1
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Freedman H, Tuszynski JA. Study of the Myosin Relay Helix Peptide by Molecular Dynamics Simulations, Pump-Probe and 2D Infrared Spectroscopy. Int J Mol Sci 2024; 25:6406. [PMID: 38928112 PMCID: PMC11203622 DOI: 10.3390/ijms25126406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The Davydov model was conjectured to describe how an amide I excitation created during ATP hydrolysis in myosin might be significant in providing energy to drive myosin's chemomechanical cycle. The free energy surfaces of the myosin relay helix peptide dissolved in 2,2,2-trifluoroethanol (TFE), determined by metadynamics simulations, demonstrate local minima differing in free energy by only ~2 kT, corresponding to broken and stabilized hydrogen bonds, respectively. Experimental pump-probe and 2D infrared spectroscopy were performed on the peptide dissolved in TFE. The relative heights of two peaks seen in the pump-probe data and the corresponding relative volumes of diagonal peaks seen in the 2D-IR spectra at time delays between 0.5 ps and 1 ps differ noticeably from what is seen at earlier or later time delays or in the linear spectrum, indicating that a vibrational excitation may influence the conformational state of this helix. Thus, it is possible that the presence of an amide I excitation may be a direct factor in the conformational state taken on by the myosin relay helix following ATP hydrolysis in myosin.
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Affiliation(s)
- Holly Freedman
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 306, Salt Lake City, UT 84112, USA
| | - Jack A. Tuszynski
- Department of Physics, University of Alberta, 11335 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada;
- DIMEAS, Politecnico di Torino, Corso Duca degli Abruzzi 24, I-1029 Turin, Italy
- Department of Data Science and Engineering, The Silesian University of Technology, 44-100 Gliwice, Poland
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2
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Konstantinovsky D, Santiago T, Tremblay M, Simpson GJ, Hammes-Schiffer S, Yan ECY. Theoretical basis for interpreting heterodyne chirality-selective sum frequency generation spectra of water. J Chem Phys 2024; 160:055102. [PMID: 38341693 PMCID: PMC10846909 DOI: 10.1063/5.0181718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/08/2024] [Indexed: 02/13/2024] Open
Abstract
Chirality-selective vibrational sum frequency generation (chiral SFG) spectroscopy has emerged as a powerful technique for the study of biomolecular hydration water due to its sensitivity to the induced chirality of the first hydration shell. Thus far, water O-H vibrational bands in phase-resolved heterodyne chiral SFG spectra have been fit using one Lorentzian function per vibrational band, and the resulting fit has been used to infer the underlying frequency distribution. Here, we show that this approach may not correctly reveal the structure and dynamics of hydration water. Our analysis illustrates that the chiral SFG responses of symmetric and asymmetric O-H stretch modes of water have opposite phase and equal magnitude and are separated in energy by intramolecular vibrational coupling and a heterogeneous environment. The sum of the symmetric and asymmetric responses implies that an O-H stretch in a heterodyne chiral SFG spectrum should appear as two peaks with opposite phase and equal amplitude. Using pairs of Lorentzian functions to fit water O-H stretch vibrational bands, we improve spectral fitting of previously acquired experimental spectra of model β-sheet proteins and reduce the number of free parameters. The fitting allows us to estimate the vibrational frequency distribution and thus reveals the molecular interactions of water in hydration shells of biomolecules directly from chiral SFG spectra.
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Affiliation(s)
| | - Ty Santiago
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Matthew Tremblay
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Garth J. Simpson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | | | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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3
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Baronio CM, Barth A. Refining protein amide I spectrum simulations with simple yet effective electrostatic models for local wavenumbers and dipole derivative magnitudes. Phys Chem Chem Phys 2024; 26:1166-1181. [PMID: 38099625 DOI: 10.1039/d3cp02018e] [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: 01/04/2024]
Abstract
Analysis of the amide I band of proteins is probably the most wide-spread application of bioanalytical infrared spectroscopy. Although highly desirable for a more detailed structural interpretation, a quantitative description of this absorption band is still difficult. This work optimized several electrostatic models with the aim to reproduce the effect of the protein environment on the intrinsic wavenumber of a local amide I oscillator. We considered the main secondary structures - α-helices, parallel and antiparallel β-sheets - with a maximum of 21 amide groups. The models were based on the electric potential and/or the electric field component along the CO bond at up to four atoms in an amide group. They were bench-marked by comparison to Hessian matrices reconstructed from density functional theory calculations at the BPW91, 6-31G** level. The performance of the electrostatic models depended on the charge set used to calculate the electric field and potential. Gromos and DSSP charge sets, used in common force fields, were not optimal for the better performing models. A good compromise between performance and the stability of model parameters was achieved by a model that considered the electric field at the positions of the oxygen, nitrogen, and hydrogen atoms of the considered amide group. The model describes also some aspects of the local conformation effect and performs similar on its own as in combination with an explicit implementation of the local conformation effect. It is better than a combination of a local hydrogen bonding model with the local conformation effect. Even though the short-range hydrogen bonding model performs worse, it captures important aspects of the local wavenumber sensitivity to the molecular surroundings. We improved also the description of the coupling between local amide I oscillators by developing an electrostatic model for the dependency of the dipole derivative magnitude on the protein environment.
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Affiliation(s)
- Cesare M Baronio
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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4
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Man VH, He X, Nguyen PH, Sagui C, Roland C, Xie XQ, Wang J. Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation. Comput Biol Med 2023; 159:106902. [PMID: 37086661 PMCID: PMC10186340 DOI: 10.1016/j.compbiomed.2023.106902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/07/2023] [Accepted: 04/09/2023] [Indexed: 04/24/2023]
Abstract
The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.
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Affiliation(s)
- Viet Hoang Man
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
| | - Xibing He
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Phuong H Nguyen
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005, Paris, France
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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5
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Hu R, Ding X, Yu P, He X, Watts A, Zhao X, Wang J. Ultrafast Two-Dimensional Infrared Spectroscopy Resolved a Structured Lysine 159 on the Cytoplasmic Surface of the Microbial Photoreceptor Bacteriorhodopsin. J Am Chem Soc 2022; 144:22083-22092. [PMID: 36399663 DOI: 10.1021/jacs.2c09435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a light-driven microbial receptor, and lysine 159 (K159) is a charged residue on the cytoplasmic (CP) side of its E-F loop. However, its conformation and function remain unknown due to fast surface dynamics. By utilizing a 13C, 15N-labeled lysine (K) as an isotope probe, we created a network of site-specific amide-I vibrational signatures (backbone carbonyl stretch) to identify the frequency contribution of the labeled residues to the amide-I excitonic band structure. Thus, the red-shifted amide-I frequency in the 13C, 15N-lysine-labeled bR (uK-bR) to the unlabeled bR (WT-bR) could be differentiated and examined by ultrafast two-dimensional vibrational echo infrared (2D IR) spectroscopy. Our results showed that the backbone carbonyl of K159 is located at a high frequency of ca. 1693 cm-1 and has a vibrational excited-state relaxation time shorter than the bulk helical amide-I mode at the same frequency, suggesting that K159 may possess a hydrogen-bonded γ-turn structure with E161, one of the carboxylate residues on the CP surface of bR. The 2D solid-state NMR study of uK-bR also revealed conformational dependent lysine residues, from which K159 was found to involve the turn motif. This γ-turn structure maintained by K159 may help to stabilize the E-F loop and support E161 in attracting protons from the bulk during the late stage of the bR photocycle. The combined spectroscopic approach illustrated in this work may be applied to map residue-specific local structures and dynamics of other receptors and large proteins.
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Affiliation(s)
- Rong Hu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaoyan Ding
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China.,Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xuemei He
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, South Park Road, Oxford OX1 3QU, U.K
| | - Xin Zhao
- Department of Physics, School of Physics and Electronic Science, East China Normal University, 500 Dongchuan Road, Minhang District, Shanghai 200241, P.R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China.,University of Chinese Academy of Sciences, Beijing 100049, P.R. China
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6
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Edun DN, Cracchiolo OM, Serrano AL. A theoretical analysis of coherent cross-peaks in polarization selective 2DIR for detection of cross-α fibrils. J Chem Phys 2022; 156:035102. [DOI: 10.1063/5.0070553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dean N. Edun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Olivia M. Cracchiolo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Arnaldo L. Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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7
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Edun DN, Flanagan MR, Serrano AL. Does liquid-liquid phase separation drive peptide folding? Chem Sci 2020; 12:2474-2479. [PMID: 34164013 PMCID: PMC8179267 DOI: 10.1039/d0sc04993j] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Proline-arginine (PR) dipeptide repeats have been shown to undergo liquid-liquid phase separation and are an example of a growing number of intrinsically disordered proteins that can assemble into membraneless organelles. These structures have been posited as nucleation sites for pathogenic protein aggregation. As such, a better understanding of the effects that the increased local concentration and volumetric crowding within droplets have on peptide secondary structure is necessary. Herein we use Fourier transform infrared (FTIR) and two-dimensional infrared (2DIR) spectroscopy to show that formation of droplets by PR20 accompanies changes in the amide-I spectra consistent with folding into poly-proline helical structures.
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Affiliation(s)
- Dean N Edun
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame Indiana 46556 USA
| | - Meredith R Flanagan
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame Indiana 46556 USA
| | - Arnaldo L Serrano
- Department of Chemistry and Biochemistry, University of Notre Dame Notre Dame Indiana 46556 USA
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8
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Biswas S, Mallik BS. Solvent-mediated dynamics and stretching profile of amide modes: QM/MM simulations of N-methylacetamide in ionic and various molecular liquids. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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9
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Baronio CM, Barth A. The Amide I Spectrum of Proteins-Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations. J Phys Chem B 2020; 124:1703-1714. [PMID: 32040320 PMCID: PMC7307917 DOI: 10.1021/acs.jpcb.9b11793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
![]()
The
amide I region of the infrared spectrum is related to the protein
backbone conformation and can provide important structural information.
However, the interpretation of the experimental results is hampered
because the theoretical description of the amide I spectrum is still
under development. Quantum mechanical calculations, for example, using
density functional theory (DFT), can be used to study the amide I
spectrum of small systems, but the high computational cost makes them
inapplicable to proteins. Other approaches that solve the eigenvalues
of the coupled amide I oscillator system are used instead. An important
interaction to be considered is transition dipole coupling (TDC).
Its calculation depends on the parameters of the transition dipole
moment. This work aims to find the optimal parameters for TDC in three
major secondary structures: α-helices, antiparallel β-sheets,
and parallel β-sheets. The parameters were suggested through
a comparison between DFT and TDC calculations. The comparison showed
a good agreement for the spectral shape and for the wavenumbers of
the normal modes for all secondary structures. The matching between
the two methods improved when hydrogen bonding to the amide oxygen
was considered. Optimal parameters for individual secondary structures
were also suggested.
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Affiliation(s)
- Cesare M Baronio
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 106 91, Sweden
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10
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Baronio CM, Baldassarre M, Barth A. Insight into the internal structure of amyloid-β oligomers by isotope-edited Fourier transform infrared spectroscopy. Phys Chem Chem Phys 2019; 21:8587-8597. [DOI: 10.1039/c9cp00717b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Isotope-edited infrared spectroscopy reveals the structural unit of amyloid-β oligomers.
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Affiliation(s)
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics
- Stockholm University
- Sweden
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11
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Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Ramesh P, Loring RF. Thermal Population Fluctuations in Two-Dimensional Infrared Spectroscopy Captured with Semiclassical Mechanics. J Phys Chem B 2018; 122:3647-3654. [DOI: 10.1021/acs.jpcb.7b12122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prashanth Ramesh
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Roger F. Loring
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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13
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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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14
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Simulation of the T-jump triggered unfolding and thermal unfolding vibrational spectroscopy related to polypeptides conformation fluctuation. Sci China Chem 2017. [DOI: 10.1007/s11426-016-9055-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Hahn S. Effective representation of amide III, II, I, and A modes on local vibrational modes: Analysis of ab initio quantum calculation results. J Chem Phys 2016; 145:164113. [PMID: 27802648 DOI: 10.1063/1.4965958] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Hamiltonian matrix for the first excited vibrational states of a protein can be effectively represented by local vibrational modes constituting amide III, II, I, and A modes to simulate various vibrational spectra. Methods for obtaining the Hamiltonian matrix from ab initio quantum calculation results are discussed, where the methods consist of three steps: selection of local vibrational mode coordinates, calculation of a reduced Hessian matrix, and extraction of the Hamiltonian matrix from the Hessian matrix. We introduce several methods for each step. The methods were assessed based on the density functional theory calculation results of 24 oligopeptides with four different peptide lengths and six different secondary structures. The completeness of a Hamiltonian matrix represented in the reduced local mode space is improved by adopting a specific atom group for each amide mode and reducing the effect of ignored local modes. The calculation results are also compared to previous models using C=O stretching vibration and transition dipole couplings. We found that local electric transition dipole moments of the amide modes are mainly bound on the local peptide planes. Their direction and magnitude are well conserved except amide A modes, which show large variation. Contrary to amide I modes, the vibrational coupling constants of amide III, II, and A modes obtained by analysis of a dipeptide are not transferable to oligopeptides with the same secondary conformation because coupling constants are affected by the surrounding atomic environment.
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Affiliation(s)
- Seungsoo Hahn
- Department of Chemistry, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu 156-756, Seoul, South Korea
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16
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Kitzig S, Thilemann M, Cordes T, Rück-Braun K. Light-Switchable Peptides with a Hemithioindigo Unit: Peptide Design, Photochromism, and Optical Spectroscopy. Chemphyschem 2016; 17:1252-63. [DOI: 10.1002/cphc.201501050] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Indexed: 12/21/2022]
Affiliation(s)
- S. Kitzig
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
| | - M. Thilemann
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
| | - T. Cordes
- Molecular Microscopy Research Group; Zernike Institute for Advanced Materials; University of Groningen; Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Karola Rück-Braun
- Institut für Chemie; Technische Universität Berlin; Str. des 17. Juni 135 10623 Berlin Germany
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17
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Dunkelberger EB, Grechko M, Zanni MT. Transition Dipoles from 1D and 2D Infrared Spectroscopy Help Reveal the Secondary Structures of Proteins: Application to Amyloids. J Phys Chem B 2015; 119:14065-75. [PMID: 26446575 DOI: 10.1021/acs.jpcb.5b07706] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Transition dipoles are an underutilized quantity for probing molecular structures. The transition dipole strengths in an extended system like a protein are modulated by the couplings and thus probe the structures. Here we measure the absolute transition dipole strengths of human and rat amylin in their solution, aggregated, membrane, and micelleular bound forms, using a combination of 1D and 2D infrared spectroscopy. We find that the vibrational modes of amyloid fibers made of human amylin can extend across as many as 12 amino acids, reflecting very ordered β-sheets in the most carefully prepared samples. Rat amylin has FTIR spectra that are nearly identical in solution, micelles, and membranes. We show that the transition dipoles of rat amylin are much larger when bound to micelles and membranes than when in solution, consistent with rat amylin adopting an α-helical structure. We interpret the transition dipole strengths as experimental measurements of the inverse participation ratio often calculated in theoretical studies. The structure of aggregating and membrane-bound proteins can be difficult to identify with existing techniques, especially during kinetics. These results demonstrate how absolute transition dipoles measured via our 1D/2D spectroscopy method can provide important structural information.
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Affiliation(s)
- Emily B Dunkelberger
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706-1396, United States
| | - Maksim Grechko
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706-1396, United States
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706-1396, United States
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18
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Alemi M, Loring RF. Two-Dimensional Vibrational Spectroscopy of a Dissipative System with the Optimized Mean-Trajectory Approximation. J Phys Chem B 2015; 119:8950-9. [PMID: 25275943 PMCID: PMC4383732 DOI: 10.1021/jp5076884] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/10/2014] [Indexed: 11/30/2022]
Abstract
The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions representing radiation-matter interactions. Here we apply this method to an anharmonic chromophore coupled to a harmonic bath. A forward-backward trajectory implementation of the OMT method is described that addresses the numerical challenges of applying the OMT to large systems with disparate frequency scales. The OMT is shown to well reproduce line shapes and waiting time dynamics in the pure dephasing limit of weak coupling to an off-resonant bath. The OMT is also shown to describe a case where energy transfer is the predominant source of line broadening.
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Affiliation(s)
- Mallory Alemi
- Department
of Chemistry and
Chemical Biology, Baker Laboratory, Cornell
University, Ithaca, New York 14853, United
States
| | - Roger F. Loring
- Department
of Chemistry and
Chemical Biology, Baker Laboratory, Cornell
University, Ithaca, New York 14853, United
States
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19
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Alemi M, Loring RF. Vibrational coherence and energy transfer in two-dimensional spectra with the optimized mean-trajectory approximation. J Chem Phys 2015; 142:212417. [PMID: 26049437 DOI: 10.1063/1.4916644] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The optimized mean-trajectory (OMT) approximation is a semiclassical method for computing vibrational response functions from action-quantized classical trajectories connected by discrete transitions that represent radiation-matter interactions. Here, we extend the OMT to include additional vibrational coherence and energy transfer processes. This generalized approximation is applied to a pair of anharmonic chromophores coupled to a bath. The resulting 2D spectra are shown to reflect coherence transfer between normal modes.
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Affiliation(s)
- Mallory Alemi
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Roger F Loring
- Baker Laboratory, Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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20
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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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21
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Chatterjee P, Bagchi S, Sengupta N. The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1. J Chem Phys 2014; 141:205103. [PMID: 25429964 DOI: 10.1063/1.4901897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
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22
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Choi JH, Cho M. Terahertz Chiroptical Spectroscopy of an α-Helical Polypeptide: A Molecular Dynamics Simulation Study. J Phys Chem B 2014; 118:12837-43. [DOI: 10.1021/jp508547y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun-Ho Choi
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-713, Korea
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23
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Wu T, Zhang R, Li H, Yang L, Zhuang W. Discriminating trpzip2 and trpzip4 peptides' folding landscape using the two-dimensional infrared spectroscopy: a simulation study. J Chem Phys 2014; 140:055101. [PMID: 24511982 DOI: 10.1063/1.4863562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB(OBC) implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors.
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Affiliation(s)
- Tianmin Wu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Ruiting Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Huanhuan Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
| | - Lijiang Yang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Wei Zhuang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning, People's Republic of China
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24
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Zhao J, Shi J, Wang J. Amide-I characteristics of helical β-peptides by linear infrared measurement and computations. J Phys Chem B 2013; 118:94-106. [PMID: 24328259 DOI: 10.1021/jp4095936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we have examined the amide-I characteristics of three β-peptide oligomers in typical helical conformations (two in 14-helix and one in 12/10-helix), solvated in water, methanol, and chloroform, respectively. Local-mode frequencies and their distributions were computed using a molecular-mechanics force field based frequency map that was constructed on the basis of molecular dynamics simulations. The local-mode frequencies were found to be determined primarily by peptide backbone and side chain, rather by solvent, suggesting their local structural sensitivities. Intermode vibrational couplings computed using a transition dipole scheme were found to be very sensitive to peptide conformation, with their signs and magnitudes varying periodically along the peptide chain. Linear infrared absorption spectra of the three peptides, simulated using a frequency-frequency time-correlation function method, were found to be in fair agreement with experimental results. Normalized potential energy distribution analysis indicated that the amide-I mode can delocalize over a few amide units. However, the IR band structure appears to be more sophisticated in helical β-peptides than in helical α-peptides.
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Affiliation(s)
- Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
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25
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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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26
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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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27
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Choi JH, Cho M. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants. J Chem Phys 2013; 138:174108. [DOI: 10.1063/1.4802991] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Han C, Wang J. Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides. Chemphyschem 2012; 13:1522-34. [DOI: 10.1002/cphc.201100995] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Indexed: 11/09/2022]
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29
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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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30
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Biancardi A, Cammi R, Cappelli C, Mennucci B, Tomasi J. Modelling vibrational coupling in DNA oligomers: a computational strategy combining QM and continuum solvation models. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1157-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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31
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Han C, Wang JP. Temperature-Dependence of the Amide-I Frequency Map for Peptides and Proteins. CHINESE J CHEM PHYS 2011. [DOI: 10.1088/1674-0068/24/05/529-537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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32
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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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33
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34
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Wang L, Middleton CT, Zanni MT, Skinner JL. Development and validation of transferable amide I vibrational frequency maps for peptides. J Phys Chem B 2011; 115:3713-24. [PMID: 21405034 DOI: 10.1021/jp200745r] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared (IR) spectroscopy of the amide I band has been widely utilized for the analysis of peptides and proteins. Theoretical modeling of IR spectra of proteins requires an accurate and efficient description of the amide I frequencies. In this paper, amide I frequency maps for protein backbone and side chain groups are developed from experimental spectra and vibrational lifetimes of N-methylacetamide and acetamide in different solvents. The frequency maps, along with established nearest-neighbor frequency shift and coupling schemes, are then applied to a variety of peptides in aqueous solution and reproduce experimental spectra well. The frequency maps are designed to be transferable to different environments; therefore, they can be used for heterogeneous systems, such as membrane proteins.
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Affiliation(s)
- L Wang
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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35
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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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36
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Ma X, Cai K, Wang J. Dynamical Structures of Glycol and Ethanedithiol Examined by Infrared Spectroscopy, Ab Initio Computation, and Molecular Dynamics Simulations. J Phys Chem B 2011; 115:1175-87. [DOI: 10.1021/jp107752a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Xiaoyan Ma
- 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
| | - Kaicong Cai
- 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
| | - Jianping Wang
- 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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37
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Abramczyk H, Brozek-Pluska B, Surmacki J, Jablonska-Gajewicz J, Kordek R. Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces. ACTA ACUST UNITED AC 2011. [DOI: 10.4236/jbpc.2011.22020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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38
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Karjalainen EL, Ravi HK, Barth A. Simulation of the amide I absorption of stacked β-sheets. J Phys Chem B 2010; 115:749-57. [PMID: 21174476 DOI: 10.1021/jp109918c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Aggregated β-sheet structures are associated with amyloid and prion diseases. Techniques capable of revealing detailed structural and dynamical information on β-sheet structure are thus of great biomedical and biophysical interest. In this work, the infrared (IR) amide I spectral characteristics of stacked β-sheets were modeled using the transition dipole coupling model. For a test set of β-sheet stacks, the simulated amide I spectrum was analyzed with respect to the following parameters; intersheet distance, relative rotation of the sheets with respect to each other and the effect of number of sheets stacked. The amide I maximum shifts about 5 cm(-1) to higher wavenumbers when the intersheet distance between two identical β-sheets decreases from 20 to 5 Å. Rotation around the normal of one of the sheets relative to the other results in maximum intersheet coupling near 0° and 180°. Upon of rotation from 0° to 90° at an intersheet distance of 9 Å, the amide I maximum shifts about 3 cm(-1). Tilting of one of the sheets by 30° from the normal results in a shift of the amide I maximum by less than 1 cm(-1). When stacking several β-sheets along the normal, the amide I maximum shifts to higher wavenumbers with increasing stack size. The amide I maximum shifts about 6 cm(-1) when stacking four sheets with an intersheet distance of 9 Å. The study provides an aid in the interpretation of the IR amide I region for experiments involving β-sheets and creates awareness of the many effects that determine the spectrum of β-sheet structures.
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Affiliation(s)
- Eeva-Liisa Karjalainen
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, SE-106 91, Sweden
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39
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Choi JH, Cho M. Polarization-Angle-Scanning Two-Dimensional Spectroscopy: Application to Dipeptide Structure Determination. J Phys Chem A 2010; 115:3766-77. [DOI: 10.1021/jp106458j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
| | - Minhaeng Cho
- Department of Chemistry and Research Institute for Natural Sciences, Korea University, Seoul 136-701, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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40
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Marai CN, Mukamel S, Wang J. Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study. PMC BIOPHYSICS 2010; 3:8. [PMID: 20302645 PMCID: PMC2851665 DOI: 10.1186/1757-5036-3-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 03/19/2010] [Indexed: 11/12/2022]
Abstract
We propose to use infrared coherent two-dimensional correlation spectroscopy (2DCS) to characterize the folding mechanism of the mini-protein Beta3s. In this study Beta3s was folded by molecular dynamics (MD) simulation and intermediate conformational ensembles were identified. The one and two-dimensional correlation spectrum was calculated for the intermediate and native states of the mini-protein. A direct structure-spectra relationship was determined by analysis of conformational properties and specific residue contributions. We identified the structural origin of diagonal and off-diagonal peaks in the 2DCS spectra for the native and intermediate conformational ensembles in the folding mechanism. This work supports the implementation of computational techniques in conjunction with experimental 2DCS to study the folding mechanism of proteins. In addition to exploring the folding mechanism the work presented here can be applied in combination with experiment to refine and validate current molecular dynamics force fields. PACS Codes: 87.15.Cc, 87.15.hm, 87.15.hp
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Affiliation(s)
- Christopher Nj Marai
- Graduate Program in Biochemistry and Structural Biology, State University of New York at Stony Brook, New York, 11794-3400, USA.
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41
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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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42
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Ha JH, Lee KK, Park KH, Choi JH, Jeon SJ, Cho M. Integrated and dispersed photon echo studies of nitrile stretching vibration of 4-cyanophenol in methanol. J Chem Phys 2009; 130:204509. [PMID: 19485459 DOI: 10.1063/1.3140402] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
By means of integrated and dispersed IR photon echo measurement methods, the vibrational dynamics of C-N stretch modes in 4-cyanophenol and 4-cyanophenoxide in methanol is investigated. The vibrational frequency-frequency correlation function (FFCF) is retrieved from the integrated photon echo signals by assuming that the FFCF is described by two exponential functions with about 400 fs and a few picosecond components. The excited state lifetimes of the C-N stretch modes of neutral and anionic 4-cyanophenols are 1.45 and 0.91 ps, respectively, and the overtone anharmonic frequency shifts are 25 and 28 cm(-1). At short waiting times, a notable underdamped oscillation, which is attributed to a low-frequency intramolecular vibration coupled to the CN stretch, in the integrated and dispersed vibrational echo as well as transient grating signals was observed. The spectral bandwidths of IR absorption and dispersed vibrational echo spectra of the 4-cyanophenoxide are significantly larger than those of its neutral form, indicating that the strong interaction between phenoxide and methanol causes large frequency fluctuation and rapid population relaxation. The resonance effects in a paradisubstituted aromatic compound would be of interest in understanding the conjugation effects and their influences on chemical reactivity of various aromatic compounds in organic solvents.
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Affiliation(s)
- Jeong-Hyon Ha
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Republic of Korea
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43
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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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44
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Zhuravlev PI, Materese CK, Papoian GA. Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins. J Phys Chem B 2009; 113:8800-12. [PMID: 19453123 DOI: 10.1021/jp810659u] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Proteins are highly complex molecules with features exquisitely selected by nature to carry out essential biological functions. Physical chemistry and polymer physics provide us with the tools needed to make sense of this complexity. Upon translation, many proteins fold to a thermodynamically stable form known as the native state. The native state is not static, but consists of a hierarchy of conformations, that are continuously explored through dynamics. In this review we provide a brief introduction to some of the core concepts required in the discussion of the protein native dynamics using energy landscapes ideas. We first discuss recent works which have challenged the structure-function paradigm by demonstrating function in disordered proteins. Next we examine the hierarchical organization in the energy landscapes using atomistic molecular dynamics simulations and principal component analysis. In particular, the role of direct and water-mediated contacts in sculpting the landscape is elaborated. Another approach to studying the native state ensemble is based on choosing high-resolution order parameters for computing one- or two-dimensional free energy surfaces. We demonstrate that 2D free energy surfaces provide rich thermodynamic and kinetic information about the native state ensemble. Brownian dynamics simulations on such a surface indicate that protein conformational dynamics is weakly activated. Finally, we briefly discuss implicit and coarse-grained protein models and emphasize the solvent role in determining native state structure and dynamics.
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Affiliation(s)
- Pavel I Zhuravlev
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA
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45
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Calculations of intermode coupling constants and simulations of amide I, II, and III vibrational spectra of dipeptides. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2009.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Cho M. Vibrational solvatochromism and electrochromism: coarse-grained models and their relationships. J Chem Phys 2009; 130:094505. [PMID: 19275407 DOI: 10.1063/1.3079609] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A theoretical description of vibrational solvatochromism and electrochromism is presented by using a coarse-grained model based on a distributed charge and multipole interaction theory. Solvatochromic frequency shift has been described by considering the interaction between distributed charges of a solute and electrostatic potential due to distributed charges of solvent molecules. Another approach was based on the expansion of the solvatochromic frequency shift in terms of solvent electric field and its gradient at distributed sites on solute. The relationship between these two approaches is elucidated and their validities are discussed. It is also shown that the distributed charge and multipole model for solvatochromism developed here can be used to describe vibrational Stark effects on frequency and transition dipole moment. The relationship between the vibrational Stark tuning rate and the parameters obtained from recent vibrational solvatochromism studies is clarified and used to determine the vibrational Stark tuning rates of a few stretching modes, which are then directly compared with experimentally measured values. We anticipate that the present theoretical model can be used to study a variety of vibrational solvatochromic and electrochromic phenomena and to extract critical information on local electrostatic environment around a small IR probe in solution or protein from linear and nonlinear IR spectroscopic studies.
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Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul, Republic of Korea.
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47
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Choi JH, Cho M. Amide I Raman optical activity of polypeptides: fragment approximation. J Chem Phys 2009; 130:014503. [PMID: 19140618 DOI: 10.1063/1.3050294] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vibrational optical activity (VOA) is an important property used to determine the absolute configuration of a chiral molecule in condensed phases. In particular, vibrational circular dichroism and Raman optical activity (ROA) are two representative VOA measurement techniques that have been extensively used to study structures and dynamics of biomolecules. Recently, the amide I vibrational circular dichroism of polypeptides was theoretically described by using fragment approximation methods, which are based on the assumption that amide I VOA can be described as a linear combination of those of constituent fragment peptide units. Here, we develop a fragment approximation theory applicable to numerical simulations of Raman and Raman optical activity spectra for the amide I vibrations in polypeptides. For an alanine dipeptide and pentapeptide analogs, we carried out density functional theory calculations of polarizability, magnetic dipole-, and electric quadrupole-ROA tensors. Numerically simulated spectra using the fragment approximation are directly compared to density functional theory results. Furthermore, the simulated ROA spectra of alanine-based right-handed alpha-helix and polyproline II polypeptides are directly compared to the previously reported experimental results. The agreements were found to be excellent, which suggests that the fragment approximation method developed for the numerical simulation of ROA spectrum of polypeptide in solution is valid and useful.
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Affiliation(s)
- Jun-Ho Choi
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Republic of Korea
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48
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Lin YS, Shorb JM, Mukherjee P, Zanni MT, Skinner JL. Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles. J Phys Chem B 2009; 113:592-602. [PMID: 19053670 PMCID: PMC2633092 DOI: 10.1021/jp807528q] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches, has long been used to probe the structures and dynamics of peptides and proteins by infrared (IR) spectroscopy. A number of ab initio-based amide I vibrational frequency maps have been developed for calculating IR line shapes. In this paper, a new empirical amide I vibrational frequency map is developed. To evaluate its performance, we applied this map to a system of isotope-edited CD3-zeta membrane peptide bundles in aqueous solution. The calculated 2D-IR diagonal line widths vary from residue to residue and show an asymmetric pattern as a function of position in the membrane. The theoretical results are in fair agreement with experiments on the same system. Through analysis of the computed frequency time-correlation functions, it is found that the 2D-IR diagonal widths are dominated by contributions from the inhomogeneous frequency distributions, from which it follows that these widths are a good probe of the extent of local structural fluctuations. Thus, the asymmetric pattern of line widths follows from the asymmetric structure of the bundle in the membrane.
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Affiliation(s)
- Y-S Lin
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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49
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Cai K, Wang J. Multiple Anharmonic Vibrational Probes of Sugar Structure and Dynamics. J Phys Chem B 2009; 113:1681-92. [DOI: 10.1021/jp8070025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kaicong Cai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
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50
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Cai K, Han C, Wang J. Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides. Phys Chem Chem Phys 2009; 11:9149-59. [DOI: 10.1039/b910269h] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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