1
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Rogers DM, Do H, Hirst JD. An Improved Diabatization Scheme for Computing the Electronic Circular Dichroism of Proteins. J Phys Chem B 2024; 128:7350-7361. [PMID: 39034688 DOI: 10.1021/acs.jpcb.4c02582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
We advance the quality of first-principles calculations of protein electronic circular dichroism (CD) through an amelioration of a key deficiency of a previous procedure that involved diabatization of electronic states on the amide chromophore (to obtain interamide couplings) in a β-strand conformation of a diamide. This yields substantially improved calculated far-ultraviolet (far-UV) electronic circular dichroism (CD) spectra for β-sheet conformations. The interamide couplings from the diabatization procedure for 13 secondary structural elements (13 diamide structures) are applied to compute the CD spectra for seven example proteins: myoglobin (α helix), jacalin (β strand), concanavalin A (β type I), elastase (β type II), papain (α + β), 310-helix bundle (310-helix) and snow flea antifreeze protein (polyproline). In all cases, except concanavalin A and papain, the CD spectra computed using the interamide couplings from the diabatization procedure yield improved agreement with experiment with respect to previous first-principles calculations.
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Affiliation(s)
- David M Rogers
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Hainam Do
- Department of Chemical and Environmental Engineering and Key Laboratory of Carbonaceous Waste Processing and Process Intensification Research of Zhejiang Province, University of Nottingham Ningbo China, Ningbo 315100, China
- New Materials Institute, University of Nottingham Ningbo China, Ningbo 315042, China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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2
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O'Neill N, Lima TA, Furlan Ferreira F, Alvarez NJ, Schweitzer-Stenner R. Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123584. [PMID: 37956526 DOI: 10.1016/j.saa.2023.123584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA; Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210-580, Brazil
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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3
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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4
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Zanetti-Polzi L, Amadei A, Daidone I. Segregation on the nanoscale coupled to liquid water polyamorphism in supercooled aqueous ionic-liquid solution. J Chem Phys 2021; 155:104502. [PMID: 34525825 DOI: 10.1063/5.0061659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The most intriguing hypothesis explaining many water anomalies is a metastable liquid-liquid phase transition (LLPT) at high pressure and low temperatures, experimentally hidden by homogeneous nucleation. Recent infrared spectroscopic experiments showed that upon addition of hydrazinium trifluoroacetate to water, the supercooled ionic solution undergoes a sharp, reversible LLPT at ambient pressure, possible offspring of that in pure water. Here, we calculate the temperature-dependent signature of the OH-stretching band, reporting on the low/high density phase of water, in neat water and in the same experimentally investigated ionic solution. The comparison between the infrared signature of the pure liquid and that of the ionic solution can be achieved only computationally, providing insight into the nature of the experimentally observed phase transition and allowing us to investigate the effects of ionic compounds on the high to low density supercooled liquid water transition. We show that the experimentally observed crossover behavior in the ionic solution can be reproduced only if the phase transition between the low- and high-density liquid states of water is coupled to a mixing-unmixing transition between the water component and the ions: at low temperatures, water and ions are separated and the water component is a low density liquid. At high temperatures, water and ions get mixed and the water component is a high-density liquid. The separation at low temperatures into ion-rich and ion-poor regions allows unveiling the polyamorphic nature of liquid water, leading to a crossover behavior resembling that observed in supercooled neat water under high pressure.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR-Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy
| | - Andrea Amadei
- Department of Chemical and Technological Sciences, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00185 Rome, Italy
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy
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5
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Pinto SMV, Tasinato N, Barone V, Zanetti-Polzi L, Daidone I. A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures. J Chem Phys 2021; 154:084105. [PMID: 33639764 DOI: 10.1063/5.0038913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Infrared spectroscopy is a widely used technique to characterize protein structures and protein mediated processes. While the amide I band provides information on proteins' secondary structure, amino acid side chains are used as infrared probes for the investigation of protein reactions and local properties. In this paper, we use a hybrid quantum mechanical/classical molecular dynamical approach based on the perturbed matrix method to compute the infrared band due to the C=O stretching mode of amide-containing side chains. We calculate, at first, the infrared band of zwitterionic glutamine in water and obtain results in very good agreement with the experimental data. Then, we compute the signal arising from glutamine side chains in a microcrystal of the yeast prion Sup35-derived peptide, GNNQQNY, with a fibrillar structure. The infrared bands obtained by selective isotopic labeling of the two glutamine residues, Q4 and Q5, of each peptide were experimentally used to investigate the local hydration in the fibrillar microcrystal. The experimental spectra of the two glutamine residues, which experience different hydration environments, feature different spectral signals that are well reproduced by the corresponding calculated spectra. In addition, the analysis of the simulated spectra clarifies the molecular origin of the experimentally observed spectroscopic differences that arise from the different local electric field experienced by the two glutamine residues, which is, in turn, determined by a different hydrogen bonding pattern.
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Affiliation(s)
- Sandra M V Pinto
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67100 L'Aquila, Italy
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6
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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7
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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8
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Nagarajan S, Xiao S, Raleigh DP, Dyer RB. Heterogeneity in the Folding of Villin Headpiece Subdomain HP36. J Phys Chem B 2018; 122:11640-11648. [PMID: 30118232 DOI: 10.1021/acs.jpcb.8b07683] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small single domain proteins that fold on the microsecond time scale have been the subject of intense interest as models for probing the complexity of folding energy landscapes. The villin headpiece subdomain (HP36) has been extensively studied because of its simple three helix structure, ultrafast folding lifetime of a few microseconds, and stable native fold. We have previously shown that folding as measured by a single 13C═18O isotopic label on residue A57 in helix 2 occurs at a different rate than that measured by global probes of folding, indicating noncooperative complexity in the folding of HP36. In order to determine whether this complexity reflects intermediates or parallel pathways over a small activation barrier, 13C═18O labels were individually incorporated at six different positions in HP36, including into all 3 helices. The equilibrium thermal unfolding transitions and the folding/unfolding dynamics were monitored using the unique IR signature of the 13C═18O label by temperature dependent FTIR and temperature jump IR spectroscopy, respectively. Equilibrium experiments reveal that the 13C═18O labels at different positions in HP36 show drastic differences in the midpoint of their transitions ( Tm), ranging from 45 to 67 °C. Heterogeneity is also observed in the relaxation kinetics; there are differences in the microsecond phase when different labeled positions are probed. At a final temperature of 45 °C, the relaxation rate for 13C═18O A57 is 2.4e + 05 s-1 whereas for 13C═18O L69 HP36 the relaxation rate is 5.1e + 05 s-1, two times faster. The observation of site-dependent midpoints for the equilibrium unfolding transitions and differences in the relaxation rates of the labeled positions enables us to probe the progressive accumulation of the folded structure, providing insight into the microscopic details of the folding mechanism.
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Affiliation(s)
- Sureshbabu Nagarajan
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
| | - Shifeng Xiao
- Shenzhen Key Laboratory of Marine Biotechnology and Ecology, College of Life Sciences and Oceanography , Shenzhen University , Shenzhen 518060 , China
| | - Daniel P Raleigh
- Department of Chemistry , State University of New York at Stony Brook , Stony Brook , New York 11794 , United States.,Institute of Structural and Molecular Biology , University College London , Gower Street , London WC1E 6BT , United Kingdom
| | - R Brian Dyer
- Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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9
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Kurouski D. Advances of Vibrational Circular Dichroism (VCD) in bioanalytical chemistry. A review. Anal Chim Acta 2017; 990:54-66. [PMID: 29029743 PMCID: PMC10389559 DOI: 10.1016/j.aca.2017.08.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/26/2022]
Abstract
Vibrational Circular Dichroism (VCD) is a unique and relatively new spectroscopic technique that is capable of determining an absolute configuration of chiral molecules. VCD can be also used to determine structure of large macromolecules. This review highlights the most recent advances of VCD in bioanalytical chemistry. It shows that VCD is capable of unraveling supramolecular organization of peptides, proteins, saccharides, glycerophospholipids, polypeptide microcrystals, as well as amyloid fibrils and DNA. This review also demonstrates how VCD can be utilized to explore molecule-molecule interactions that determine mechanisms of chiral separations in chromatography. It aims to attract attention of scientists from all different research areas demonstrating the strength and capability of this very powerful spectroscopic technique.
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Affiliation(s)
- Dmitry Kurouski
- Department Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843, USA.
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10
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Lomont JP, Ostrander JS, Ho JJ, Petti MK, Zanni MT. Not All β-Sheets Are the Same: Amyloid Infrared Spectra, Transition Dipole Strengths, and Couplings Investigated by 2D IR Spectroscopy. J Phys Chem B 2017; 121:8935-8945. [PMID: 28851219 DOI: 10.1021/acs.jpcb.7b06826] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the transition dipole strengths and frequencies of the amyloid β-sheet amide I mode for the aggregated proteins amyloid-β1-40, calcitonin, α-synuclein, and glucagon. According to standard vibrational coupling models for proteins, the frequencies of canonical β-sheets are set by their size and structural and environmental disorder, which determines the delocalization length of the vibrational excitons. The larger the delocalization the lower the frequency of the main infrared-allowed transition, A⊥. The models also predict an accompanying increase in transition dipole strength. For the proteins measured here, we find no correlation between transition dipole strengths and amyloid β-sheet transition frequency. To understand this observation, we have extracted from the protein data bank crystal structures of amyloid peptides from which we calculate the amide I vibrational couplings, and we use these in a model β-sheet Hamiltonian to simulate amyloid vibrational spectra. We find that the variations in amyloid β-sheet structures (e.g., dihedral angles, interstrand distances, and orientations) create significant differences in the average values for interstrand and nearest neighbor couplings, and that those variations encompass the variation in measured A⊥ frequencies. We also find that off-diagonal disorder about the average values explains the range of transition dipole strengths observed experimentally. Thus, we conclude that the lack of correlation between transition dipole-strength and frequency is caused by variations in amyloid β-sheet structure. Taken together, these results indicate that the amide I frequency is very sensitive to amyloid β-sheet structure, the β-sheets of these 4 proteins are not identical, and the assumption that frequency of amyloids scales with β-sheet size cannot be adopted without an accompanying measurement of transition dipole strengths.
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Affiliation(s)
- Justin P Lomont
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Joshua S Ostrander
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Jia-Jung Ho
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Megan K Petti
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, WI 53706, United States
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11
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Shukla A, Khan E, Tandon P, Sinha K. Study of vibrational spectra and hydrogen bonding network in dimeric and tetrameric model of ampicillin using DFT and AIM approach. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Jose KVJ, Raghavachari K. Molecules-in-molecules fragment-based method for the calculation of chiroptical spectra of large molecules: Vibrational circular dichroism and Raman optical activity spectra of alanine polypeptides. Chirality 2016; 28:755-768. [DOI: 10.1002/chir.22651] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 12/17/2022]
Affiliation(s)
- K. V. Jovan Jose
- Department of Chemistry; Indiana University; Bloomington Indiana USA
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13
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Jose KVJ, Beckett D, Raghavachari K. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach. J Chem Theory Comput 2015; 11:4238-47. [DOI: 10.1021/acs.jctc.5b00647] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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14
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Daidone I, Thukral L, Smith JC, Amadei A. Monitoring the Folding Kinetics of a β-Hairpin by Time-Resolved IR Spectroscopy in Silico. J Phys Chem B 2015; 119:4849-56. [DOI: 10.1021/acs.jpcb.5b01477] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Isabella Daidone
- Department
of Physical and Chemical Sciences, University of L’Aquila, via
Vetoio (Coppito 1), 67010 L’Aquila, Italy
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, South Campus, Mathura Road, New Delhi 110020, India
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Andrea Amadei
- Department
of Chemical Sciences and Technologies, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, 00133 Rome, Italy
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15
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Scherrer A, Vuilleumier R, Sebastiani D. Nuclear Velocity Perturbation Theory of Vibrational Circular Dichroism. J Chem Theory Comput 2013; 9:5305-12. [DOI: 10.1021/ct400700c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Scherrer
- UMR 8640 ENS-CNRS-UPMC, Département de
Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
| | - R. Vuilleumier
- UMR 8640 ENS-CNRS-UPMC, Département de
Chimie, 24 rue Lhomond, École Normale Supérieure, 75005 Paris, France
- UPMC Université Paris 06, 4, Place Jussieu, 75005 Paris, France
| | - D. Sebastiani
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
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16
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Zanetti-Polzi L, Aschi M, Amadei A, Daidone I. Simulation of the Amide I Infrared Spectrum in Photoinduced Peptide Folding/Unfolding Transitions. J Phys Chem B 2013; 117:12383-90. [DOI: 10.1021/jp406708p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Laura Zanetti-Polzi
- Dipartimento
di Scienze Fisiche e Chimiche, University of L’Aquila, via
Vetoio (Coppito 1), 67010 Coppito (AQ), Italy
- Center
S3, Institute of Nanoscience - CNR, Via Campi 213/A, 41125 Modena, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, University of L’Aquila, via
Vetoio (Coppito 1), 67010 Coppito (AQ), Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, University of Rome ”Tor Vergata”, via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Isabella Daidone
- Dipartimento
di Scienze Fisiche e Chimiche, University of L’Aquila, via
Vetoio (Coppito 1), 67010 Coppito (AQ), Italy
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17
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Bee S, Agarwal P, Gupta A, Tandon P. Use of vibrational spectroscopy to study 2-[4-(N-dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole: a combined theoretical and experimental approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 114:236-255. [PMID: 23770512 DOI: 10.1016/j.saa.2013.05.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Quantum chemical calculations of geometric structure and vibrational wavenumbers of 2-[4-(N-dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole (AF51) were carried out by using density functional theory (DFT/B3LYP/6-311G(d,p) method. The fundamental vibrational modes were characterized depending on their potential energy distribution (PED). In order to predict the reactive sites for electrophilic and nucleophilic attacks of the title molecule, electrostatic potential surface has been plotted. The UV absorption spectrum was examined in chloroform solvent and compared with the calculated one in gas phase as well as in solvent environment using TD-DFT/ PCM approach. The (1)H NMR spectra was recorded. Comparison between the experimental and the theoretical results is satisfactory. The thermodynamic properties of the title compound at different temperatures have been calculated. A relationship between molecular structural features, non-linear responses and hyperpolarizability of AF51 has been established using vibrational spectra with emphasis on the role of intramolecular charge transfer mechanism in such organic NLO materials.
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Affiliation(s)
- Saba Bee
- Department of Applied Physics, Institute of Engineering and Technology, MJP Rohilkhand University, Bareilly, India
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18
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Sethi A, Anunciado D, Tian J, Vu DM, Gnanakaran S. Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics. Chem Phys 2013; 422:10.1016/j.chemphys.2013.05.005. [PMID: 24187427 PMCID: PMC3810979 DOI: 10.1016/j.chemphys.2013.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
As it remains practically impossible to generate ergodic ensembles for large intrinsically disordered proteins (IDP) with molecular dynamics (MD) simulations, it becomes critical to compare spectroscopic characteristics of the theoretically generated ensembles to corresponding measurements. We develop a Bayesian framework to infer the ensemble properties of an IDP using a combination of conformations generated by MD simulations and its measured infrared spectrum. We performed 100 different MD simulations totaling more than 10 µs to characterize the conformational ensemble of αsynuclein, a prototypical IDP, in water. These conformations are clustered based on solvent accessibility and helical content. We compute the amide-I band for these clusters and predict the thermodynamic weights of each cluster given the measured amide-I band. Bayesian analysis produces a reproducible and non-redundant set of thermodynamic weights for each cluster, which can then be used to calculate the ensemble properties. In a rigorous validation, these weights reproduce measured chemical shifts.
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Affiliation(s)
- Anurag Sethi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Divina Anunciado
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Jianhui Tian
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Dung M. Vu
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
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19
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Hudecová J, Profant V, Novotná P, Baumruk V, Urbanová M, Bouř P. CH Stretching Region: Computational Modeling of Vibrational Optical Activity. J Chem Theory Comput 2013; 9:3096-108. [PMID: 26583989 DOI: 10.1021/ct400285n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Most organic compounds provide vibrational spectra within the CH stretching region, yet the signal is difficult to interpret because of multiple difficulties in experiment and modeling. To better understand various factors involved, the ability of several harmonic and anharmonic computational approaches to describe these vibrations was explored for α-pinene, fenchone, and camphor as test compounds. Raman, Raman optical activity (ROA), infrared absorption (IR), and vibrational circular dichroism (VCD) spectra were measured and compared to quantum chemical computations. Surprisingly, the harmonic vibrational approach reasonably well reproduced the measured spectral patterns, including the vibrational optical activity (VOA). The CH stretching, however, appeared to be more sensitive to the basis set and solvent variations than lower-frequency vibrations. For a higher accuracy in frequencies and spectral shapes, anharmonic corrections were necessary. Accurate harmonic and anharmonic force fields were obtained with the mPW2PLYP double-hybrid functional. A limited vibrational configuration interaction (LVCI) where the CH stretching motion was decoupled from other vibrations provided the best simulated spectra. A balanced harmonic oscillator basis set had to be used, containing also states indirectly interacting with fundamental vibrations. A simpler second-order perturbational approach (PT2) appeared less useful. The modeling provided unprecedented agreement with experimental vibrational frequencies; spectral shapes were reproduced less faithfully. The possibility of ab initio interpretation of the CH spectral region for relatively large molecules further broadens the application span of vibrational spectroscopy.
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Affiliation(s)
- Jana Hudecová
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Václav Profant
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Pavlína Novotná
- Department of Physics and Measurements and Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Vladimír Baumruk
- Faculty of Mathematics and Physics, Institute of Physics, Charles University , Ke Karlovu 5, 12116, Prague 2, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements and Department of Analytical Chemistry, Institute of Chemical Technology , Technická 5, 16628 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences , Flemingovo náměstí 2, 16610 Prague, Czech Republic
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20
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Kim H, Cho M. Infrared Probes for Studying the Structure and Dynamics of Biomolecules. Chem Rev 2013; 113:5817-47. [DOI: 10.1021/cr3005185] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute,
Seoul 136-713, Korea
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21
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Dezhahang Z, Poopari MR, Xu Y. Vibrational Circular Dichroism Spectroscopy of Three Multidentate Nitrogen Donor Ligands: Conformational Flexibility and Solvent Effects. Chem Asian J 2013; 8:1205-12. [DOI: 10.1002/asia.201300070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Indexed: 11/08/2022]
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22
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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23
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Kessler J, Dračínský M, Bouř P. Parallel variable selection of molecular dynamics clusters as a tool for calculation of spectroscopic properties. J Comput Chem 2012; 34:366-71. [DOI: 10.1002/jcc.23143] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 08/30/2012] [Accepted: 09/07/2012] [Indexed: 11/10/2022]
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24
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Hudecová J, Horníček J, Buděšínský M, Šebestík J, Šafařík M, Zhang G, Keiderling TA, Bouř P. Three types of induced tryptophan optical activity compared in model dipeptides: theory and experiment. Chemphyschem 2012; 13:2748-60. [PMID: 22706803 DOI: 10.1002/cphc.201200201] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 04/27/2012] [Indexed: 11/08/2022]
Abstract
The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp-containing cyclic dipeptides c-(Trp-X) (where X = Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π-π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm(-1) indicates the local χ(2) angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion-corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion-DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.
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Affiliation(s)
- Jana Hudecová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague 6, Czech Republic.
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25
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Kobus M, Lieder M, Nguyen PH, Stock G. Simulation of transient infrared spectra of a photoswitchable peptide. J Chem Phys 2012; 135:225102. [PMID: 22168727 DOI: 10.1063/1.3664747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In transient infrared (IR) experiments, a molecular system may be photoexcited in a nonstationary conformational state, whose time evolution is monitored via IR spectroscopy with high temporal and structural resolution. As a theoretical formulation of these experiments, this work derives explicit expressions for transient one- and two-dimensional IR spectra and discusses various levels of approximation and sampling strategies. Adopting a photoswitchable octapeptide in water as a representative example, nonequilibrium molecular dynamics simulations are performed and the photoinduced conformational dynamics and associated IR spectra are discussed in detail. Interestingly, it is found that the time scales of dynamics and spectra may differ from residue to residue by up to an order of magnitude. Considering merely the cumulative spectrum of all residues, the contributions of the individual residues largely compensate each other, which may explain the surprisingly small frequency shifts and short photoproduct rise times found in experiment. Even when a localized amide I mode is probed (e.g., via isotope labeling), the vibrational frequency shift is shown to depend in a complicated way on the conformation of the entire peptide as well as on the interaction with the solvent. In this context, various issues concerning the interpretation of transient IR spectra and conformational dynamics in terms of a few exponential time scales are discussed.
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Affiliation(s)
- Maja Kobus
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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26
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Schweitzer-Stenner R. Simulated IR, Isotropic and Anisotropic Raman, and Vibrational Circular Dichroism Amide I Band Profiles of Stacked β-Sheets. J Phys Chem B 2012; 116:4141-53. [DOI: 10.1021/jp2112445] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department
of Chemistry, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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27
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Zanetti Polzi L, Daidone I, Amadei A. A Theoretical Reappraisal of Polylysine in the Investigation of Secondary Structure Sensitivity of Infrared Spectra. J Phys Chem B 2012; 116:3353-60. [DOI: 10.1021/jp211063x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Zanetti Polzi
- Department of Chemistry, Chemical
Engineering and Materials, University of L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy
| | - Isabella Daidone
- Department of Chemistry, Chemical
Engineering and Materials, University of L’Aquila, via Vetoio (Coppito 1), 67010 L’Aquila, Italy
| | - Andrea Amadei
- Department of Chemical Sciences
and Technology, University of Rome “Tor Vergata”, via della Ricerca Scientifica 1, 00133 Rome, Italy
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28
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Yamamoto S, Li X, Ruud K, Bouř P. Transferability of Various Molecular Property Tensors in Vibrational Spectroscopy. J Chem Theory Comput 2012; 8:977-85. [DOI: 10.1021/ct200714h] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shigeki Yamamoto
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
166 10 Prague, Czech Republic
| | - Xiaojun Li
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Kenneth Ruud
- Centre
for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Petr Bouř
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences,
166 10 Prague, Czech Republic
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29
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Schweitzer-Stenner R, Soffer JB, Verbaro D. Structure analysis of unfolded peptides I: vibrational circular dichroism spectroscopy. Methods Mol Biol 2012; 895:271-313. [PMID: 22760325 DOI: 10.1007/978-1-61779-927-3_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).
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30
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Choi JH, Cho M. Direct Calculations of Mid- and Near-IR Absorption and Circular Dichroism Spectra of Chiral Molecules Using QM/MM Molecular Dynamics Simulation Method. J Chem Theory Comput 2011; 7:4097-103. [DOI: 10.1021/ct200660s] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 1360-713, Korea
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31
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Zanetti Polzi L, Daidone I, Anselmi M, Carchini G, Di Nola A, Amadei A. Analysis of Infrared Spectra of β-Hairpin Peptides As Derived from Molecular Dynamics Simulations. J Phys Chem B 2011; 115:11872-8. [DOI: 10.1021/jp202332z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
| | - Isabella Daidone
- Dipartimento di Chimica Ingegneria Chimica e Materiali, University of L′Aquila, Coppito (AQ), Italy
| | | | - Giuliano Carchini
- Dipartimento di Chimica, University of Rome “La Sapienza”, Rome, Italy
| | - Alfredo Di Nola
- Dipartimento di Chimica, University of Rome “La Sapienza”, Rome, Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome “Tor Vergata”, Rome, Italy
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32
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Bieler NS, Haag MP, Jacob CR, Reiher M. Analysis of the Cartesian Tensor Transfer Method for Calculating Vibrational Spectra of Polypeptides. J Chem Theory Comput 2011; 7:1867-81. [DOI: 10.1021/ct2001478] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Noah S. Bieler
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Moritz P. Haag
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Christoph R. Jacob
- Karlsruhe Institute of Technology (KIT), Center for Functional Nanostructures, Wolfgang-Gaede-Str. 1a, 76131 Karlsruhe, Germany
| | - Markus Reiher
- ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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33
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Magyarfalvi G, Tarczay G, Vass E. Vibrational circular dichroism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.39] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Kobus M, Nguyen PH, Stock G. Coherent vibrational energy transfer along a peptide helix. J Chem Phys 2011; 134:124518. [DOI: 10.1063/1.3574395] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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35
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Santiveri CM, Jiménez MA. Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides. Biopolymers 2011; 94:779-90. [PMID: 20564027 DOI: 10.1002/bip.21436] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid 28006, Spain
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36
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Jiang N, Tan RX, Ma J. Simulations of Solid-State Vibrational Circular Dichroism Spectroscopy of (S)-Alternarlactam by Using Fragmentation Quantum Chemical Calculations. J Phys Chem B 2011; 115:2801-13. [DOI: 10.1021/jp110152q] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nan Jiang
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
| | - Ren Xiang Tan
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu 210093, People’s Republic of China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Institute of Theoretical and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry of MOE, Nanjing University, Nanjing, Jiangsu, 210093, People’s Republic of China
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37
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Yamamoto S, Watarai H, Bouř P. Monitoring the Backbone Conformation of Valinomycin by Raman Optical Activity. Chemphyschem 2011; 12:1509-18. [DOI: 10.1002/cphc.201000917] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 01/18/2011] [Indexed: 11/11/2022]
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38
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Amadei A, Daidone I, Zanetti-Polzi L, Aschi M. Modeling quantum vibrational excitations in condensed-phase molecular systems. Theor Chem Acc 2011. [DOI: 10.1007/s00214-010-0882-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Zhao J, Wang J. Amide vibrations and their conformational dependences in β-peptide. J Phys Chem B 2010; 114:16011-9. [PMID: 21070067 DOI: 10.1021/jp108324p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The characteristics of the amide-A and amide-I modes in a β-homoalanine dipeptide (β-HADP) have been examined as a function of backbone dihedral angles. The harmonic frequencies were obtained using the density functional theory. The anharmonic frequencies and diagonal anharmonicities were obtained by using the Morse potential. Local-mode frequencies and intermode couplings were obtained using the computed normal-mode frequencies and eigenvectors. It was found that the vibrational frequencies for the two types of amide modes are both conformational-dependent. The inter-amide-A and inter-amide-I couplings in the β-peptides were predicted to be generally weaker than those in the α-peptides. Structural bases of the amide-A and amide-I local modes in the β-peptides are discussed.
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Affiliation(s)
- Juan Zhao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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40
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Kaminský J, Bouř P, Kubelka J. Simulations of the Temperature Dependence of Amide I Vibration. J Phys Chem A 2010; 115:30-4. [DOI: 10.1021/jp1084839] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jakub Kaminský
- University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071, United States, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic
| | - Petr Bouř
- University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071, United States, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic
| | - Jan Kubelka
- University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071, United States, and Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic
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41
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Grahnen JA, Amunson KE, Kubelka J. DFT-Based Simulations of IR Amide I′ Spectra for a Small Protein in Solution. Comparison of Explicit and Empirical Solvent Models. J Phys Chem B 2010; 114:13011-20. [DOI: 10.1021/jp106639s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan A. Grahnen
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
| | - Krista E. Amunson
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
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42
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Chi H, Lakhani A, Roy A, Nakaema M, Keiderling TA. Inter-residue Coupling and Equilibrium Unfolding of PPII Helical Peptides. Vibrational Spectra Enhanced with 13C Isotopic Labeling. J Phys Chem B 2010; 114:12744-53. [DOI: 10.1021/jp106095q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heng Chi
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Ahmed Lakhani
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Anjan Roy
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Marcelo Nakaema
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St. (m/c111), Chicago, Illinois 60607-7061
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43
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Kobus M, Nguyen PH, Stock G. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J Chem Phys 2010; 133:034512. [DOI: 10.1063/1.3462961] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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44
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Hatfield MPD, Murphy RF, Lovas S. VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents. Biopolymers 2010; 93:442-50. [PMID: 19937759 PMCID: PMC4499852 DOI: 10.1002/bip.21356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.
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Affiliation(s)
| | - Richard. F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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45
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Daidone I, Aschi M, Zanetti-Polzi L, Di Nola A, Amadei A. On the origin of IR spectral changes upon protein folding. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.02.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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46
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Dracínský M, Kaminský J, Bour P. Structure of the alanine hydration shell as probed by NMR chemical shifts and indirect spin-spin coupling. J Phys Chem B 2010; 113:14698-707. [PMID: 19863140 DOI: 10.1021/jp9034198] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The structure of the alanine hydration shell was modeled by Carr-Parinello molecular dynamics (CPMD) to explain subtle differences in NMR chemical shifts and indirect spin-spin coupling constants of the neutral (zwitterionic), cationic, and anionic forms of this amino acid. In comparison with classical molecular dynamics (MD), the quantum mechanical CPMD approach revealed a more structured solvent and significant differences in the radial and angular distributions of the water molecules around the solute. In particular, the solvent was predicted to be organized around the uncharged COOH and NH(2) residues to a similar degree as that for the charged ones. This was not the case with MD. For snapshot CPMD configurations, the NMR parameters were computed by density functional theory (DFT) and averaged. Obtained values were significantly closer to experimental parameters known for (15)N and (13)C isotopically labeled alanine than those calculated by the conventional implicit dielectric solvent model. The NMR results also quantitatively reflect a superiority of the CPMD over the MD explicit solvent treatment. A further improvement of the computed spin-spin coupling constants could be achieved by taking into account vibrational averaging beyond the harmonic approximation. Differently positioned water molecules in the clusters cause an unexpectedly large scattering of the NMR parameters. About 10-15 dynamics snapshots were required for a satisfactory convergence of the shifts and couplings. The NMR chemical shift was found to be much more sensitive to the molecular hydration than the coupling. The results thus indicate a large potential of the NMR spectroscopy and quantum simulations to probe not only the structure of molecules but also their interactions with the environment.
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Affiliation(s)
- Martin Dracínský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic.
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Yamamoto S, Straka M, Watarai H, Bouř P. Formation and structure of the potassium complex of valinomycin in solution studied by Raman optical activity spectroscopy. Phys Chem Chem Phys 2010; 12:11021-32. [DOI: 10.1039/c003277h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Kudo M, Hanashima T, Muranaka A, Sato H, Uchiyama M, Azumaya I, Hirano T, Kagechika H, Tanatani A. Identification of Absolute Helical Structures of Aromatic Multilayered Oligo(m-phenylurea)s in Solution. J Org Chem 2009; 74:8154-63. [DOI: 10.1021/jo901934r] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mayumi Kudo
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Takayuki Hanashima
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Atsuya Muranaka
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hisako Sato
- Faculty of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
| | - Masanobu Uchiyama
- Advanced Elements Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Isao Azumaya
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomoya Hirano
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Hiroyuki Kagechika
- School of Biomedical Science, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Aya Tanatani
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
- PRESTO, Japan Science and Technology Agency (JST), Japan
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Yang S, Cho M. Direct calculations of vibrational absorption and circular dichroism spectra of alanine dipeptide analog in water: Quantum mechanical/molecular mechanical molecular dynamics simulations. J Chem Phys 2009; 131:135102. [DOI: 10.1063/1.3243078] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
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Torii H. Nature of vibrational frequency modulations and the related one- and two-dimensional vibrational spectral features analysed for the amide I mode of tetraalanine in aqueous solution. Mol Phys 2009. [DOI: 10.1080/00268970902804542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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