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Morozova TI, García NA, Matsarskaia O, Roosen-Runge F, Barrat JL. Structural and Dynamical Properties of Elastin-Like Peptides near Their Lower Critical Solution Temperature. Biomacromolecules 2023; 24:1912-1923. [PMID: 36877869 DOI: 10.1021/acs.biomac.3c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Elastin-like peptides (ELPs) are artificially derived intrinsically disordered proteins (IDPs) mimicking the hydrophobic repeat unit in the protein elastin. ELPs are characterized by a lower critical solution temperature (LCST) in aqueous media. Here, we investigate the sequence GVG(VPGVG)3 over a wide range of temperatures (below, around, and above the LCST) and peptide concentrations employing all-atom molecular dynamics simulations, where we focus on the role of intra- and interpeptide interactions. We begin by investigating the structural properties of a single peptide that demonstrates a hydrophobic collapse with temperature, albeit moderate, because the sequence length is short. We observe a change in the interaction between two peptides from repulsive to attractive with temperature by evaluating the potential of mean force, indicating an LCST-like behavior. Next, we explore dynamical and structural properties of peptides in multichain systems. We report the formation of dynamical aggregates with coil-like conformation, in which valine central residues play an important role. Moreover, the lifetime of contacts between chains strongly depends on the temperature and can be described by a power-law decay that is consistent with the LCST-like behavior. Finally, the peptide translational and internal motion are slowed by an increase in the peptide concentration and temperature.
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Affiliation(s)
| | - Nicolás A García
- Instituto de Física del Sur (IFISUR), Departamento de Física, Universidad Nacional del Sur (UNS), CONICET, Av. L. N. Alem 1253, B8000CPB Bahía Blanca, Argentina
| | - Olga Matsarskaia
- Institut Laue-Langevin, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Felix Roosen-Runge
- Department of Biomedical Science and Biofilms Research Center for Biointerfaces (BRCB), Malmö University, 20506 Malmö, Sweden
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2
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Yang H, Graham NJD, Wang W, Liu M, Yu W. Evaluating and improving the reliability of the UV-persulfate method for the determination of TOC/DOC in surface waters. WATER RESEARCH 2021; 196:116918. [PMID: 33765497 DOI: 10.1016/j.watres.2021.116918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
The UV-persulfate oxidation method is widely used for determining the total organic carbon concentration of aqueous samples (denoted for convenience as UVP-TOC). However, for some surface water samples, the measurement of TOC by this method can be unreliable, deviating significantly from the true carbon content. In this study, the performance of the UVP-TOC method has been investigated by comparing the results from the analysis of a variety of aqueous samples that included two kinds of surface water samples and related surface water model substances: bovine serum albumin (BSA), sodium alginate (SA), humic acid (HA), tannic acid (TA), benzoic acid (BA) and citric acid (CA), with those from a high-temperature combustion method (elemental analysis); the latter providing the true carbon content value. By comparing the above data, it was found that the UVP-TOC method significantly underestimated the TOC value of the surface water samples, and it was also found that the model components BSA (protein) and HA (humic substances, HS) had a substantial influence on the TOC underestimation, while the SA (polysaccharide), TA (complex organic molecule) and CA/BA (small molecules) had little effect. The results showed that the agglomeration within and between BSA and HA molecules was an important reason for the inaccurate UVP-TOC values of BSA and HA. A further limitation was that for BSA, surfactants (e.g. sodium dodecylbenzene sulfonate, SDBS) and other surfactant-like substances, foam was formed during the CO2 removal purging process by N2 that seriously interfered with the determination of TOC. The study provides new information and insight into the causes of inaccuracies in the UVP-TOC analysis of surface waters and possible approaches to improve the accuracy.
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Affiliation(s)
- Hankun Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Nigel J D Graham
- Department of Civil and Environmental Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Wenyu Wang
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Separation Membrane and Membrane Processes, School of Environmental Science and Engineering, Tiangong University, Tianjin 300387, China
| | - Mengjie Liu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wenzheng Yu
- State Key Laboratory of Environmental Aquatic Chemistry, Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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3
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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4
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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: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [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. Two-dimensional infrared spectroscopy reveals folding of an intrinsically disordered peptide when sequestered into a model “membrane-less” organelle.![]()
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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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5
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Biswas S, Mallik BS. Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Hernández B, Crowet JM, Thiery J, Kruglik SG, Belloy N, Baud S, Dauchez M, Debelle L. Structural Analysis of Nonapeptides Derived from Elastin. Biophys J 2020; 118:2755-2768. [PMID: 32396850 DOI: 10.1016/j.bpj.2020.04.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/09/2020] [Accepted: 04/13/2020] [Indexed: 12/28/2022] Open
Abstract
Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex located at the surface of cells. Besides these elastokines, another class of peptides has been identified. This group of bioactive elastin peptides presents the XGXPGXGXG consensus sequence, but the reason for their bioactivity remains unexplained. To better understand their nature and structure-function relationships, herein we searched the current databases for this nonapeptide motif and observed that the XGXPGXGXG elastin peptides define a specific group of tandemly repeated patterns. Further, we focused on four tandemly repeated human elastin nonapeptides, i.e., AGIPGLGVG, VGVPGLGVG, AGVPGLGVG, and AGVPGFGAG. These peptides were analyzed by means of optical spectroscopies and molecular dynamics. Ultraviolet-circular dichroism and Raman spectra are consistent with a mixture of β-turn, β-strand, and random-chain secondary elements in aqueous media. Quantitative analysis of their conformations suggested that turns corresponded to half of the total population of structural elements, whereas the remaining half were equally distributed between β-strand and unordered chains. These distributions were confirmed by molecular dynamics simulations. Altogether, our data suggest that these highly dynamic peptides harbor a type II β-turn located in their central part. We hypothesize that this structural element could explain their specific bioactivity.
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Affiliation(s)
- Belén Hernández
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Groupe de Biophysique Moléculaire, Sorbonne Paris Cité, Université Paris 13, UFR Santé-Médecine-Biologie Humaine, Bobigny, France
| | - Jean-Marc Crowet
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Multiscale Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Joseph Thiery
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Sergei G Kruglik
- UMR CNRS 8237, Laboratoire Jean-Perrin, Sorbonne Université, UPMC Paris 06, Paris, France
| | - Nicolas Belloy
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Multiscale Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Stéphanie Baud
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Multiscale Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Manuel Dauchez
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Multiscale Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France
| | - Laurent Debelle
- UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire, Université de Reims Champagne Ardenne, UFR Sciences Exactes et Naturelles, Reims, France; Multiscale Molecular Modeling Platform, Université de Reims Champagne Ardenne, Reims, France.
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7
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Qin XY, Zhang JT, Li GM, Cai MY, Lu J, Gu RZ, Liu WY. Selenium-chelating corn oligopeptide as a potential antioxidant supplement: investigation of the protein conformational changes and identification of the antioxidant fragment composition. INTERNATIONAL JOURNAL OF FOOD ENGINEERING 2020. [DOI: 10.1515/ijfe-2019-0166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AbstractA selenium-chelating corn oligopeptide (Se-COP) with high protein and low molecular weight was prepared as a selenium supplement. We utilized infrared (IR), ultraviolet (UV), and circular dichroism (CD) spectroscopy, 1-anilinonaphthalene-8-sulfonate (ANS)-binding fluorescence spectra, and isothermal titration calorimetry (ITC) to analyze and describe Se-COP and its reactions. It was concluded that the chelation reaction was a spontaneous process driven by enthalpy and entropy, with ΔH=3.79 × 104 ± 4075 cal/mol, ΔS = 146 cal/mol, ΔG = –23356.30 ± 126.94 cal/mol, binding constant Ka = 1.18 × 104 ± 855 M–1, and binding site number n = 0.13 ± 0.0126, and described as coordination bonds forming and hydrophobic interaction, as well as protein conformational changes including secondary and tertiary hydrophobic structure. Se-COP had strong antioxidant capacity, and mass spectrometry (MS) was used to identify the antioxidant peptide fragment, which was characterized as LLPPY and quantified at 428.95 ng/mg. This study indicated that Se-COP prepared by chelation may be a Se supplement with antioxidant capacity that can be applied in functional foods or ingredients.
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Affiliation(s)
- Xiu-Yuan Qin
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Jiang-Tao Zhang
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Guo-Ming Li
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Mu-Yi Cai
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Jun Lu
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Rui-Zeng Gu
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
| | - Wen-Ying Liu
- Beijing Engineering Research Center of Protein and Functional Peptides, China National Research Institute of Food and Fermentation Industries Co. Ltd., Beijing 100015, People's Republic of China
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8
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Biswas S, Mallik BS. Aqueous hydroxyl group as the vibrational probe to access the hydrophobicity of amide derivatives. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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Lim J, Lee KK, Liang C, Park KH, Kim M, Kwak K, Cho M. Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation Studies of Nonaqueous Lithium Ion Battery Electrolytes. J Phys Chem B 2019; 123:6651-6663. [DOI: 10.1021/acs.jpcb.9b02026] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Joonhyung Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyung-Koo Lee
- Department of Chemistry, Kunsan National University, Kunsan, Jeonbuk 573-701, Korea
| | - Chungwen Liang
- Computational Modeling Core, Institute for Applied Life Sciences (IALS), University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Kwang-Hee Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minjoo Kim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Korea
- Department of Chemistry, Korea University, Seoul 02841, Korea
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10
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Selig O, Cunha AV, van Eldijk MB, van Hest JCM, Jansen TLC, Bakker HJ, Rezus YLA. Temperature-Induced Collapse of Elastin-like Peptides Studied by 2DIR Spectroscopy. J Phys Chem B 2018; 122:8243-8254. [PMID: 30067028 PMCID: PMC6143280 DOI: 10.1021/acs.jpcb.8b05221] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Indexed: 12/21/2022]
Abstract
Elastin-like peptides are hydrophobic biopolymers that exhibit a reversible coacervation transition when the temperature is raised above a critical point. Here, we use a combination of linear infrared spectroscopy, two-dimensional infrared spectroscopy, and molecular dynamics simulations to study the structural dynamics of two elastin-like peptides. Specifically, we investigate the effect of the solvent environment and temperature on the structural dynamics of a short (5-residue) elastin-like peptide and of a long (450-residue) elastin-like peptide. We identify two vibrational energy transfer processes that take place within the amide I' band of both peptides. We observe that the rate constant of one of the exchange processes is strongly dependent on the solvent environment and argue that the coacervation transition is accompanied by a desolvation of the peptide backbone where up to 75% of the water molecules are displaced. We also study the spectral diffusion dynamics of the valine(1) residue that is present in both peptides. We find that these dynamics are relatively slow and indicative of an amide group that is shielded from the solvent. We conclude that the coacervation transition of elastin-like peptides is probably not associated with a conformational change involving this residue.
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Affiliation(s)
- Oleg Selig
- AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Mark B. van Eldijk
- Institute
for Molecules and Materials, Radboud University
Nijmegen, Heyendaalseweg
135, 6525 AJ Nijmegen, The Netherlands
| | - Jan C. M. van Hest
- Department
of Chemical Engineering and Chemistry Kranenveld, Eindhoven University of Technology, Building 14, 5600 MB Eindhoven, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Huib J. Bakker
- FOM
institute AMOLF, Science
Park 104, 1098 XG Amsterdam, The Netherlands
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11
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Weißheit S, Kahse M, Kämpf K, Tietze A, Vogel M, Winter R, Thiele CM. Elastin-like Peptide in Confinement: FT-IR and NMR T
1 Relaxation Data. Z PHYS CHEM 2018. [DOI: 10.1515/zpch-2017-1047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
We employed FT-IR and NMR experiments to investigate the influence of a cell-mimicking crowding environment on the structure and dynamics of an elastin-like peptide (ELP) with the sequence GVG(VPGVG)3, which – due to a high number of hydrophobic amino acid side chains – exhibits an inverse temperature transition (ITT). As simplified crowding agent, we used 30 wt% Ficoll. The FT-IR data revealed the well-known broad ITT above ~25°C, as observed by the decrease of the relative population of random coil structures and the concomitant increase of type II β-turns. Interestingly, the addition of Ficoll leads to a destabilizing effect of type II β-turn structures. This is in contrast to the expected excluded-volume effect of the macromolecular crowder, but can be explained by weak interactions of the peptide with the polysaccharide chains of the crowding agent. Further, the crowding agent leads to the onset of a reversal of the folding transition at high temperatures. The full assignment of the ELP allowed for a residue-specific investigation of the dynamic behavior of ELP by NMR. Due to a strong change of microscopic viscosity between native/buffered conditions and crowded conditions, relaxation data remain inconclusive with respect to the observation of an ITT. Hence, no quantitative details in terms of internal conformational changes can be obtained. However, temperature dependent differences in the 13C relaxation behavior between core and terminal parts of the peptide indicate temperature induced changes in the internal dynamics with generally higher internal mobility at chain ends: This is in full agreement with FT-IR data. In harmony with the FT-IR analysis, macromolecular crowding does not lead to significant changes in the relaxation behavior.
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Affiliation(s)
- Susann Weißheit
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt, Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Marie Kahse
- Physical Chemistry I – Biophysical Chemistry, Faculty of Chemistry and Chemical Biology , TU Dortmund University, Otto-Hahn-Str. 4a , 44227 Dortmund , Germany
| | - Kerstin Kämpf
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Alesia Tietze
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt, Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
| | - Michael Vogel
- Institut für Festkörperphysik , Technische Universität Darmstadt, Hochschulstr. 6 , 64289 Darmstadt , Germany
| | - Roland Winter
- Physical Chemistry I – Biophysical Chemistry, Faculty of Chemistry and Chemical Biology , TU Dortmund University, Otto-Hahn-Str. 4a , 44227 Dortmund , Germany
| | - Christina Marie Thiele
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie , Technische Universität Darmstadt, Alarich-Weiss-Str. 16 , 64287 Darmstadt , Germany
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12
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Salamatova E, Cunha AV, Bloem R, Roeters SJ, Woutersen S, Jansen TLC, Pshenichnikov MS. Hydrophobic Collapse in N-Methylacetamide-Water Mixtures. J Phys Chem A 2018; 122:2468-2478. [PMID: 29425450 PMCID: PMC6028151 DOI: 10.1021/acs.jpca.8b00276] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Indexed: 11/28/2022]
Abstract
Aqueous N-methylacetamide solutions were investigated by polarization-resolved pump-probe and 2D infrared spectroscopy (2D IR), using the amide I mode as a reporter. The 2D IR results are compared with molecular dynamics simulations and spectral calculations to gain insight into the molecular structures in the mixture. N-Methylacetamide and water molecules tend to form clusters with "frozen" amide I dynamics. This is driven by a hydrophobic collapse as the methyl groups of the N-methylacetamide molecules cluster in the presence of water. Since the studied system can be considered as a simplified model for the backbone of proteins, the present study forms a convenient basis for understanding the structural and vibrational dynamics in proteins. It is particularly interesting to find out that a hydrophobic collapse as the one driving protein folding is observed in such a simple system.
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Affiliation(s)
- Evgeniia Salamatova
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robbert Bloem
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Steven J. Roeters
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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13
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Ho JJ, Ghosh A, Zhang TO, Zanni MT. Heterogeneous Amyloid β-Sheet Polymorphs Identified on Hydrogen Bond Promoting Surfaces Using 2D SFG Spectroscopy. J Phys Chem A 2018; 122:1270-1282. [DOI: 10.1021/acs.jpca.7b11934] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jia-Jung Ho
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Ayanjeet Ghosh
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tianqi O. Zhang
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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14
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Liang C, Kwak K, Cho M. Revealing the Solvation Structure and Dynamics of Carbonate Electrolytes in Lithium-Ion Batteries by Two-Dimensional Infrared Spectrum Modeling. J Phys Chem Lett 2017; 8:5779-5784. [PMID: 29131650 DOI: 10.1021/acs.jpclett.7b02623] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Carbonate electrolytes in lithium-ion batteries play a crucial role in conducting lithium ions between two electrodes. Mixed solvent electrolytes consisting of linear and cyclic carbonates are commonly used in commercial lithium-ion batteries. To understand how the linear and cyclic carbonates introduce different solvation structures and dynamics, we performed molecular dynamics simulations of two representative electrolyte systems containing either linear or cyclic carbonate solvents. We then modeled their two-dimensional infrared (2DIR) spectra of the carbonyl stretching mode of these carbonate molecules. We found that the chemical exchange process involving formation and dissociation of lithium-ion/carbonate complexes is responsible for the growth of 2DIR cross peaks with increasing waiting time. In addition, we also found that cyclic carbonates introduce faster dynamics of dissociation and formation of lithium-ion/carbonate complexes than linear carbonates. These findings provide new insights into understanding the lithium-ion mobility and its interplay with solvation structure and ultrafast dynamics in carbonate electrolytes used in lithium-ion batteries.
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Affiliation(s)
- Chungwen Liang
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University , Seoul 02841, Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
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15
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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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16
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Cunha AV, Salamatova E, Bloem R, Roeters SJ, Woutersen S, Pshenichnikov MS, Jansen TLC. Interplay between Hydrogen Bonding and Vibrational Coupling in Liquid N-Methylacetamide. J Phys Chem Lett 2017; 8:2438-2444. [PMID: 28510458 PMCID: PMC5462486 DOI: 10.1021/acs.jpclett.7b00731] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
Intrinsically disordered proteins play an important role in biology, and unraveling their labile structure presents a vital challenge. However, the dynamical structure of such proteins thwarts their study by standard techniques such as X-ray diffraction and NMR spectroscopy. Here, we use a neat liquid composed of N-methylacetamide molecules as a model system to elucidate dynamical and structural properties similar to those one can expect to see in intrinsically disordered proteins. To examine the structural dynamics in the neat liquid, we combine molecular dynamics, response-function-based spectral simulations, and two-dimensional polarization-resolved infrared spectroscopy in the amide I (CO stretch) region. The two-dimensional spectra reveal a delicate interplay between hydrogen bonding and intermolecular vibrational coupling effects, observed through a fast anisotropy decay. The present study constitutes a general platform for understanding the structure and dynamics of highly disordered proteins.
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Affiliation(s)
- Ana V. Cunha
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Evgeniia Salamatova
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robbert Bloem
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Steven J. Roeters
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Sander Woutersen
- Van
’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - Maxim S. Pshenichnikov
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L. C. Jansen
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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17
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Reppert M, Roy AR, Tempkin JOB, Dinner AR, Tokmakoff A. Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides. J Phys Chem B 2016; 120:11395-11404. [PMID: 27736076 DOI: 10.1021/acs.jpcb.6b08678] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The characterization of intrinsically disordered protein (IDP) ensembles is complicated both by inherent heterogeneity and by the fact that many common experimental techniques function poorly when applied to IDPs. For this reason, the development of alternative structural tools for probing IDP ensembles has attracted considerable attention. Here we describe our recent work in developing experimental and computational tools for characterizing IDP ensembles using Amide I (backbone carbonyl stretch) vibrational spectroscopy. In this approach, the infrared (IR) absorption frequencies of isotope-labeled amide bonds probe their local electrostatic environments and structures. Empirical frequency maps allow us to use this spectroscopic data as a direct experimental test of atomistic structural models. We apply these methods to a family of short elastin-like peptides (ELPs), fragments of the elastin protein based around the Pro-Gly turn motif characteristic of the elastomeric segments of the full protein. Using a maximum entropy analysis that applies constraints from experimental spectra to weighting predicted spectra from molecular dynamics (MD) ensembles, we find that peptides with Ala or Val side chains preceding the Pro-Gly turn unit exhibit a stronger tendency toward extended structures than do Gly-Pro-Gly motifs, suggesting an important role for steric interactions in tuning the molecular properties of elastin.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States.,Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Anish R Roy
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States
| | - Jeremy O B Tempkin
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States
| | - Aaron R Dinner
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department of Chemistry and James Franck Institute, University of Chicago , Chicago, Illinois 60637, United States
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18
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Stingel AM, Petersen PB. Couplings Across the Vibrational Spectrum Caused by Strong Hydrogen Bonds: A Continuum 2D IR Study of the 7-Azaindole–Acetic Acid Heterodimer. J Phys Chem B 2016; 120:10768-10779. [DOI: 10.1021/acs.jpcb.6b05049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ashley M. Stingel
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Poul B. Petersen
- Department
of Chemistry and
Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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19
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Cunha AV, Bondarenko AS, Jansen TLC. Assessing Spectral Simulation Protocols for the Amide I Band of Proteins. J Chem Theory Comput 2016; 12:3982-92. [PMID: 27348022 DOI: 10.1021/acs.jctc.6b00420] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.
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Affiliation(s)
- Ana V Cunha
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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20
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Edington SC, Flanagan JC, Baiz CR. An Empirical IR Frequency Map for Ester C═O Stretching Vibrations. J Phys Chem A 2016; 120:3888-96. [DOI: 10.1021/acs.jpca.6b02887] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sean C. Edington
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Jennifer C. Flanagan
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
| | - Carlos R. Baiz
- Department
of Chemistry, University of Texas at Austin, 105 E. 24th St. Stop A5300, Austin, Texas 78712-1224, United States
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21
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Reppert M, Tokmakoff A. Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics. Annu Rev Phys Chem 2016; 67:359-86. [DOI: 10.1146/annurev-physchem-040215-112055] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mike Reppert
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637;
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22
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Bondarenko AS, Jansen TLC. Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins. J Chem Phys 2016; 142:212437. [PMID: 26049457 DOI: 10.1063/1.4919716] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.
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Affiliation(s)
- Anna S Bondarenko
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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23
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Daily MD, Baer MD, Mundy CJ. Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer. J Phys Chem B 2016; 120:2198-208. [DOI: 10.1021/acs.jpcb.5b12277] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Michael D. Daily
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department
of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Marcel D. Baer
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher J. Mundy
- Physical
Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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24
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Roy S, Skoff D, Perroni DV, Mondal J, Yethiraj A, Mahanthappa MK, Zanni MT, Skinner JL. Water Dynamics in Gyroid Phases of Self-Assembled Gemini Surfactants. J Am Chem Soc 2016; 138:2472-5. [DOI: 10.1021/jacs.5b12370] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Santanu Roy
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - David Skoff
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Dominic V. Perroni
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Jagannath Mondal
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Mahesh K. Mahanthappa
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
| | - James L. Skinner
- Department of Chemistry, University of Wisconsin, 1101 University
Avenue, Madison, Wisconsin 53706, United States
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25
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Liang C. Catching protein structural dynamics by two-dimensional infrared spectroscopy. Biophys J 2016; 108:1577-1579. [PMID: 25863046 DOI: 10.1016/j.bpj.2015.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 02/01/2023] Open
Affiliation(s)
- Chungwen Liang
- Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California.
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26
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Baiz CR, Tokmakoff A. Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling. Biophys J 2016; 108:1747-1757. [PMID: 25863066 DOI: 10.1016/j.bpj.2014.12.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 12/05/2014] [Accepted: 12/19/2014] [Indexed: 01/14/2023] Open
Abstract
The conformational heterogeneity of the N-terminal domain of the ribosomal protein L9 (NTL91-39) in its folded state is investigated using isotope-edited two-dimensional infrared spectroscopy. Backbone carbonyls are isotope-labeled ((13)C=(18)O) at five selected positions (V3, V9, V9G13, G16, and G24) to provide a set of localized spectroscopic probes of the structure and solvent exposure at these positions. Structural interpretation of the amide I line shapes is enabled by spectral simulations carried out on structures extracted from a recent Markov state model. The V3 label spectrum indicates that the β-sheet contacts between strands I and II are well folded with minimal disorder. The V9 and V9G13 label spectra, which directly probe the hydrogen-bond contacts across the β-turn, show significant disorder, indicating that molecular dynamics simulations tend to overstabilize ideally folded β-turn structures in NTL91-39. In addition, G24-label spectra provide evidence for a partially disordered α-helix backbone that participates in hydrogen bonding with the surrounding water.
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Affiliation(s)
- Carlos R Baiz
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois.
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27
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Ragnoni E, Palombo F, Green E, Winlove CP, Di Donato M, Lapini A. Coacervation of α-elastin studied by ultrafast nonlinear infrared spectroscopy. Phys Chem Chem Phys 2016; 18:27981-27990. [DOI: 10.1039/c6cp04049g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Elastin is the main protein to confer elasticity to biological tissues, through the formation of a hierarchical network of fibres.
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Affiliation(s)
- Elena Ragnoni
- LENS, European Laboratory for Nonlinear Spectroscopies
- Via Nello Carrara 1
- I-50019 Sesto Fiorentino
- Italy
- Department of Physics
| | | | - Ellen Green
- School of Physics and Astronomy
- University of Exeter
- Exeter EX4 4QJ
- UK
| | - C. Peter Winlove
- School of Physics and Astronomy
- University of Exeter
- Exeter EX4 4QJ
- UK
| | - Mariangela Di Donato
- LENS, European Laboratory for Nonlinear Spectroscopies
- Via Nello Carrara 1
- I-50019 Sesto Fiorentino
- Italy
- Department of Chemistry
| | - Andrea Lapini
- LENS, European Laboratory for Nonlinear Spectroscopies
- Via Nello Carrara 1
- I-50019 Sesto Fiorentino
- Italy
- INO
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28
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Affiliation(s)
- Juan Zhao
- Beijing
National Laboratory
for Molecular Sciences; 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; Laboratory of Molecular Reaction Dynamics,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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29
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Cyran JD, Nite JM, Krummel AT. Characterizing Anharmonic Vibrational Modes of Quinones with Two-Dimensional Infrared Spectroscopy. J Phys Chem B 2015; 119:8917-25. [PMID: 25697689 DOI: 10.1021/jp506900n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Two-dimensional infrared (2D IR) spectroscopy was used to study the vibrational modes of three quinones--benzoquinone, naphthoquinone, and anthraquinone. The vibrations of interest were in the spectral range of 1560-1710 cm(-1), corresponding to the in-plane carbonyl and ring stretching vibrations. Coupling between the vibrational modes is indicated by the cross peaks in the 2D IR spectra. The diagonal and off-diagonal anharmonicities range from 4.6 to 17.4 cm(-1) for the quinone series. In addition, there is significant vibrational coupling between the in-plane carbonyl and ring stretching vibrations. The diagonal anharmonicity, off-diagonal anharmonicity, and vibrational coupling constants are reported for benzoquinone, naphthoquinone, and anthraquinone.
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Affiliation(s)
- Jenée D Cyran
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Jacob M Nite
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Amber T Krummel
- Chemistry Department, Colorado State University, Fort Collins, Colorado 80523-1872, United States
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30
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Rezende Valim L, Davies JA, Tveen Jensen K, Guo R, Willison KR, Spickett CM, Pitt AR, Klug DR. Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy. J Phys Chem B 2014; 118:12855-64. [PMID: 25347525 DOI: 10.1021/jp509053q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy.
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31
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Li NK, Quiroz FG, Hall CK, Chilkoti A, Yingling YG. Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide. Biomacromolecules 2014; 15:3522-30. [DOI: 10.1021/bm500658w] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Felipe García Quiroz
- Department
of Biomedical Engineering, Duke University, P.O. Box 90281, Durham, North Carolina 27708, United States
| | | | - Ashutosh Chilkoti
- Department
of Biomedical Engineering, Duke University, P.O. Box 90281, Durham, North Carolina 27708, United States
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32
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Lotze S, Olijve LLC, Voets IK, Bakker HJ. Observation of vibrational energy exchange in a type-III antifreeze protein. J Phys Chem B 2014; 118:8962-71. [PMID: 25051212 DOI: 10.1021/jp503481e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We performed time- and polarization-resolved pump-probe and two-dimensional infrared (2D-IR) experiments to study the dynamics of the amide I vibration of a 7 kDa type-III antifreeze protein. In the pump-probe experiments, we used femtosecond mid-infrared pulses to investigate the vibrational relaxation dynamics of the amide mode. The transient spectra show the presence of two spectral components that decay with different lifetimes, indicative of the presence of two distinct amide subbands. The 2D-IR experiments reveal the coupling between the two bands in the form of cross-peaks. On the basis of previous work by Demirdöven et al. ( J. Am. Chem. Soc. 2004 , 126 , 7981 - 7990 ), we assign the observed bands to the two infrared-active modes α(-) and α(+) found in protein β-sheets. The amplitudes of the cross-peak were found to increase with delay time, indicating that the cross-peaks originate from population transfer between the coupled amide oscillators. The time constant of the energy transfer was found to be 6-7 ps.
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Affiliation(s)
- S Lotze
- FOM-Institute for Atomic and Molecular Physics AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
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33
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Jansen TLC. Linear absorption and two-dimensional infrared spectra of N-methylacetamide in chloroform revisited: polarizability and multipole effects. J Phys Chem B 2014; 118:8162-9. [PMID: 24666193 DOI: 10.1021/jp5012445] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effect of solvent polarizability and multipole effects on the amide I vibrational spectra of a peptide unit is investigated. Four molecular dynamics force fields of increasing complexity for the solvent are used to model both the linear absorption and two-dimensional infrared spectra. It is observed that, at least in chloroform solution, the predicted solvent shift is considerably improved when accounting for the polarizabiltiy and multipole effects. The latter are typically connected with halogen bonding. Significant deviations are still observed for more sensitive line shape parameters such as the spectral width and line skewness. However, the findings demonstrate that previously observed deviations have an origin in the force field treatment rather than in the electrostatic mapping procedure frequently employed to simulate linear absorption and two-dimensional infrared spectroscopy.
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Affiliation(s)
- Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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34
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Reppert M, Tokmakoff A. Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment. J Chem Phys 2013; 138:134116. [PMID: 23574217 DOI: 10.1063/1.4798938] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The interpretation of protein amide I infrared spectra has been greatly assisted by the observation that the vibrational frequency of a peptide unit reports on its local electrostatic environment. However, the interpretation of spectra remains largely qualitative due to a lack of direct quantitative connections between computational models and experimental data. Here, we present an empirical parameterization of an electrostatic amide I frequency map derived from the infrared absorption spectra of 28 dipeptides. The observed frequency shifts are analyzed in terms of the local electrostatic potential, field, and field gradient, evaluated at sites near the amide bond in molecular dynamics simulations. We find that the frequency shifts observed in experiment correlate very well with the electric field in the direction of the C=O bond evaluated at the position of the amide oxygen atom. A linear best-fit mapping between observed frequencies and electric field yield sample standard deviations of 2.8 and 3.7 cm(-1) for the CHARMM27 and OPLS-AA force fields, respectively, and maximum deviations (within our data set) of 9 cm(-1). These results are discussed in the broader context of amide I vibrational models and the effort to produce quantitative agreement between simulated and experimental absorption spectra.
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Affiliation(s)
- Mike Reppert
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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35
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Meuzelaar H, Marino KA, Huerta-Viga A, Panman MR, Smeenk LEJ, Kettelarij AJ, van Maarseveen JH, Timmerman P, Bolhuis PG, Woutersen S. Folding dynamics of the Trp-cage miniprotein: evidence for a native-like intermediate from combined time-resolved vibrational spectroscopy and molecular dynamics simulations. J Phys Chem B 2013; 117:11490-501. [PMID: 24050152 DOI: 10.1021/jp404714c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Trp-cage is a synthetic 20-residue miniprotein which folds rapidly and spontaneously to a well-defined globular structure more typical of larger proteins. Due to its small size and fast folding, it is an ideal model system for experimental and theoretical investigations of protein folding mechanisms. However, Trp-cage's exact folding mechanism is still a matter of debate. Here we investigate Trp-cage's relaxation dynamics in the amide I' spectral region (1530-1700 cm(-1)) using time-resolved infrared spectroscopy. Residue-specific information was obtained by incorporating an isotopic label ((13)C═(18)O) into the amide carbonyl group of residue Gly11, thereby spectrally isolating an individual 310-helical residue. The folding-unfolding equilibrium is perturbed using a nanosecond temperature-jump (T-jump), and the subsequent re-equilibration is probed by observing the time-dependent vibrational response in the amide I' region. We observe bimodal relaxation kinetics with time constants of 100 ± 10 and 770 ± 40 ns at 322 K, suggesting that the folding involves an intermediate state, the character of which can be determined from the time- and frequency-resolved data. We find that the relaxation dynamics close to the melting temperature involve fast fluctuations in the polyproline II region, whereas the slower process can be attributed to conformational rearrangements due to the global (un)folding transition of the protein. Combined analysis of our T-jump data and molecular dynamics simulations indicates that the formation of a well-defined α-helix precedes the rapid formation of the hydrophobic cage structure, implying a native-like folding intermediate, that mainly differs from the folded conformation in the orientation of the C-terminal polyproline II helix relative to the N-terminal part of the backbone. We find that the main free-energy barrier is positioned between the folding intermediate and the unfolded state ensemble, and that it involves the formation of the α-helix, the 310-helix, and the Asp9-Arg16 salt bridge. Our results suggest that at low temperature (T ≪ Tm) a folding path via formation of α-helical contacts followed by hydrophobic clustering becomes more important.
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Affiliation(s)
- Heleen Meuzelaar
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam , Science Park 904, 1098 XH Amsterdam, The Netherlands
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36
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Wu T, Yang L, Zhang R, Shao Q, Zhuang W. Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation. J Phys Chem A 2013; 117:6256-63. [PMID: 23496267 DOI: 10.1021/jp400625a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.
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Affiliation(s)
- Tianmin Wu
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
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37
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Liang C, Jansen TLC. Simulation of Two-Dimensional Sum-Frequency Generation Response Functions: Application to Amide I in Proteins. J Phys Chem B 2013; 117:6937-45. [DOI: 10.1021/jp403111j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Chungwen Liang
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH - 4056 Basel,
Switzerland
| | - Thomas L. C. Jansen
- Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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38
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Roeters SJ, van Dijk CN, Torres-Knoop A, Backus EHG, Campen RK, Bonn M, Woutersen S. Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment. J Phys Chem A 2013; 117:6311-22. [DOI: 10.1021/jp401159r] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- S. J. Roeters
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - C. N. van Dijk
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - A. Torres-Knoop
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - E. H. G. Backus
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - R. K. Campen
- Department of Physical
Chemistry, Fritz Haber Institute, Faradayweg
4-6, 14195 Berlin,
Germany
| | - M. Bonn
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz,
Germany
| | - S. Woutersen
- Van’t Hoff Institute
for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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39
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Han C, Zhao J, Yang F, Wang J. Structural Dynamics of N-Propionyl-d-glucosamine Probed by Infrared Spectroscopies and Ab Initio Computations. J Phys Chem A 2013; 117:6105-15. [DOI: 10.1021/jp400096a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chen Han
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Fan Yang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences,
Molecular Reaction Dynamics Laboratory, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, People’s
Republic of China
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40
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Studying Biomacromolecules with Two-Dimensional Infrared Spectroscopy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:1-36. [DOI: 10.1016/b978-0-12-416596-0.00001-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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41
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Baiz CR, Reppert M, Tokmakoff A. Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins. J Phys Chem A 2012; 117:5955-61. [DOI: 10.1021/jp310689a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Mike Reppert
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Andrei Tokmakoff
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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42
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Aizpurua JM, Palomo C, Balentová E, Jimenez A, Andreieff E, Sagartzazu-Aizpurua M, Miranda JI, Linden A. Chirality-Driven Folding of Short β-Lactam Pseudopeptides. J Org Chem 2012; 78:224-37. [DOI: 10.1021/jo302368y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jesus M. Aizpurua
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Claudio Palomo
- Departamento de Química Orgánica-I, Joxe Mari Korta R&D Center, Universidad del País Vasco UPV/EHU, Avda Tolosa-72, 20018 San Sebastian, Spain
| | - Eva Balentová
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Azucena Jimenez
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Elena Andreieff
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Maialen Sagartzazu-Aizpurua
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - José Ignacio Miranda
- Departamento
de Química
Orgánica-I, Facultad de Química, Universidad del País Vasco UPV/EHU, Paseo Manuel Lardizabal-3,
20018 San Sebastian, Spain
| | - Anthony Linden
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190,
CH-8057 Zürich, Switzerland
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43
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Welch WRW, Kubelka J. DFT-Based Simulations of Amide I′ IR Spectra of a Small Protein in Solution Using Empirical Electrostatic Map with a Continuum Solvent Model. J Phys Chem B 2012; 116:10739-47. [DOI: 10.1021/jp305387x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- William R. W. Welch
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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44
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Wang L, Skinner JL. Thermally induced protein unfolding probed by isotope-edited IR spectroscopy. J Phys Chem B 2012; 116:9627-34. [PMID: 22853174 PMCID: PMC3463243 DOI: 10.1021/jp304613b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infrared (IR) spectroscopy has been widely utilized for the study of protein folding, unfolding, and misfolding processes. We have previously developed a theoretical method for calculating IR spectra of proteins in the amide I region. In this work, we apply this method, in combination with replica-exchange molecular dynamics simulations, to study the equilibrium thermal unfolding transition of the villin headpiece subdomain (HP36). Temperature-dependent IR spectra and spectral densities are calculated. The spectral densities correctly reflect the unfolding conformational changes in the simulation. With the help of isotope labeling, we are able to capture the feature that helix 2 of HP36 loses its secondary structure before global unfolding occurs, in agreement with experiment.
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Affiliation(s)
- Lu Wang
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
| | - James L. Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, WI 53706 USA
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