1
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Xiong Q, Stupp SI, Schatz GC. Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons. J Phys Chem Lett 2021; 12:11238-11244. [PMID: 34762436 DOI: 10.1021/acs.jpclett.1c03243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine-glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine's role in suppressing right-handed β-sheet formation. This study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.
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Affiliation(s)
- Qinsi Xiong
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Samuel I Stupp
- Department of Chemistry, Center for BioInspired Energy Science, and Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611, United States
| | - George C Schatz
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, United States
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2
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Schweitzer-Stenner R, Alvarez NJ. Short Peptides as Tunable, Switchable, and Strong Gelators. J Phys Chem B 2021; 125:6760-6775. [PMID: 34133176 DOI: 10.1021/acs.jpcb.1c01447] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This Perspective outlines our current understanding of molecular gels composed of short and ultrashort peptides over the past 20 years. We discuss in detail the state of the art regarding self-assembly mechanisms, structure, thermal stability, and kinetics of fibril and/or network formation. Emphasis is put on the importance of the combined use of spectroscopy and rheology for characterizing and validating self-assembly models. While a range of peptide chemistries are reviewed, we focus our discussion on a unique new class of ultrashort peptide gelators, denoted GxG peptides (x: guest residue), which are capable of forming self-assembled fibril networks. The storage moduli of GxG gels are tunable up to 100 kPa depending on concentration, pH, and/or cosolvent. The sheet structures of the fibrils differ from canonical β-sheets. When appropriate, each section highlights opportunities for additional research and technologies that would further our understanding.
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3
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Hesser M, Thursch LJ, Lewis TR, Lima TA, Alvarez NJ, Schweitzer-Stenner R. Concentration Dependence of a Hydrogel Phase Formed by the Deprotonation of the Imidazole Side Chain of Glycylhistidylglycine. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:6935-6946. [PMID: 34077210 DOI: 10.1021/acs.langmuir.1c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Upon deprotonation of its imidazole group at ∼pH 6, the unblocked tripeptide glycylhistidylglycine (GHG) self-assembles into very long crystalline fibrils on a 10-1000 μm scale which are capable of forming a volume spanning network, that is, hydrogel. The critical peptide concentration for self-assembly at a pH of 6 lies between 50 and 60 mM. The fraction of peptides that self-assemble into fibrils depends on the concentration of deprotonated GHG. While IR spectra seem to indicate the formation of fibrils with standard amyloid fibril β-sheet structures, vibrational circular dichroism spectra show a strongly enhanced amide I' signal, suggesting that the formed fibrils exhibit significant chirality. The fibril chirality appears to be a function of peptide concentration. Rheological measurements reveal that the rate of gelation is concentration-dependent and that there is an optimum gel strength at intermediate peptide concentrations of ca. 175 mM. This paper outlines the unique properties of the GHG gel phase which is underlain by a surprisingly dense fibril network with an exceptionally strong modulus that make them potential additives for biomedical applications.
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Affiliation(s)
- Morgan Hesser
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Lavenia J Thursch
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Todd R Lewis
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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4
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Vosough F, Barth A. Characterization of Homogeneous and Heterogeneous Amyloid-β42 Oligomer Preparations with Biochemical Methods and Infrared Spectroscopy Reveals a Correlation between Infrared Spectrum and Oligomer Size. ACS Chem Neurosci 2021; 12:473-488. [PMID: 33455165 PMCID: PMC8023574 DOI: 10.1021/acschemneuro.0c00642] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
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Soluble oligomers of the amyloid-β(1-42)
(Aβ42) peptide,
widely considered to be among the relevant neurotoxic species involved
in Alzheimer’s disease, were characterized with a combination
of biochemical and biophysical methods. Homogeneous and stable Aβ42
oligomers were prepared by treating monomeric solutions of the peptide
with detergents. The prepared oligomeric solutions were analyzed with
blue native and sodium dodecyl sulfate polyacrylamide gel electrophoresis,
as well as with infrared (IR) spectroscopy. The IR spectra indicated
a well-defined β-sheet structure of the prepared oligomers.
We also found a relationship between the size/molecular weight of
the Aβ42 oligomers and their IR spectra: The position of the
main amide I′ band of the peptide backbone correlated with
oligomer size, with larger oligomers being associated with lower wavenumbers.
This relationship explained the time-dependent band shift observed
in time-resolved IR studies of Aβ42 aggregation in the absence
of detergents, during which the oligomer size increased. In addition,
the bandwidth of the main IR band in the amide I′ region was
found to become narrower with time in our time-resolved aggregation
experiments, indicating a more homogeneous absorption of the β-sheets
of the oligomers after several hours of aggregation. This is predominantly
due to the consumption of smaller oligomers in the aggregation process.
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Affiliation(s)
- Faraz Vosough
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
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5
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Hesser M, Thursch L, Lewis T, DiGuiseppi D, Alvarez NJ, Schweitzer-Stenner R. The tripeptide GHG as an unexpected hydrogelator triggered by imidazole deprotonation. SOFT MATTER 2020; 16:4110-4114. [PMID: 32322858 DOI: 10.1039/d0sm00224k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The tripeptide glycyl-histidyl-glycine (GHG) self-assembles into long, crystalline fibrils forming a strong hydrogel (G'∼ 50 kPa) above a critical concentration of 40 mM upon the deprotonation of its imidazole group. Spectroscopic data reveal a mixture of helically twisted β-sheets and monomers to coexist in the gel phase.
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Affiliation(s)
- Morgan Hesser
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA.
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6
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Koenis MAJ, Visscher L, Buma WJ, Nicu VP. Analysis of Vibrational Circular Dichroism Spectra of Peptides: A Generalized Coupled Oscillator Approach of a Small Peptide Model Using VCDtools. J Phys Chem B 2020; 124:1665-1677. [PMID: 32037822 PMCID: PMC7061330 DOI: 10.1021/acs.jpcb.9b11261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Vibrational circular dichroism (VCD) is one of the major spectroscopic tools to study peptides. Nevertheless, a full understanding of what determines the signs and intensities of VCD bands of these compounds in the amide I and amide II spectral regions is still far from complete. In the present work, we study the origin of these VCD signals using the general coupled oscillator (GCO) analysis, a novel approach that has recently been developed. We apply this approach to the ForValNHMe model peptide in both α-helix and β-sheet configurations. We show that the intense VCD signals observed in the amide I and amide II spectral regions essentially have the same underlying mechanism, namely, the through-space coupling of electric dipoles. The crucial role played by intramolecular hydrogen bonds in determining VCD intensities is also illustrated. Moreover, we find that the contributions to the rotational strengths, considered to be insignificant in standard VCD models, may have sizable magnitudes and can thus not always be neglected. In addition, the VCD robustness of the amide I and II modes has been investigated by monitoring the variation of the rotational strength and its contributing terms during linear transit scans and by performing calculations with different computational parameters. From these studies-and in particular, the decomposition of the rotational strength made possible by the GCO analysis-it becomes clear that one should be cautious when employing measures of robustness as proposed previously.
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Affiliation(s)
- Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling, Section Theoretical Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Wybren J Buma
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.,Institute for Molecules and Materials, FELIX Laboratory, Radboud University, Toernooiveld 7c, 6525 ED Nijmegen, The Netherlands
| | - Valentin P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport, Lucian Blaga University of Sibiu, loan Ratiu Street, Nr. 7-9, 550012 Sibiu, Romania
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7
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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8
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Xing R, Yuan C, Li S, Song J, Li J, Yan X. Charge-Induced Secondary Structure Transformation of Amyloid-Derived Dipeptide Assemblies from β-Sheet to α-Helix. Angew Chem Int Ed Engl 2018; 57:1537-1542. [DOI: 10.1002/anie.201710642] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/12/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Ruirui Xing
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
| | - Jingwen Song
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Junbai Li
- Key Laboratory of Colloid and Interface Science, Center for Molecular Sciences; Institute of Chemistry; Chinese Academy of Sciences; 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
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9
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Xing R, Yuan C, Li S, Song J, Li J, Yan X. Charge-Induced Secondary Structure Transformation of Amyloid-Derived Dipeptide Assemblies from β-Sheet to α-Helix. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201710642] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Ruirui Xing
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Chengqian Yuan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Shukun Li
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
| | - Jingwen Song
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
| | - Junbai Li
- Key Laboratory of Colloid and Interface Science, Center for Molecular Sciences; Institute of Chemistry; Chinese Academy of Sciences; 100190 Beijing China
| | - Xuehai Yan
- State Key Laboratory of Biochemical Engineering; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- Center for Mesoscience; Institute of Process Engineering; Chinese Academy of Sciences; 100190 Beijing China
- University of Chinese Academy of Sciences; 100049 Beijing China
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10
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Baldassarre M, Baronio CM, Morozova-Roche LA, Barth A. Amyloid β-peptides 1-40 and 1-42 form oligomers with mixed β-sheets. Chem Sci 2017; 8:8247-8254. [PMID: 29568473 PMCID: PMC5857929 DOI: 10.1039/c7sc01743j] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/12/2017] [Indexed: 12/16/2022] Open
Abstract
Two main amyloid-β peptides of different length (Aβ40 and Aβ42) are involved in Alzheimer's disease. Their relative abundance is decisive for the severity of the disease and mixed oligomers may contribute to the toxic species. However, little is know about the extent of mixing. To study whether Aβ40 and Aβ42 co-aggregate, we used Fourier transform infrared spectroscopy in combination with 13C-labeling and spectrum calculation and focused on the amide I vibration, which is sensitive to backbone structure. Mixtures of monomeric labeled Aβ40 and unlabeled Aβ42 (and vice versa) were co-incubated for ∼20 min and their infrared spectrum recorded. The position of the main 13C-amide I' band shifted to higher wavenumbers with increasing admixture of 12C-peptide due to the presence of 12C-amides in the vicinity of 13C-amides. The results indicate that Aβ40 and Aβ42 form mixed oligomers with a largely random distribution of Aβ40 and Aβ42 strands in their β-sheets. The structures of the mixed oligomers are intermediate between those of the pure oligomers. There is no indication that one of the peptides forces the backbone structure of its oligomers on the other peptide when they are mixed as monomers. We also demonstrate that isotope-edited infrared spectroscopy can distinguish aggregation modulators that integrate into the backbone structure of their interaction partner from those that do not. As an example for the latter case, the pro-inflammatory calcium binding protein S100A9 is shown not to incorporate into the β-sheets of Aβ42.
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Affiliation(s)
- Maurizio Baldassarre
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
| | - Cesare M Baronio
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
| | | | - Andreas Barth
- Department of Biochemistry and Biophysics , Stockholm University , Arrhenius Laboratories , 10691 Stockholm , Sweden .
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11
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DiGuiseppi D, Kraus J, Toal SE, Alvarez N, Schweitzer-Stenner R. Investigating the Formation of a Repulsive Hydrogel of a Cationic 16mer Peptide at Low Ionic Strength in Water by Vibrational Spectroscopy and Rheology. J Phys Chem B 2016; 120:10079-10090. [DOI: 10.1021/acs.jpcb.6b07673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Siobhan E. Toal
- Department
of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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12
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Farrell S, DiGuiseppi D, Alvarez N, Schweitzer-Stenner R. The interplay of aggregation, fibrillization and gelation of an unexpected low molecular weight gelator: glycylalanylglycine in ethanol/water. SOFT MATTER 2016; 12:6096-6110. [PMID: 27363780 DOI: 10.1039/c6sm00879h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrogels formed by polypeptides could be much-favored tools for drug delivery because their main ingredients are generally biodegradable. However, the gelation of peptides in aqueous solution generally requires a minimal length of the peptide as well as distinct sequences of hydrophilic and hydrophobic residues. The aggregation of short peptides like tripeptides, which are relatively cheap and offer a high degree of biodegradability, are generally thought to require a high hydrophobicity of their residues. We found that contrary to this expectation cationic glycylalanylglycine in 55 mol% ethanol/45 mol% water forms a gel below a melting temperature of ca. 36 °C. A pure hydrogel state can be obtained after allowing the ethanol component to evaporate. The gel phase consists of crystalline fibrils of several 100 μm, which form a sample-spanning network. Rheological data reveal a soft elastic solid gel. We investigated the kinetics of the various processes that lead to the final gel state of the ternary mixture by a unique combination of UV circular dichroism, infrared, vibrational circular dichroism (VCD) and rheological measurements. A mathematical analysis of our data show that gelation is preceded by the formation of peptide β-sheet like tapes or ribbons, which give rise to a significant enhancement of the amide I' VCD signal, and the subsequent formation of rather thick and long fibrils. The VCD signals indicate that the tapes exhibit a right-handed helicity at temperatures above 16 °C and a left-handed helicity below. The tapes'/ribbons' helicity change occurs at a temperature where the UVCD data reflect a relatively long nucleation process. The kinetics of gel formation probed by the storage and loss moduli are composed of a fast process that follows tape/ribbon/fibril formation and is clearly identifiable in a movie that shows the gelation process and a slow process that causes an additional gel stabilization. The rheological data indicate that left-handed fibrils observed at low temperatures form a more solid-like structure than their right-handed counterparts formed at higher temperatures. Taken together our data reveal GAG as an unexpected gelator, the formation of which is underlied by a set of distinguishable kinetic processes.
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Affiliation(s)
- Stefanie Farrell
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
| | - David DiGuiseppi
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
| | - Nicolas Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
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13
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Góbi S, Magyarfalvi G, Tarczay G. VCD Robustness of the Amide-I and Amide-II Vibrational Modes of Small Peptide Models. Chirality 2015; 27:625-34. [DOI: 10.1002/chir.22475] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 04/21/2015] [Accepted: 05/08/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Sándor Góbi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - Gábor Magyarfalvi
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
| | - György Tarczay
- Laboratory of Molecular Spectroscopy; Institute of Chemistry, Eötvös University; Budapest Hungary
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14
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Piccirilli F, Schirò G, Vetri V, Lupi S, Perucchi A, Militello V. Decoding vibrational states of Concanavalin A amyloid fibrils. Biophys Chem 2015; 199:17-24. [DOI: 10.1016/j.bpc.2015.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/04/2015] [Accepted: 02/13/2015] [Indexed: 10/24/2022]
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15
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Parchaňský V, Kapitán J, Bouř P. Inspecting chiral molecules by Raman optical activity spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra10416a] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
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Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
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17
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Welch WRW, Kubelka J, Keiderling TA. Infrared, vibrational circular dichroism, and Raman spectral simulations for β-sheet structures with various isotopic labels, interstrand, and stacking arrangements using density functional theory. J Phys Chem B 2013; 117:10343-58. [PMID: 23924300 DOI: 10.1021/jp4056126] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infrared (IR), Raman, and vibrational circular dichroism (VCD) spectral variations for different β-sheet structures were studied using simulations based on density functional theory (DFT) force field and intensity computations. The DFT vibrational parameters were obtained for β-sheet fragments containing nine-amides and constrained to a variety of conformations and strand arrangements. These were subsequently transferred onto corresponding larger β-sheet models, normally consisting of five strands with ten amides each, for spectral simulations. Further extension to fibril models composed of multiple stacked β-sheets was achieved by combining the transfer of DFT parameters for each sheet with dipole coupling methods for interactions between sheets. IR spectra of the amide I show different splitting patterns for parallel and antiparallel β-sheets, and their VCD, in the absence of intersheet stacking, have distinct sign variations. Isotopic labeling by (13)C of selected residues yields spectral shifts and intensity changes uniquely sensitive to relative alignment of strands (registry) for antiparallel sheets. Stacking of multiple planar sheets maintains the qualitative spectral character of the single sheet but evidences some reduction in the exciton splitting of the amide I mode. Rotating sheets with respect to each other leads to a significant VCD enhancement, whose sign pattern and intensity is dependent on the handedness and degree of rotation. For twisted β-sheets, a significant VCD enhancement is computed even for sheets stacked with either the same or opposite alignments and the inter-sheet rotation, depending on the sense, can either further increase or weaken the enhanced VCD intensity. In twisted, stacked structures (without rotation), similar VCD amide I patterns (positive couplets) are predicted for both parallel and antiparallel sheets, but different IR intensity distributions still enable their differentiation. Our simulation results prove useful for interpreting experimental vibrational spectra in terms of β-sheet and fibril structure, as illustrated in the accompanying paper.
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Affiliation(s)
- William R W Welch
- Department of Chemistry, University of Wyoming , Laramie, Wyoming 82071, United States
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18
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Schweitzer-Stenner R. Different Degrees of Disorder in Long Disordered Peptides Can Be Discriminated by Vibrational Spectroscopy. J Phys Chem B 2013; 117:6927-36. [DOI: 10.1021/jp402869k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department
of Chemistry, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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19
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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20
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Pagba CV, Barry BA. Redox-Induced Conformational Switching in Photosystem-II-Inspired Biomimetic Peptides: A UV Resonance Raman Study. J Phys Chem B 2012; 116:10590-9. [DOI: 10.1021/jp303607b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Cynthia V. Pagba
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Bridgette A. Barry
- School of Chemistry and
Biochemistry and the Parker
H. Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
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21
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Schweitzer-Stenner R. Simulated IR, Isotropic and Anisotropic Raman, and Vibrational Circular Dichroism Amide I Band Profiles of Stacked β-Sheets. J Phys Chem B 2012; 116:4141-53. [DOI: 10.1021/jp2112445] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department
of Chemistry, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United
States
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22
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Fulara A, Lakhani A, Wójcik S, Nieznańska H, Keiderling TA, Dzwolak W. Spiral superstructures of amyloid-like fibrils of polyglutamic acid: an infrared absorption and vibrational circular dichroism study. J Phys Chem B 2011; 115:11010-6. [PMID: 21842891 DOI: 10.1021/jp206271e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Amyloid fibrils, which are often associated with certain degenerative disorders, reveal a number of intriguing spectral properties. However, the relationship between the structure of fibrils and their optical traits remains poorly understood. Poly(L-glutamic) acid is a model polypeptide shown recently to form amyloid-like fibrils with an atypical infrared amide I' band at 1595 cm(-1), which has been attributed to the presence of bifurcated hydrogen bonds coupling C═O and N-D groups of the main chains to glutamate side chains. Here we show that this unusual amide I' band is observed only for fibrils grown from pure enantiomers of the polypeptide, whereas fibrils precipitating from equimolar mixtures of poly(L-glutamic) and poly(D-glutamic) acids have amide I' bands at 1684 and 1612 cm(-1), which are indicative of a typical intermolecular antiparallel β-sheet. Pure enantiomers of polyglutamic acid form spirally twisted superstructures whose handedness is correlated to the amino acid chirality, while fibrils prepared from the racemate do not form scanning electron microscopy (SEM)-detectable mesoscopically ordered structures. Vibrational circular dichroism (VCD) spectra of β-aggregates prepared from mixtures of all L- or D-polyglutamic acid in varying ratios indicate that the enhancement of VCD intensity correlates with the presence of the twisted superstructures. Our results demonstrate that both IR absorption and enhanced VCD are sensitive to subtle packing defects taking place within the compact structure of amyloid fibrils.
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Affiliation(s)
- Aleksandra Fulara
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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23
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Magyarfalvi G, Tarczay G, Vass E. Vibrational circular dichroism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.39] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Formation of β-sheets in glutamine and alanine tripeptides. Biochem Biophys Res Commun 2011; 406:348-52. [DOI: 10.1016/j.bbrc.2011.02.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 02/10/2011] [Indexed: 11/20/2022]
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25
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Zhang L, Moo-Young M, Chou CP. Molecular manipulation associated with disulfide bond formation to enhance the stability of recombinant therapeutic protein. Protein Expr Purif 2011; 75:28-39. [PMID: 20719248 DOI: 10.1016/j.pep.2010.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 08/10/2010] [Accepted: 08/11/2010] [Indexed: 11/17/2022]
Abstract
Cys²⁷ in the extracellular domain of human CD83 (hCD83ext), a potential therapeutic protein, was identified as a target for molecular manipulation. Two Escherichia coli strains of BL21(DE3) and Origami B(DE3), respectively, with a reducing and an oxidative cytoplasm were used as the expression host to produce the Cys²⁷ mutants. It was observed that Cys²⁷ was involved in the in vivo formation of intramolecular disulfide bonds when hCD83ext was expressed in Origami B(DE3). The Origami-derived protein products had a higher tendency than the BL21-derived counterparts for multimerization via the in vitro formation of intermolecular disulfide bonds. Various analyses were conducted to identify the structural differences among these mutant variants. Most importantly, molecular stability was enhanced by the Cys²⁷ mutations since the Cys²⁷ mutants derived from either BL21 or Origami were much less susceptible to degradation compared to wild-type hCD83ext. This study highlights the implications of aberrant disulfide bond formation on the production of therapeutic proteins.
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Affiliation(s)
- Lin Zhang
- Department of Chemical Engineering, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
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26
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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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27
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Andrushchenko V, Matějka P, Anderson DT, Kaminský J, Horníček J, Paulson LO, Bouř P. Solvent Dependence of the N-Methylacetamide Structure and Force Field. J Phys Chem A 2009; 113:9727-36. [DOI: 10.1021/jp9045512] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Valery Andrushchenko
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Pavel Matějka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - David T. Anderson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Jan Horníček
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Leif O. Paulson
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences,
Flemingovo nám. 2, 16610, Praha 6, Czech Republic, Department
of Analytical Chemistry, Institute of Chemical Technology, Technická
5, 166 28, Prague 6, Czech Republic, and Department of Chemistry,
University of Wyoming, 1000 East University Avenue, Laramie, Wyoming
82071
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28
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Lakhani A, Malon P, Keiderling TA. Comparison of vibrational circular dichroism instruments: development of a new dispersive VCD. APPLIED SPECTROSCOPY 2009; 63:775-785. [PMID: 19589215 DOI: 10.1366/000370209788701189] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A dispersive vibrational circular dichroism (VCD) instrument has been designed and optimized for the measurement of mid-infrared (MIR) bands such as the amide I and amide II vibrational modes of peptides and proteins. The major design considerations were to construct a compact VCD instrument for biological molecules, to increase signal-to-noise (S/N) ratio, to simultaneously collect and digitize the sample transmission and polarization modulation signals, and to digitally ratio them to yield a VCD spectrum. These were realized by assembling new components using design factors adapted from previous VCD instruments. A collection of spectra for peptides and proteins having different dominant secondary structures (alpha-helix, beta-sheet, and random coil) measured for identical samples under the same conditions showed that the new instrument had substantially improved S/N as compared with our previous dispersive VCD instrument. These instruments both provide protein VCD for the amide I that are comparable to or somewhat better than those measurable with commercial Fourier transform (FT) VCD instruments if just the amide I band in the spectra is obtained at modest resolution (8 cm(-1)) with the same total data collection time on each type of instrument.
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Affiliation(s)
- Ahmed Lakhani
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c 111), Chicago, Illinois 60607-7061, USA
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29
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Šebek J, Kapitán J, Šebestík J, Baumruk V, Bouř P. l-Alanyl-l-alanine Conformational Changes Induced by pH As Monitored by the Raman Optical Activity Spectra. J Phys Chem A 2009; 113:7760-8. [DOI: 10.1021/jp902739r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jiří Šebek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 166 10, Prague 6, Czech Republic, Faculty of Mathematics and Physics, Institute of Physics, Charles University, Ke Karlovu 5, 12116, Prague, Czech Republic, and Department of Analytical Chemistry, Institute of Chemical Technology, Technická 5, 166 28, Prague 6, Czech Republic
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30
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Petrovic AG, Polavarapu PL, Mahalakshmi R, Balaram P. Characterization of folded conformations in a tetrapeptide containing two tryptophan residues by vibrational circular dichroism. Chirality 2009; 21 Suppl 1:E76-85. [DOI: 10.1002/chir.20779] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Vener MV, Egorova AN, Fomin DP, Tsirelson VG. Hierarchy of the non-covalent interactions in the alanine-based secondary structures. DFT study of the frequency shifts and electron-density features. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1445] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Two-dimensional infrared spectra of isotopically diluted amyloid fibrils from Abeta40. Proc Natl Acad Sci U S A 2008; 105:7720-5. [PMID: 18499799 DOI: 10.1073/pnas.0802993105] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 2D IR spectra of the amide-I vibrations of amyloid fibrils from Abeta40 were obtained. The matured fibrils formed from strands having isotopic substitution by (13)C (18)O at Gly-38, Gly-33, Gly-29, or Ala-21 show vibrational exciton spectra having reduced dimensionality. Indeed, linear chain excitons of amide units are seen, for which the interamide vibrational coupling is measured in fibrils grown from 50% and 5% mixtures of labeled and unlabeled strands. The data prove that the 1D excitons are formed from parallel in-register sheets. The coupling constants show that for each of the indicated residues the amide carbonyls in the chains are separated by 0.5 +/- 0.05 nm. The isotope replacement of Gly-25 does not reveal linear excitons, consistent with the region of the strand having a different structure distribution. The vibrational frequencies of the amide-I modes, freed from effects of amide vibrational excitation exchange by 5% dilution experiments, point to there being a component of an electric field along the fibril axis that increases through the sequence Gly-38, Gly-33, Gly-29. The field is dominated by side chains of neighboring residues.
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33
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Affiliation(s)
- Minhaeng Cho
- Department of Chemistry and Center for Multidimensional Spectroscopy, Korea University, Seoul 136-701, Korea.
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34
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Huang R, Setnička V, Etienne MA, Kim J, Kubelka J, Hammer RP, Keiderling TA. Cross-Strand Coupling of a β-Hairpin Peptide Stabilized with an Aib-Gly Turn Studied Using Isotope-Edited IR Spectroscopy. J Am Chem Soc 2007; 129:13592-603. [DOI: 10.1021/ja0736414] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong Huang
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Vladimir Setnička
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Marcus A. Etienne
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Joohyun Kim
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Jan Kubelka
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Robert P. Hammer
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
| | - Timothy A. Keiderling
- Contribution from the Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (m/c111), Chicago, Illinois 60607-7061, Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803-1804
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35
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Parthasarathi R, Raman SS, Subramanian V, Ramasami T. Bader's Electron Density Analysis of Hydrogen Bonding in Secondary Structural Elements of Protein. J Phys Chem A 2007; 111:7141-8. [PMID: 17602540 DOI: 10.1021/jp071513w] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrogen-bonding (H-bonding) interactions in alpha-helical and beta-sheet model peptides have been studied by using the atoms-in-molecule (AIM) approach. The relative importance of NH...O and CH...O H-bonding interactions in the different secondary elements such as alpha-helix, parallel, and antiparallel beta-sheets have been assessed. The electron density values at the NH...O bond are higher than those of the CH...O bonds in the alpha-helical conformation. The electron density values at the H-bonded critical points (HBCPs) corresponding to NH...O and CH...O interactions are nearly equal in the parallel beta-sheet of the order of 10(-3) au, whereas in the case of antiparallel beta-sheets, rho(rc) values for NH...O and CH...O interactions are of the order of 10(-2) and 10(-3) au, respectively. It is interesting to point out here that the weakening of NH...O interactions in the parallel beta-sheet arrangement is evident from the AIM analysis. This is concomitant with the increase in the NH...O distance in the parallel beta-sheet conformation. In addition to the clear description of H-bonding by electron density at the HBCP, possible good linear relationships between the electron density at ring critical points (RCP) and stabilization energy (SE) have been observed corresponding to the various beta-sheet conformations.
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Affiliation(s)
- R Parthasarathi
- Chemical Laboratory, Central Leather Research Institute, Adyar, Chennai 600 020, India
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36
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Smith AW, Tokmakoff A. Amide I two-dimensional infrared spectroscopy of beta-hairpin peptides. J Chem Phys 2007; 126:045109. [PMID: 17286519 DOI: 10.1063/1.2428300] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this report, spectral simulations and isotope labeling are used to describe the two-dimensional IR spectroscopy of beta-hairpin peptides in the amide I spectral region. 2D IR spectra of Gramicidin S, PG12, Trpzip2 (TZ2), and TZ2-T3(*)T10(*), a dual (13)C(') isotope label, are qualitatively described by a model based on the widely used local mode amide I Hamiltonian. The authors' model includes methods for calculating site energies for individual amide oscillators on the basis of hydrogen bonding, nearest neighbor and long-range coupling between sites, and disorder in the site energy. The dependence of the spectral features on the peptide backbone structure is described using disorder-averaged eigenstates, which are visualized by mapping back onto the local amide I sites. beta-hairpin IR spectra are dominated by delocalized vibrations that vary by the phase of adjacent oscillators parallel and perpendicular to the strands. The dominant nu(perpendicular) band is sensitive to the length of the hairpin and the amount of twisting in the backbone structure, while the nu(parallel) band is composed of several low symmetry modes that delocalize along the strands. The spectra of TZ2-T3(*)T10(*) are used to compare coupling models, from which we conclude that transition charge coupling is superior to transition dipole coupling for amide groups directly hydrogen bound across the beta strands. The 2D IR spectra of TZ2-T3(*)T10(*) are used to resolve the redshifted amide I band and extract the site energy of the labeled groups. This allows the authors to compare several methods for calculating the site energies used in excitonic treatments of the amide I band. Gramicidin S is studied in dimethyl sulfoxide to test the role of solvent on the spectral simulations.
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Affiliation(s)
- Adam W Smith
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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37
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Tight β-turns in peptides. DFT-based study of infrared absorption and vibrational circular dichroism for various conformers including solvent effects. Theor Chem Acc 2006. [DOI: 10.1007/s00214-006-0183-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Kim J, Huang R, Kubelka J, Bou Rcaron P, Keiderling TA. Simulation of Infrared Spectra for β-Hairpin Peptides Stabilized by an Aib-Gly Turn Sequence: Correlation between Conformational Fluctuation and Vibrational Coupling. J Phys Chem B 2006; 110:23590-602. [PMID: 17107215 DOI: 10.1021/jp0640575] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational spectra of a 12-residue beta-hairpin peptide, RYVEVBGKKILQ (HBG), stabilized by an Aib-Gly turn sequence (B = Aib) were investigated theoretically using a combination of molecular dynamics (MD) and density functional theory (DFT) calculations. Selected conformations of HBG were extracted from a classical MD trajectory and used for spectral simulations. DFT calculations, based on the Cartesian coordinate spectral property transfer protocol, were carried out for peptide structures in which all residues are replaced with Ala, except for the Aib and Gly residues, but the backbone (phi, psi, omega) structure of the original configuration is retained. The simulations provide a basis for interpretation of the HBG amide I infrared spectra in terms of structural variables such as detailed secondary structure and thermal conformational fluctuation as well as vibrational coupling as indicated by spectra of 13C isotope-labeled variants. The characteristic amide I band shape of such small beta-hairpin peptides appears to arise from the structure of the short antiparallel beta-sheet strands. The role of structural parameter fluctuation in vibrational coupling is evaluated by comparison of DFT-derived amide coupling constants for selected configurations and from transition dipole coupling calculations of coupling parameters between (13)C isotopically labeled residues for a MD-derived ensemble of configurations. Calculated results were compared with the experimentally obtained spectra for several (13)C isotope-labeled peptides of this sequence.
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Affiliation(s)
- Joohyun Kim
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061, USA
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39
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Measey TJ, Schweitzer-Stenner R. Aggregation of the Amphipathic Peptides (AAKA)n into Antiparallel β-Sheets. J Am Chem Soc 2006; 128:13324-5. [PMID: 17031922 DOI: 10.1021/ja0632411] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helical wheel projections of peptides based on the repeating unit Ac-(AAKA)n-NH2 clearly illustrate an amphipathic nature. One should therefore expect these peptides to form helices if the number of residues exceeds a certain threshold value. Indeed, ECD measurements show that Ac-(AAKA)4-NH2 and, to a minor extent, also Ac-(AAKA)3-NH2 exhibit some helical content at millimolar concentrations in aqueous solution. Surprisingly, however, these peptides were found to form hydrogels with an antiparallel beta-sheet conformation at centimolar concentrations. This occurs despite the positively charged lysine side chain which would be expected to inhibit the formation of extended beta-sheet layers.
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Affiliation(s)
- Thomas J Measey
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA
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40
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Du D, Tucker MJ, Gai F. Understanding the mechanism of beta-hairpin folding via phi-value analysis. Biochemistry 2006; 45:2668-78. [PMID: 16489760 DOI: 10.1021/bi052039s] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The folding kinetics of a 16-residue beta-hairpin (trpzip4) and five mutants were studied by a laser-induced temperature-jump infrared method. Our results indicate that mutations which affect the strength of the hydrophobic cluster lead to a decrease in the thermal stability of the beta-hairpin, as a result of increased unfolding rates. For example, the W45Y mutant has a phi-value of approximately zero, implying a folding transition state in which the native contacts involving Trp45 are not yet formed. On the other hand, mutations in the turn or loop region mostly affect the folding rate. In particular, replacing Asp46 with Ala leads to a decrease in the folding rate by roughly 9 times. Accordingly, the phi-value for D46A is determined to be approximately 0.77, suggesting that this residue plays a key role in stabilizing the folding transition state. This is most likely due to the fact that the main chain and side chain of Asp46 form a characteristic hydrogen bond network with other residues in the turn region. Taken together, these results support the folding mechanism we proposed before, which suggests that the turn formation is the rate-limiting step in beta-hairpin folding and, consequently, a stronger turn-promoting sequence increases the stability of a beta-hairpin primarily by increasing its folding rate, whereas a stronger hydrophobic cluster increases the stability of a beta-hairpin primarily by decreasing its unfolding rate. In addition, we have examined the compactness of the thermally denatured and urea-denatured states of another 16-residue beta-hairpin, using the method of fluorescence resonance energy transfer. Our results show that the thermally denatured state of this beta-hairpin is significantly more compact than the urea-denatured state, suggesting that the very first step in beta-hairpin folding, when initiated from an extended conformation, probably corresponds to a process of hydrophobic collapse.
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Affiliation(s)
- Deguo Du
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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41
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Bour P, Keiderling TA. Vibrational Spectral Simulation for Peptides of Mixed Secondary Structure: Method Comparisons with the Trpzip Model Hairpin. J Phys Chem B 2005; 109:23687-97. [PMID: 16375349 DOI: 10.1021/jp054107q] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Infrared absorption and vibrational circular dichroism (IR and VCD) spectra of model fragments of TrpZip-style beta-hairpin structures are simulated using density functional theory (DFT) methods to estimate the influence of fragment size, end effects, conformational irregularities, peptide side chains, and solvent. Different fragmentation schemes, computing the strands and turn segments separately, were tested by varying the sizes of each and their respective overlaps. For suitably overlapping fragments, atomic property tensors were found to be reliably transferable, as tested by their ability to generate simulated spectra in good agreement with results from ab initio DFT computations for the entire peptide. This fragment approach significantly reduces computational times and opens up a wider range of systems that can be studied with a DFT-based approach as compared to previous methods based on uniform repeating sequences. However, vacuum calculations do not adequately represent the frequency dispersion of solvated molecules, and thus, some alternate strategies for solvation correction are explored for improving the simulation accuracy. Unlike for regular periodic secondary structure, the solvent significantly impacts the spectral shapes of hairpins, due to the different degrees of hydration of individual amide groups, which can be exposed to or shielded from water due to external vs internal hydrogen bonding. This is amplified by the shielding of selected amides from the solvent due to bulky side chains. The peptide plus solvent was structurally modeled with molecular dynamics methods, and then an electrostatic field-based parametrization correction was added to the force field and intensity tensors to compensate for the solvent dipolar field. The effect of the shielding and subsequent reordering of modes has a larger impact on VCD than IR band shapes.
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Affiliation(s)
- Petr Bour
- Institute for Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo námestí 2, 16610 Praha 6, Czech Republic.
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Koch O, Bocola M, Klebe G. Cooperative effects in hydrogen-bonding of protein secondary structure elements: A systematic analysis of crystal data using Secbase. Proteins 2005; 61:310-7. [PMID: 16121398 DOI: 10.1002/prot.20613] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A systematic analysis of the hydrogen-bonding geometry in helices and beta sheets has been performed. The distances and angles between the backbone carbonyl O and amide N atoms were correlated considering more than 1500 protein chains in crystal structures determined to a resolution better than 1.5 A. They reveal statistically significant trends in the H-bond geometry across the different secondary structural elements. The analysis has been performed using Secbase, a modular extension of Relibase (Receptor Ligand Database) which integrates information about secondary structural elements assigned to individual protein structures with the various search facilities implemented into Relibase. A comparison of the mean hydrogen-bond distances in alpha helices and 3(10) helices of increasing length shows opposing trends. Whereas in alpha helices the mean H-bond distance shrinks with increasing helix length and turn number, the corresponding mean dimension in 3(10) helices expands in a comparable series. Comparing similarly the hydrogen-bond lengths in beta sheets there is no difference to be found between the mean H-bond length in antiparallel and parallel beta sheets along the strand direction. In contrast, an interesting systematic trend appears to be given for the hydrogen bonds perpendicular to the strands bridging across an extended sheet. With increasing number of accumulated strands, which results in a growing number of back-to-back piling hydrogen bonds across the strands, a slight decrease of the mean H-bond distance is apparent in parallel beta sheets whereas such trends are obviously not given in antiparallel beta sheets. This observation suggests that cooperative effects mutually polarizing spatially well-aligned hydrogen bonds are present either in alpha helices and parallel beta sheets whereas such influences seem to be lacking in 3(10) helices and antiparallel beta sheets.
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Affiliation(s)
- O Koch
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35032 Marburg, Germany
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Hahn S, Kim SS, Lee C, Cho M. Characteristic two-dimensional IR spectroscopic features of antiparallel and parallel β-sheet polypeptides: Simulation studies. J Chem Phys 2005; 123:084905. [PMID: 16164328 DOI: 10.1063/1.1997151] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The antiparallel and parallel beta sheets are two of the most abundant secondary structures found in proteins. Although various spectroscopic methods have been used to distinguish these two different structures, the linear spectroscopic measurements could not provide incisive information for distinguishing an antiparallel beta sheet from a parallel beta sheet. After carrying out quantum-chemistry calculations and model simulations, we show that the polarization-controlled two-dimensional (2D) IR photon echo spectroscopy can be of critical use in distinguishing these two different beta sheets. Particularly, the ratio between the diagonal peak and the cross peak is found to be strongly dependent on the quasi-2D array of the amide I local-mode transition dipole vectors. The relative intensities of the cross peaks in the 2D difference spectrum of an antiparallel beta sheet are significantly larger than those of the diagonal peaks, whereas the cross-peak amplitudes in the 2D difference spectrum of a parallel beta sheet are much weaker than the main diagonal-peak amplitudes. A detailed discussion on the origin of the diagonal- and cross-peak intensity distributions of both the antiparallel and parallel beta sheets is presented by examining vibrational exciton delocalization, relative angles between two different normal-mode transition dipoles, and natures of the cross peaks in the 2D difference spectrum.
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Affiliation(s)
- Seungsoo Hahn
- Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
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Bour P, Michalík D, Kapitán J. Empirical solvent correction for multiple amide group vibrational modes. J Chem Phys 2005; 122:144501. [PMID: 15847539 DOI: 10.1063/1.1877272] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Praha 6, Czech Republic.
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Measey T, Hagarman A, Eker F, Griebenow K, Schweitzer-Stenner R. Side Chain Dependence of Intensity and Wavenumber Position of Amide I‘ in IR and Visible Raman Spectra of XA and AX Dipeptides. J Phys Chem B 2005; 109:8195-205. [PMID: 16851958 DOI: 10.1021/jp045762l] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A series of AX and XA dipeptides in D2O have been investigated by FTIR, isotropic, and anisotropic Raman spectroscopy at acidic, neutral, and alkaline pD, to probe the influence of amino acid side chains on the amide I' band. We obtained a set of spectral parameters for each peptide, including intensities, wavenumbers, half-widths, and dipole moments, and found that these amide I' parameters are indeed dependent on the side chain. Side chains with similar characteristic properties were found to have similar effects on the amide I'. For example, dipeptides with aliphatic side chains were found to exhibit a downshift of the amide I' wavenumber, while those containing polar side chains experienced an increase in wavenumber. The N-terminal charge causes a substantial upshift of amide I', whereas the C-terminal charge causes a moderate decrease of the transition dipole moment. Density functional theory (DFT) calculations on the investigated dipeptides in vacuo yielded different correlations between theoretically and experimentally obtained wavenumbers for aliphatic/aromatic and polar/charged side chains, respectively. This might be indicative of a role of the hydration shell in transferring side chain-backbone interactions. For Raman bands, we found a correlation between amide I' depolarization ratio and wavenumber which reflects that some side chains (valine, histidine) have a significant influence on the Raman tensor. Altogether, the obtained data are of utmost importance for utilizing amide I as a tool for secondary structure analysis of polypeptides and proteins and providing an experimental basis for theoretical modeling of this important backbone mode. This is demonstrated by a rather accurate modeling for the amide I' band profiles of the IR, isotropic Raman, and anisotropic Raman spectra of the beta-amyloid fragment Abeta(1-82).
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Affiliation(s)
- Thomas Measey
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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Bour P, Keiderling TA. Ab Initio Modeling of Amide I Coupling in Antiparallel β-Sheets and the Effect of 13C Isotopic Labeling on Infrared Spectra. J Phys Chem B 2005; 109:5348-57. [PMID: 16863201 DOI: 10.1021/jp0446837] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.
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Affiliation(s)
- Petr Bour
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610, Praha 6, Czech Republic.
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Schmidt P, Dybal J, Rodriguez-Cabello JC, Reboto V. Role of Water in Structural Changes of Poly(AVGVP) and Poly(GVGVP) Studied by FTIR and Raman Spectroscopy and ab Initio Calculations. Biomacromolecules 2005; 6:697-706. [PMID: 15762632 DOI: 10.1021/bm049461t] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two elastin-like poly(pentapeptides), poly(AV1GV2P) and poly(G1V1G2V2P), have been studied in water and in solid state by ATR FTIR and Raman spectroscopy in combination with model ab initio calculations. In aqueous solutions below the transition temperature T(t), a part of the amide groups and of the methyl groups of both polypentapeptides interacts with neighboring water molecules, whereas the other part of amide groups mutually interacts forming a beta-sheetlike structure. Below T(t), poly(AV1GV2P) is dissolved more perfectly, and the water shells around the polymer chains are more closely structured. The suspension of poly(AV1GV2P) formed above T(t) is more compact and, on cooling, resists more to the reverse dissolution, whereas the suspension of poly(G1V1G2V2P) contains more water molecules bound to the carbonyl of amide groups and on backward cooling dissolves fairly reversibly. The measured poly(pentapeptides) tend to form beta-turns due to the conformational transition on the residue between P and V1.
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Affiliation(s)
- Pavel Schmidt
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovský Sq. 2, Prague 6, Czech Republic.
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Bouř P. Convergence Properties of the Normal Mode Optimization and Its Combination with Molecular Geometry Constraints. ACTA ACUST UNITED AC 2005. [DOI: 10.1135/cccc20051315] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Optimization in the normal mode coordinates has been established as a useful tool for modeling of vibrational spectra (J. Chem. Phys. 2002, 117, 4126). In this work the algorithm is extended with the aid of harmonic penalty functions to allow for multiple restraints of geometry parameters, such as bond lengths, bond and dihedral angles, and for simultaneous optimization of more molecules. Additionally, geometry optimization when atomic nuclei are maintained on the constant electrostatic potential surface was implemented and its applications for solvent models are discussed. Model systems include small molecules, water cluster, antiparallel β-sheet peptide containing intermolecular hydrogen bonds, periodic α-helix and a parallel β-sheet segments. The normal mode method provided better numerical stability than the conventional redundant internal coordinates, especially for weakly hydrogen-bonded systems, while the speed of the optimization was found similar as for the Cartesian coordinates.
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Petrovic AG, Bose PK, Polavarapu PL. Vibrational circular dichroism of carbohydrate films formed from aqueous solutions. Carbohydr Res 2004; 339:2713-20. [PMID: 15519330 DOI: 10.1016/j.carres.2004.09.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 09/20/2004] [Indexed: 11/28/2022]
Abstract
Vibrational circular dichroism (VCD) spectra in the entire 2000-900 cm(-1) region have been recorded, for the first time, for films of carbohydrates prepared from aqueous solutions. Eight different carbohydrates, alpha-D-glucopyranosyl-(1-->4)-D-glucose, cyclomaltohexaose, alpha-D-glucopyranosyl alpha-D-glucopyranoside, beta-D-glucopyranosyl-(1-->6)-D-glucose, beta-D-glucopyranosyl-(1-->4)-D-glucose, D-glucose, and both enantiomers of 6-deoxygalactose and of allose, were investigated. The VCD spectra obtained for films are found to be identical to the corresponding spectra obtained for aqueous solutions of carbohydrates. These measurements demonstrate several advantages of significant importance. The strong infrared absorption of water has prevented, in the past, the pursuit for routine applications of VCD in determining the structures of carbohydrates in aqueous solutions. This limitation is not present for film studies because water solvent is removed in the process of preparing the films. Also, strong infrared absorption of water at 1650 cm(-1) requires the use of very short-pathlength (6 microm) cells for measurements on aqueous solutions. This requirement and concomitant inconveniences (such as laborious assembling of a demountable liquid cell or purchasing an expensive variable pathlength liquid cell) have been eliminated for film measurements. The removal of interfering water absorption in film studies resulted in higher light throughput and better signal-to-noise ratios for VCD measurements. Another point of significance is that the amount of carbohydrate sample required for VCD measurements on films is approximately one to two orders of magnitude smaller than that required for corresponding VCD measurements on aqueous solutions. Since carbohydrate samples can now be studied as films, VCD spectroscopy becomes much more broadly applicable for carbohydrates than previously believed. The present work, in combination with other film measurements in our laboratory, indicate that VCD studies on films can be used more generally, providing a convenient and powerful approach for probing structural information for biologically important compounds.
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Affiliation(s)
- Ana G Petrovic
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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Schweitzer-Stenner R. Secondary Structure Analysis of Polypeptides Based on an Excitonic Coupling Model to Describe the Band Profile of Amide I‘ of IR, Raman, and Vibrational Circular Dichroism Spectra. J Phys Chem B 2004. [DOI: 10.1021/jp0477654] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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