule state remains stable and how it facilitates proper folding remains difficult due to a lack of amenable spectroscopic techniques to characterize this class of partially unfolded proteins. Previously, deep-UV resonance Raman (dUVRR) spectroscopy has proven useful in the resolution of global and local structural fluctuations in the secondary structure of proteins. In this work, dUVRR was employed to study the molten globule to ordered transition of a model four-helix bundle protein, HP7. Both the average ensemble secondary structure and types of local disorder were monitored, without perturbation of the solvent, pH, or temperature. The molten globule to ordered transition is induced by stepwise coordination of two heme molecules. Persistent dUVRR spectral features in the amide III region at 1295-1301 and 1335-1338 cm-1 confirm previous observations that HP7 remains predominantly helical in the molten globule versus the fully ordered state. Additionally, these spectra represent the first demonstration of conserved helical content in a molten globule protein. With successive heme binding significant losses are observed in the spectral intensity of the amide III3 and S regions (1230-1260 and 1390 cm-1, respectively), which are known to be sensitive to local disorder. These observations indicate that there is a decrease in the structural populations able to explore various extended conformations, with successive heme binding events. DUVRR spectra indicate that the first heme coordination between two helical segments diminishes exploration of more elongated backbone structural conformations in the inter-helical regions. A second heme coordination by the remaining two helices further restricts protein motion.
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Affiliation(s)
- Mia C. Brown
- Department of Chemistry, University of Missouri, Columbia, MO 65211
| | - Andrew Mutter
- Department of Physics, The City College of New York, New York, NY 10031
| | - Ronald L. Koder
- Department of Physics, The City College of New York, New York, NY 10031
| | - Renee D. JiJi
- Department of Chemistry, University of Missouri, Columbia, MO 65211
| | - Jason W. Cooley
- Department of Chemistry, University of Missouri, Columbia, MO 65211
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133
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Hong Z, Wert J, Asher SA. UV resonance Raman and DFT studies of arginine side chains in peptides: insights into arginine hydration. J Phys Chem B 2013; 117:7145-56. [PMID: 23676082 PMCID: PMC3715884 DOI: 10.1021/jp404030u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examined the UV resonance Raman (UVRR) spectra of four models of the Arg side chain, guanidinium (Gdn), ethylguanidinium (EG), arginine (Arg), and Ac-Arg-OMe (AAO) in H2O and D2O, in order to identify spectral markers that report on the environment of the Arg side chain. To elucidate the resonance Raman enhancement mechanism of the Arg side chain, we used density functional theory (DFT) to calculate the equilibrium geometries of the electronic ground state and the first excited state. We determined the vibrational mode frequencies of the ground state and the first derivative of the first electronic excited state potential energy with respect to each vibrational normal mode of the electronic ground state at the electronic ground state equilibrium geometry. The DFT calculations and the potential energy distributions reveal that, in addition to the Gdn group C-N stretching vibrations, the C-N bond stretching vibration of the Gdn group-methylene linkage is also strongly resonance-enhanced in EG, Arg, and AAO. From the UVRR spectra, we find that the Raman cross section and frequency of the ~1170 cm(-1) vibration of the Arg side chain depends on its hydration state and can be used to determine the hydration state of the Arg side chain in peptides and proteins. We examined the hydration of the Arg side chain in two polyAla peptides and found that in the α-helical conformation the Arg side chain in the AEP peptide (sequence: A9RA3EA4RA2) is less hydrated than that in the AP peptide (sequence: A8RA4RA4RA2).
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Affiliation(s)
- Zhenmin Hong
- Department of Chemistry, University of Pittsburgh, Pennsylvania 15260, USA
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134
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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135
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Prigozhin MB, Gruebele M. Microsecond folding experiments and simulations: a match is made. Phys Chem Chem Phys 2013; 15:3372-88. [PMID: 23361200 PMCID: PMC3632410 DOI: 10.1039/c3cp43992e] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
For the past two decades, protein folding experiments have been speeding up from the second or millisecond time scale to the microsecond time scale, and full-atom simulations have been extended from the nanosecond to the microsecond and even millisecond time scale. Where the two meet, it is now possible to compare results directly, allowing force fields to be validated and refined, and allowing experimental data to be interpreted in atomistic detail. In this perspective we compare recent experiments and simulations on the microsecond time scale, pointing out the progress that has been made in determining native structures from physics-based simulations, refining experiments and simulations to provide more quantitative underlying mechanisms, and tackling the problems of multiple reaction coordinates, downhill folding, and complex underlying structure of unfolded or misfolded states.
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Affiliation(s)
- M. B. Prigozhin
- Department of Chemistry, Center for Biophsyics and Computational Biology, 600 South Mathews Ave. Box 5–6, Urbana IL 61801, USA
| | - M. Gruebele
- Department of Chemistry, Center for Biophsyics and Computational Biology, 600 South Mathews Ave. Box 5–6, Urbana IL 61801, USA
- Department of Physics, Center for Biophsyics and Computational Biology, 600 South Mathews Ave. Box 5–6, Urbana IL 61801, USA
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136
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Lednev IK, Kurouski D. 146 Amyloid fibril polymorphism probed by advanced vibrational spectroscopy. J Biomol Struct Dyn 2013. [DOI: 10.1080/07391102.2013.786388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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137
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Ye S, Wei F, Li H, Tian K, Luo Y. Structure and Orientation of Interfacial Proteins Determined by Sum Frequency Generation Vibrational Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:213-55. [DOI: 10.1016/b978-0-12-416596-0.00007-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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138
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Srinivasan S, Patke S, Wang Y, Ye Z, Litt J, Srivastava SK, Lopez MM, Kurouski D, Lednev IK, Kane RS, Colón W. Pathogenic serum amyloid A 1.1 shows a long oligomer-rich fibrillation lag phase contrary to the highly amyloidogenic non-pathogenic SAA2.2. J Biol Chem 2012; 288:2744-55. [PMID: 23223242 DOI: 10.1074/jbc.m112.394155] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Serum amyloid A (SAA) is best known for being the main component of amyloid in the inflammation-related disease amyloid A (AA) amyloidosis. Despite the high sequence identity among different SAA isoforms, not all SAA proteins are pathogenic. In most mouse strains, the AA deposits mostly consist of SAA1.1. Conversely, the CE/J type mouse expresses a single non-pathogenic SAA2.2 protein that is 94% identical to SAA1.1. Here we show that SAA1.1 and SAA2.2 differ in their quaternary structure, fibrillation kinetics, prefibrillar oligomers, and fibril morphology. At 37 °C and inflammation-related SAA concentrations, SAA1.1 exhibits an oligomer-rich fibrillation lag phase of a few days, whereas SAA2.2 shows virtually no lag phase and forms small fibrils within a few hours. Deep UV resonance Raman, far UV-circular dichroism, atomic force microscopy, and fibrillation cross-seeding experiments suggest that SAA1.1 and SAA2.2 fibrils possess different morphology. Both the long-lived oligomers of pathogenic SAA1.1 and the fleeting prefibrillar oligomers of non-pathogenic SAA2.2, but not their respective amyloid fibrils, permeabilized synthetic bilayer membranes in vitro. This study represents the first comprehensive comparison between the biophysical properties of SAA isoforms with distinct pathogenicities, and the results suggest that structural and kinetic differences in the oligomerization-fibrillation of SAA1.1 and SAA2.2, more than their intrinsic amyloidogenicity, may contribute to their diverse pathogenicity.
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Affiliation(s)
- Saipraveen Srinivasan
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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139
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Balakrishnan G, Hu Y, Spiro TG. His26 protonation in cytochrome c triggers microsecond β-sheet formation and heme exposure: implications for apoptosis. J Am Chem Soc 2012; 134:19061-9. [PMID: 23094892 PMCID: PMC3529097 DOI: 10.1021/ja307100a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytochrome c unfolds locally and reversibly upon heating at pH 3. UV resonance Raman (UVRR) spectra reveal that instead of producing unordered structure, unfolding converts turns and some helical elements to β-sheet. It also disrupts the Met80-heme bond, and has been previously shown to induce peroxidase activity. Aromatic residues that are H-bonded to a heme propionate (Trp59 and Tyr48) alter their orientation, indicating heme displacement. T-jump/UVRR measurements give time constants of 0.2, 3.9, and 67 μs for successive phases of β-sheet formation and concomitant reorientation of Trp59. UVRR spectra reveal protonation of histidines, and specifically of His26, whose H-bond to Pro44 anchors the 40s Ω loop; this loop is known to be the least stable 'foldon' in the protein. His26 protonation is proposed to disrupt its H-bond with Pro44, triggering the extension of a short β-sheet segment at the 'neck' of the 40s Ω loop into the loop itself and back into the 60s and 70s helices. The secondary structure change displaces the heme via H-bonds from residues in the growing β-sheet, thereby exposing it to exogenous ligands, and inducing peroxidase activity. This unfolding mechanism may play a role in cardiolipin peroxidation by cyt c during apoptosis.
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140
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Kurouski D, Deckert-Gaudig T, Deckert V, Lednev IK. Structure and composition of insulin fibril surfaces probed by TERS. J Am Chem Soc 2012; 134:13323-9. [PMID: 22813355 DOI: 10.1021/ja303263y] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Amyloid fibrils associated with many neurodegenerative diseases are the most intriguing targets of modern structural biology. Significant knowledge has been accumulated about the morphology and fibril-core structure recently. However, no conventional methods could probe the fibril surface despite its significant role in the biological activity. Tip-enhanced Raman spectroscopy (TERS) offers a unique opportunity to characterize the surface structure of an individual fibril due to a high depth and lateral spatial resolution of the method in the nanometer range. Herein, TERS is utilized for characterizing the secondary structure and amino acid residue composition of the surface of insulin fibrils. It was found that the surface is strongly heterogeneous and consists of clusters with various protein conformations. More than 30% of the fibril surface is dominated by β-sheet secondary structure, further developing Dobson's model of amyloid fibrils (Jimenez et al. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9196-9201). The propensity of various amino acids to be on the fibril surface and specific surface secondary structure elements were evaluated. β-sheet areas are rich in cysteine and aromatic amino acids, such as phenylalanine and tyrosine, whereas proline was found only in α-helical and unordered protein clusters. In addition, we showed that carboxyl, amino, and imino groups are nearly equally distributed over β-sheet and α-helix/unordered regions. Overall, this study provides valuable new information about the structure and composition of the insulin fibril surface and demonstrates the power of TERS for fibril characterization.
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Affiliation(s)
- Dmitry Kurouski
- University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, USA
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141
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Pagba CV, Barry BA. Redox-Induced Conformational Switching in Photosystem-II-Inspired Biomimetic Peptides: A UV Resonance Raman Study. J Phys Chem B 2012; 116:10590-9. [DOI: 10.1021/jp303607b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Cynthia V. Pagba
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Bridgette A. Barry
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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142
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Al-Saidi WA, Asher SA, Norman P. Resonance Raman Spectra of TNT and RDX Using Vibronic Theory, Excited-State Gradient, and Complex Polarizability Approximations. J Phys Chem A 2012; 116:7862-72. [DOI: 10.1021/jp303920c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- W. A. Al-Saidi
- Department of Chemical and Petroleum
Engineering, University of Pittsburgh,
Pittsburgh, Pennsylvania 15261, United States
| | - Sanford A. Asher
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania
15260, United States
| | - Patrick Norman
- Department
of Physics, Chemistry
and Biology, Linköping University, SE-581 83 Linköping, Sweden
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