1
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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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2
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O'Neill N, Lima TA, Ferreira FF, Thursch L, Alvarez N, Schweitzer-Stenner R. Forbidden Secondary Structures Found in Gel-Forming Fibrils of Glycylphenylalanylglycine. J Phys Chem B 2022; 126:8080-8093. [PMID: 36194765 DOI: 10.1021/acs.jpcb.2c05010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The zwitterionic l-tripeptide glycylphenylalanylglycine self-assembles into very long crystalline fibrils in an aqueous solution, which causes the formation of an exceptionally strong gel phase (G' ∼ 5 × 106 Pa). The Rietveld refinement analysis of its powder X-ray diffraction (PXRD) pattern reveals a unit cell with four peptides forming a P212121 space group and adopting an inverse polyproline II conformation, that is, a right-handed helical structure that occupies the "forbidden" region of the Ramachandran plot. This unusual structure is stabilized by a plethora of intermolecular interactions facilitated by the large number of different functional groups of the unblocked tripeptide. Comparisons of simulated and experimental Fourier transform infrared and vibrational circular dichroism (VCD) amide I' profiles corroborate the PXRD structure. Our experimental setup reduces the sample to a quasi-two-dimensional network of fibrils. We exploited the influence of this reduced dimensionality on the amide I VCD to identify the main fibril axis. We demonstrate that PXRD, vibrational spectroscopy, and amide I simulations provide a powerful toolset for secondary structure and fibril axis determination.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States.,Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Thamires A Lima
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Fabio Furlan Ferreira
- Center for Natural and Human Sciences (CCNH), Federal University of ABC (UFABC), Av. Dos Estados, 5001, S622-3, Santo André, São Paulo09210-580, Brazil
| | - Lavenia Thursch
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Nicolas Alvarez
- Department of Chemical Engineering, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania19104, United States
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3
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Levine MS, Ghosh M, Hesser M, Hennessy N, DiGuiseppi DM, Adler-Abramovich L, Schweitzer-Stenner R. Formation of peptide-based oligomers in dimethylsulfoxide: identifying the precursor of fibril formation. SOFT MATTER 2020; 16:7860-7868. [PMID: 32761042 DOI: 10.1039/d0sm00035c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The well-studied dipeptide fluorenylmethyloxycarbonyl-di-phenylalanine (FmocFF) forms a rigid hydrogel upon dissolving in dimethylsulfoxide (DMSO) and dilution in H2O. Here, we explored the pre-aggregation of the peptide in pure DMSO by vibrational spectroscopies, X-ray powder diffraction and dynamic light scattering. Our results show an equilibrium between a dominant population of amorphous oligomers (on a length scale of 2 nm) and a small number of protofibrils/fibrils (on a length scale of 30 nm in the centimolar and of 200 nm in the sub-molar region). To probe the mechanism underlying the formation of these protofilaments, we measured the 1H-NMR, IR and visible Raman spectra of DMSO containing different FmocFF concentrations, ranging between 10 and 300 mM. Our data reveal that interpeptide hydrogen bonding leads to the self-assembly of FmocFF in the centimolar region, while π-π stacking between Fmoc-groups is observed above 100 mM. The high 3J(HNHCα) coupling constant of the N-terminal amide proton indicates that the Fmoc end-cap of the peptide locks the N-terminal residue into a conformational ensemble centered at a φ-value of ca. -120°, which corresponds to a parallel β-sheet type conformation. The 3J(HNHCα) coupling constant of the C-terminal residue is indicative of a polyproline II (pPII)/βt mixture. Our results suggest that the gelation of FmocFF caused by the addition of a small amount of water to DMSO mixtures is facilitated by the formation of disordered protofibrils in pure DMSO.
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Affiliation(s)
- Matthew S Levine
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA.
| | - Moumita Ghosh
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Morgan Hesser
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA.
| | - Nathan Hennessy
- Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield S3 7HF, United Kingdom
| | - David M DiGuiseppi
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104, USA.
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel.
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4
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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5
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Cai K, Zheng X, Liu J, Du F, Yan G, Zhuang D, Yan S. Mapping the amide-I vibrations of model dipeptides with secondary structure sensitivity and amino acid residue specificity, and its application to amyloid β-peptide in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 219:391-400. [PMID: 31059891 DOI: 10.1016/j.saa.2019.04.070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
Vibrational spectroscopy has been known as particularly well-suited for deciphering the polypeptide's structure. To decode structural information encoded in IR spectra, we developed amide-I frequency maps on the basis of model dipeptides to correlate the amide-I frequency of interest to the combination of the calculated secondary structure dependent amide-I frequency by using DFT method and the electrostatic potentials that projected onto the amide unit from the micro-environment within molecular mechanics force field. The constructed maps were applied to model dipeptides and amyloid β-peptide fragment (Aβ25-35). The dipeptide specified map (DS map) and the hybrid map (HYB map) predicted amide-I bands of Aβ25-35 in solution satisfactorily reproduce experimental observation, and indicate the preference of forming β-sheet and random coil structure for Aβ25-35 in D2O just as the results of cluster analysis suggested. These maps with secondary structural sensitivity and amino acid residue specificity open up a way for the interpretation of amide-I vibrations and show their potentials in the understanding of molecular structure of polypeptides in solution.
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Affiliation(s)
- Kaicong Cai
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China; Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China.
| | - Xuan Zheng
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Jia Liu
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Fenfen Du
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Guiyang Yan
- Fujian Provincial Key Laboratory of Featured Materials in Biochemical Industry, Ningde Normal University, Ningde 352100, PR China
| | - Danling Zhuang
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
| | - Siyi Yan
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, Fujian 350007, PR China; Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen, Fujian 361005, PR China
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6
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Acharyya A, DiGiuseppi D, Stinger BL, Schweitzer-Stenner R, Vaden TD. Structural Destabilization of Azurin by Imidazolium Chloride Ionic Liquids in Aqueous Solution. J Phys Chem B 2019; 123:6933-6945. [DOI: 10.1021/acs.jpcb.9b04113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, 231 S. 34 Street, Philadelphia, Pennsylvania 19104, United States
| | - David DiGiuseppi
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Brittany L. Stinger
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32 S. 32nd Street, Philadelphia, Pennsylvania 19104, United States
| | - Timothy D. Vaden
- Department of Chemistry and Biochemistry, Rowan University, 201 Mullica Hill Road, Glassboro, New Jersey 08028, United States
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7
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Stevenson P, Tokmakoff A. Ultrafast Fluctuations of High Amplitude Electric Fields in Lipid Membranes. J Am Chem Soc 2017; 139:4743-4752. [DOI: 10.1021/jacs.6b12412] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paul Stevenson
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Ave., Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
| | - Andrei Tokmakoff
- Department
of Chemistry, James Frank Institute, and The Institute
for Biophysical Dynamics, The University of Chicago, 929 E 57th Street, Chicago, Illinois 60637, United States
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8
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Anderson BA, Literati A, Ball B, Kubelka J. Temperature dependence of C-terminal carboxylic group IR absorptions in the amide I' region. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 134:473-483. [PMID: 25036456 DOI: 10.1016/j.saa.2014.06.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 05/13/2014] [Accepted: 06/16/2014] [Indexed: 06/03/2023]
Abstract
Studies of structural changes in peptides and proteins using IR spectroscopy often rely on subtle changes in the amide I' band as a function of temperature. However, these changes can be obscured by the overlap with other absorptions, namely the side-chain and terminal carboxylic groups. The former were the subject of our previous report (Anderson et al., 2014). In this paper we investigate the IR spectra of the asymmetric stretch of α-carboxylic groups for amino acids representing all major types (Gly, Ala, Val, Leu, Ser, Thr, Asp, Glu, Lys, Asn, His, Trp, Pro) as well as the C-terminal groups of three dipeptides (Gly-Gly, Gly-Ala, Ala-Gly) in D₂O at neutral pH. Experimental temperature dependent IR spectra were analyzed by fitting of both symmetric and asymmetric pseudo-Voigt functions. Qualitatively the spectra exhibit shifts to higher frequency, loss in intensity and narrowing with increased temperature, similar to that observed previously for the side-chain carboxylic groups of Asp. The observed dependence of the band parameters (frequency, intensity, width and shape) on temperature is in all cases linear: simple linear regression is therefore used to describe the spectral changes. The spectral parameters vary between individual amino acids and show systematic differences between the free amino acids and dipeptides, particularly in the absolute peak frequencies, but the temperature variations are comparable. The relative variations between the dipeptide spectral parameters are most sensitive to the C-terminal amino acid, and follow the trends observed in the free amino acid spectra. General rules for modeling the α-carboxylic IR absorption bands in peptides and proteins as the function of temperature are proposed.
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Affiliation(s)
- Benjamin A Anderson
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Alex Literati
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Borden Ball
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States
| | - Jan Kubelka
- University of Wyoming, 1000 E. University Ave, Laramie, WY 82071, United States.
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10
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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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11
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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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12
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Rybka K, Toal SE, Verbaro DJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations. Proteins 2013; 81:968-83. [PMID: 23229867 DOI: 10.1002/prot.24226] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/07/2012] [Accepted: 11/21/2012] [Indexed: 11/08/2022]
Abstract
In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides.
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Affiliation(s)
- Karin Rybka
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt/Main, Germany
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13
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Verbaro DJ, Mathieu D, Toal SE, Schwalbe H, Schweitzer-Stenner R. Ionized Trilysine: A Model System for Understanding the Nonrandom Structure of Poly-l-lysine and Lysine-Containing Motifs in Proteins. J Phys Chem B 2012; 116:8084-94. [DOI: 10.1021/jp303794s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel J. Verbaro
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Daniel Mathieu
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Siobhan E. Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
| | - Harald Schwalbe
- Institute for Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe University, Max-von-Laue-Strasse
7, 60438 Frankfurt, Germany
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia,
Pennsylvania 19104, United States
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14
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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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15
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Schweitzer-Stenner R, Soffer JB, Verbaro D. Structure analysis of unfolded peptides I: vibrational circular dichroism spectroscopy. Methods Mol Biol 2012; 895:271-313. [PMID: 22760325 DOI: 10.1007/978-1-61779-927-3_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is an invaluable spectroscopic techniques utilized to exploit the optical strength of vibrational transitions for structure analysis. In this chapter, we describe the protocol for measuring and self-consistently analyzing VCD and the corresponding FT-IR spectra of short peptides. This process involves the decomposition of the IR spectrum as well as simulations of the amide I band profiles in both spectra based on structural models of the peptides investigated. This type of spectral analysis should be complemented with similar investigations of Raman spectra, which are described in the subsequent chapter. The structural analysis of short, unfolded peptides described in this chapter can easily be extended for the analysis of longer unfolded peptides or even proteins. This is particularly important in view of the demonstrated biological relevance of intrinsically disordered peptides and proteins (IDPs).
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16
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Abstract
Raman spectroscopy has positioned itself as an invaluable tool in the study of complex biological systems, consistently being used to obtain information illustrating a vast array of fundamental properties. Of primary interest, with respect to the focus of this chapter, are conformational changes of peptide backbones. For short peptides to larger biological systems this understanding can be extended to local hydrogen bonding interactions and the probing of other structural or organizational properties. With regard to unfolded peptides Raman spectroscopy can be used as a technique complementary to infrared (IR) and vibrational circular dichroism (VCD) spectroscopy. This chapter describes how high quality polarized Raman spectra of peptide can be recorded with a Raman microspectrometer and how the structure sensitive amide I band profiles of isotropic and anisotropic Raman scattering can be analyzed in conjunction with the respective IR and VCD profiles to obtain conformational distributions of short unfolded peptides.
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17
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Measey TJ, Schweitzer-Stenner R. Vibrational circular dichroism as a probe of fibrillogenesis: the origin of the anomalous intensity enhancement of amyloid-like fibrils. J Am Chem Soc 2010; 133:1066-76. [PMID: 21186804 DOI: 10.1021/ja1089827] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Amyloid fibrils are affiliated with various human pathologies. Knowledge of their molecular architecture is necessary for a detailed understanding of the mechanism of fibril formation. Vibrational circular dichroism (VCD) spectroscopy has recently shown sensitivity to amyloid fibrils [Ma et al. J. Am. Chem. Soc. 2007, 129, 12364 and Measey et al. J. Am. Chem. Soc. 2009, 131, 18218]. In particular, amyloid fibrils give rise to an intensity enhanced signal in the amide I band region of the corresponding VCD spectrum, offering promise of utilizing such a method for probing fibrillogenesis and the chiral structure of fibrils. Herein, we further investigate this phenomenon and demonstrate the use of VCD to probe the fibril formation kinetics of a short alanine-rich peptide. To elucidate the origin of the anomalous VCD intensity enhancement, we use an excitonic coupling model to simulate the VCD spectrum of stacked β-sheets containing one (Ising-like model) and two amide I oscillators per strand, as models for the underlying amyloid-fibril secondary structure. With this simple model, we show that the VCD intensity enhancement of amyloid-like fibrils results from intrasheet and, to a more limited extent, also from intersheet vibrational coupling between stacked β-sheets. The enhancement requires helically twisted sheets and is most pronounced for arrangements with parallel-oriented strands. Both the intersheet distance and the orientation of the amide I transition dipole moments of neighboring sheets are found to modulate the intensity enhancement of the amide I VCD signal. Moreover, our simulations suggest that, depending on the three-dimensional arrangement of the β-strands, the sign of the VCD signal of amyloid-like fibrils can be used to distinguish between right- and left-handed helical twists of parallel-oriented β-sheets. We compare the results of our simulation to experimental spectra of two short peptides, GNNQQNY, the N-terminal peptide fragment of the yeast prion protein Sup35, and an amyloidogenic alanine-rich peptide, AKY8. Our results demonstrate the advantages of using VCD spectroscopy to probe the kinetics of peptide and protein aggregation as well as the chirality of the resulting supramolecular structure.
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Affiliation(s)
- Thomas J Measey
- Department of Chemistry, Drexel University, 3201 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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18
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Verbaro D, Ghosh I, Nau WM, Schweitzer-Stenner R. Discrepancies between Conformational Distributions of a Polyalanine Peptide in Solution Obtained from Molecular Dynamics Force Fields and Amide I′ Band Profiles. J Phys Chem B 2010; 114:17201-8. [PMID: 21138254 DOI: 10.1021/jp109404r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Daniel Verbaro
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States, and School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Indrajit Ghosh
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States, and School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Werner M. Nau
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States, and School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States, and School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany
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19
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Grahnen JA, Amunson KE, Kubelka J. DFT-Based Simulations of IR Amide I′ Spectra for a Small Protein in Solution. Comparison of Explicit and Empirical Solvent Models. J Phys Chem B 2010; 114:13011-20. [DOI: 10.1021/jp106639s] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Johan A. Grahnen
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
| | - Krista E. Amunson
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
| | - Jan Kubelka
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82070
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20
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Hagarman A, Measey TJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Intrinsic propensities of amino acid residues in GxG peptides inferred from amide I' band profiles and NMR scalar coupling constants. J Am Chem Soc 2010; 132:540-51. [PMID: 20014772 DOI: 10.1021/ja9058052] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A reliable intrinsic propensity scale of amino acid residues is indispensable for an assessment of how local conformational distributions in the unfolded state can affect the folding of peptides and proteins. Short host-guest peptides, such as GxG tripeptides, are suitable tools for probing such propensities. To explore the conformational distributions sampled by the central amino acid residue in these motifs, we combined vibrational (IR, Raman, and VCD) with NMR spectroscopy. The data were analyzed in terms of a superposition of two-dimensional Gaussian distribution functions in the Ramachandran space pertaining to subensembles of polyproline II, beta-strand, right- and left-handed helical, and gamma-turn-like conformations. The intrinsic propensities of eight amino acid residues (x = A, V, F, L, S, E, K, and M) in GxG peptides were determined as mole fractions of these subensembles. Our results show that alanine adopts primarily (approximately 80%) a PPII-like conformation, while valine and phenylalanine were found to sample PPII and beta-strand-like conformations equally. The centers of the respective beta-strand distributions generally do not coincide with canonical values of dihedral angles of residues in parallel or antiparallel beta-strands. In fact, the distributions for most residues found in the beta-region significantly overlap the PPII-region. A comparison with earlier reported results for trivaline reveals that the terminal valines increase the beta-strand propensity of the central valine residue even further. Of the remaining investigated amino acids, methionine preferred PPII the most (0.64), and E, S, L, and K exhibit moderate (0.56-0.45) PPII propensities. Residues V, F, S, E, and L sample, to a significant extent, a region between the canonical PPII and (antiparallel) beta-strand conformations. This region coincides with the sampling reported for L and V using theoretical predictions (Tran et al. Biochemistry 2005, 44, 11369). The distributions of all investigated residues differ from coil library and computationally predicted distributions in that they do not exhibit a substantial sampling of helical conformations. We conclude that this sampling of helical conformations arises from the context dependence, for example, neighboring residues, in proteins and longer peptides, some of which is long-range.
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Affiliation(s)
- Andrew Hagarman
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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21
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Maekawa H, De Poli M, Moretto A, Toniolo C, Ge NH. Toward detecting the formation of a single helical turn by 2D IR cross peaks between the amide-I and -II modes. J Phys Chem B 2010; 113:11775-86. [PMID: 19642666 DOI: 10.1021/jp9045879] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have combined two-dimensional infrared (2D IR) spectroscopy and isotope substitutions to reveal the vibrational couplings between a pair of amide-I and -II modes that are several residues away but directly connected through a hydrogen bond in a helical peptide. This strategy is demonstrated on a 3(10)-helical hexapeptide, Z-Aib-L-Leu-(Aib)2-Gly-Aib-OtBu, and its 13C=18O-Leu monolabeled and 13C=18O-Leu/15N-Gly bis-labeled isotopomers in CDCl3. The isotope-dependent amide-I/II cross peaks clearly show that the second and fourth peptide linkages are vibrationally coupled as they are in proximity, forming a 3(10)-helical turn. The experimental spectra are compared to simulations based on a vibrational exciton Hamiltonian model that fully takes into account the amide-I and -II modes. The amide-II local mode frequency is evaluated by a new model based on the effects of hydrogen-bond geometry and sites. Ab initio nearest-neighbor coupling maps of the amide-I/I, -I/II, -II/I and -II/II modes are generated by isotopically isolating the local modes of N-acetyl-glycine N'-methylamide (AcGlyNHMe). Longer range couplings are modeled by transition charge interactions. The effects of the capping groups are incorporated and isotope effects are analyzed based on ab initio calculations of six model compounds. The main features of the 2D IR spectra are reproduced by this modeling. The conformational sensitivity of the isotope-dependent amide-I/II cross peaks is discussed in comparison with the calculated spectra for a semiextended structure. Our experimental and theoretical study demonstrates that the combination of 2D IR and 13C=18O/15N labeling is a useful structural method for detecting helical turn formation with residue-level specificity.
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Affiliation(s)
- Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, California 92697-2025, USA
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22
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Schweitzer-Stenner R. Distribution of conformations sampled by the central amino acid residue in tripeptides inferred from amide I band profiles and NMR scalar coupling constants. J Phys Chem B 2009; 113:2922-32. [PMID: 19243204 DOI: 10.1021/jp8087644] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The conformational preference of individual amino acid residues in the unfolded state of peptides and proteins is the subject of a continuous debate. Research has mostly been focused on alanine, owing to its abundance in proteins and its relevance for the understanding of helix <----> coil transitions. In the current study, we have analyzed the amide I band profiles of the IR, isotropic and anisotropic Raman, and VCD profiles of trialanine in terms of a conformational model which, for the first time, explicitly considers the entire ensemble of possible conformations rather than representative structures. The distribution function utilized for a satisfactory simulation of the amide I band profiles was found to also reproduce a set of five J coupling constants reported by Graf et al. (Graf, J.; et al. J. Am. Chem. Soc. 2007, 129, 1179). The results of our analysis reveal a PPII fraction of approximately 0.84 for the central alanine residue, which strongly corroborates the notion that alanine has a very high PPII propensity, exceeding the values obtained from restricted coil libraries. We performed a similar analysis for trivaline and found that the dominant fraction of its central residue is a beta-strand. The fraction of the respective distribution is 0.68. The remaining fraction contains contributions from helical and PPII conformations. The results of our analysis enable us to decide on the suitability of force fields used for MD simulations of short alanine-containing peptides. The paper establishes vibrational spectroscopy as a suitable method to explore the energy landscape of amino acid residues.
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Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32nd and Chestnut Streets, Philadelphia, Pennsylvania 19104, USA.
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23
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Schweitzer-Stenner R, Gonzales W, Bourne GT, Feng JA, Marshall GR. Conformational Manifold of α-Aminoisobutyric Acid (Aib) Containing Alanine-Based Tripeptides in Aqueous Solution Explored by Vibrational Spectroscopy, Electronic Circular Dichroism Spectroscopy, and Molecular Dynamics Simulations. J Am Chem Soc 2007; 129:13095-109. [PMID: 17918837 DOI: 10.1021/ja0738430] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Widalys Gonzales
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Gregory T. Bourne
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Jianwen A. Feng
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Garland R. Marshall
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
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24
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Schweitzer-Stenner R, Measey TJ. The alanine-rich XAO peptide adopts a heterogeneous population, including turn-like and polyproline II conformations. Proc Natl Acad Sci U S A 2007; 104:6649-54. [PMID: 17416675 PMCID: PMC1871840 DOI: 10.1073/pnas.0700006104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Indexed: 11/18/2022] Open
Abstract
The solution structure of the hepta-alanine polypeptide Ac-X(2)A(7)O(2)-NH(2) (XAO) has been a matter of controversy in the current literature. On one side of the argument is a claim that the peptide adopts a mostly polyproline II (PPII) structure, with a <20% population of beta conformations at room temperature [Shi Z, Olson CA, Rose GA, Baldwin RL, Kallenbach NR (2002) Proc Natl Acad Sci USA 99:9190-9195], whereas the other side of the argument insists that the peptide exists as an ensemble of conformations, including multiple beta-turn structures [Makowska J, Rodziewicz-Motowidlo S, Baginska K, Vila JA, Liwo A, Chmurzynski L, Scheraga HA (2006) Proc Natl Acad Sci USA 103:1744-1749]. We have used an excitonic coupling model to simulate the amide I band of the FTIR, vibrational circular dichroism, and isotropic and anisotropic Raman spectra of XAO, where, for each residue, the backbone dihedral angle varphi was constrained by using the reported (3)J(CalphaHNH) values and a modified Karplus relation. The best reproduction of the experimental data could only be achieved by assuming an ensemble of conformations, which contains various beta-turn conformations ( approximately 26%), in addition to beta-strand ( approximately 23%) and PPII ( approximately 50%) conformations. PPII is the dominant conformation in segments not involved in turn formations. Most of the residues were found to sample the bridge region connecting the PPII and right-handed helix troughs in the Ramachandran plot, which is part of the very heterogeneous ensemble of conformations generally termed type IV beta-turn.
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25
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Bagchi S, Kim YS, Charnley AK, Smith AB, Hochstrasser RM. Two-Dimensional Infrared Investigation of N-Acetyl Tryptophan Methyl Amide in Solution. J Phys Chem B 2007; 111:3010-8. [PMID: 17388413 DOI: 10.1021/jp067348m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The linear infrared and two-dimensional infrared (2D IR) spectra in the amide-I region of N-acetyl tryptophan methyl amide (NATMA) in solvents of varying polarity are reported. The two amide-I transitions have been assigned unambiguously by using 13C isotopic substitution of the carbonyl group. The amide unit at the amino end shows a lower transition frequency in CH2Cl2 and methanol, while the acetyl end has a lower transition frequency in D2O. Multiple conformers exist in CH2Cl2 and methanol, but only one conformer is evident in D2O. The 2D IR cross peaks from the intermode coupling yield off-diagonal anharmonicities 2.5 +/- 0.5, 3.25 +/- 0.5, and 3.0 +/- 0.5 cm(-1) in CH2Cl2, methanol, and D2O, respectively, which by simple matrix diagonalization yield the coupling constants 8.0 +/- 0.5, 8.0 +/- 1.0, and 5.5 +/- 1.0 cm(-1). The major conformer in CH2Cl2 corresponds to a C7 structure, in agreement with that found in the gas phase [Dian, B. C.; Longarte, A.; Mercier, S.; Evans, D. A.; Wales, D. J.; Zwier, T. S. J. Chem. Phys. 2002, 117, 10688-10702] with intramolecular hydrogen bonding between the acetyl end C=O and the amino end N-H. The backbone dihedral angles (phi, psi) are determined to be in the ranges of (-55 +/- 5 degrees , 30 +/- 5 degrees ), (120 +/- 10 degrees , -20 +/- 10 degrees ), and (+/-160 +/- 10 degrees , +/-75 +/- 10 degrees ) in CH2Cl2, methanol, and D2O, respectively.
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Affiliation(s)
- Sayan Bagchi
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA
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26
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Turner DR, Kubelka J. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent. J Phys Chem B 2007; 111:1834-45. [PMID: 17256894 DOI: 10.1021/jp0666840] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins at very low temperatures, but overestimate the effects of solvent on the protein spectra at ambient temperatures, where the peptide-water hydrogen bonds are weakened by thermal motion.
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Affiliation(s)
- David R Turner
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, USA
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27
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Schweitzer-Stenner R, Measey T, Kakalis L, Jordan F, Pizzanelli S, Forte C, Griebenow K. Conformations of Alanine-Based Peptides in Water Probed by FTIR, Raman, Vibrational Circular Dichroism, Electronic Circular Dichroism, and NMR Spectroscopy. Biochemistry 2007; 46:1587-96. [PMID: 17279623 DOI: 10.1021/bi062224l] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used a combination of FTIR, VCD, ECD, Raman, and NMR spectroscopies to probe the solution conformations sampled by H-(AAKA)-OH by utilizing an excitonic coupling model and constraints imposed by the 3JCalphaHNH coupling constants of the central residues to simulate the amide I' profile of the IR, isotropic Raman, anisotropic Raman, and VCD spectra in terms of a mixture of three conformations, i.e., polyproline II, beta-strand and right-handed helical. The representative coordinates of the three conformations were obtained from published coil libraries. Alanine was found to exhibit PPII fractions of 0.60 or greater, mixed with smaller fractions of helices and beta-strand conformations. Lysine showed no clear conformational propensity in that it samples polyproline II, beta-strand, and helical conformations with comparable probability. This is at variance with results obtained earlier for ionized polylysine, which suggest a high polyproline II propensity. We reanalyzed previously investigated tetra- and trialanine by combining published vibrational spectroscopy data with 3JCalphaHNH coupling constants and obtained again blends dominated by PPII with smaller admixtures of beta-strand and right-handed helical conformations. The polyproline II propensity of alanine was found to be higher in tetraalanine than in trialanine. For all peptides investigated, our results rule out a substantial population of turn-like conformations. Our results are in excellent agreement with MD simulations on short alanine peptides by Gnanakaran and Garcia [(2003) J. Phys. Chem. B 107, 12555-12557] but at variance with multiple MD simulations particularly for the alanine dipeptide.
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Schweitzer-Stenner R, Measey T, Hagarman A, Eker F, Griebenow K. Salmon calcitonin and amyloid beta: two peptides with amyloidogenic capacity adopt different conformational manifolds in their unfolded states. Biochemistry 2006; 45:2810-9. [PMID: 16503636 DOI: 10.1021/bi052282r] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular conformations of salmon calcitonin in aqueous solution have been investigated by exploiting the different influences of excitonic coupling on the amide I band profile in the isotropic and anisotropic Raman, FTIR, and vibrational circular dichroism spectra of a polypeptide. The N-terminal loop, caused by a disulfide bridge between cysteines at positions 1 and 7, was modeled by performing a conformational search by molecular mechanics calculations. The remaining part of the peptide chain was modeled as a mixture of three sequences containing different fractions of residues adopting poly-l-proline II (PPII), extended beta-strand, and alpha-helix-like conformations. This yielded an excellent reproduction of the experimentally observed amide I' band profiles. A comparison with recent data on the beta-amyloid fragment Abeta(1)(-)(28) revealed a lower PPII content and more conformational heterogeneity for calcitonin. Thus, our results underscore the notion that individual structural propensities of amino acid residues give rise to structural differences between the unfolded states of even long peptide chains, at variance with expectations based on a random or statistical coil model.
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Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University, 32nd and Chestnut Streets, Philadelphia, Pennsylvania 19104, USA.
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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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