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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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Schweitzer-Stenner R, Pecht I, Guo C. Orientation of Oligopeptides in Self-Assembled Monolayers Inferred from Infrared Reflection-Absorption Spectroscopy. J Phys Chem B 2019; 123:860-868. [PMID: 30607951 DOI: 10.1021/acs.jpcb.8b09180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of a single tryptophan containing oligo-alanine peptides were recently characterized as conductive molecules that enable electron transport between electrodes. IR reflection-absorption of self-assembled monolayers of such peptides on gold surfaces revealed that the relative intensities of amide I and II bands in the respective spectra depend on the tryptophan residue position in the oligopeptide sequence. This indicates different average peptide orientations with respect to the normal onto the carrying gold surface. We developed a model which calculates the polarized reflectivities of the amide I and II bands as function of the angle of the incident light, the average peptide orientation and the relative orientations of peptide group at the N-terminal. The orientation and strength of vibrational transition dipole moments were calculated by employing an excitonic coupling approach which considers probable conformational distributions of the disordered peptides. Our results revealed that the position of the tryptophan can affect the effective tilt angle of the peptide as well as the orientation of transition dipole moments with respect to the reflection plane. We have also calculated the average end to end distances of the examined peptides and found them to be in reasonable agreement with experimental values determined by ellipsometry. Some evidence is obtained for the notion that increasing the tilt angle of the investigated peptides reduces their conductivity.
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Affiliation(s)
- Reinhard Schweitzer-Stenner
- Department of Chemistry , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
| | - Israel Pecht
- Department of Chemical Immunology , The Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Cunlan Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , P. R. China
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Bonhommeau S, Lecomte S. Tip-Enhanced Raman Spectroscopy: A Tool for Nanoscale Chemical and Structural Characterization of Biomolecules. Chemphyschem 2017; 19:8-18. [DOI: 10.1002/cphc.201701067] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Sébastien Bonhommeau
- University of Bordeaux; Institut des Sciences Moléculaires; CNRS UMR 5255; 351 cours de la Libération 33405 Talence cedex France
| | - Sophie Lecomte
- University of Bordeaux; Institut de Chimie et Biologie des Membranes et des Nano-objets; CNRS UMR 5248; Allée Geoffroy Saint Hilaire 33600 Pessac France
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Toal SE, Kubatova N, Richter C, Linhard V, Schwalbe H, Schweitzer-Stenner R. Randomizing the unfolded state of peptides (and proteins) by nearest neighbor interactions between unlike residues. Chemistry 2015; 21:5173-92. [PMID: 25728043 DOI: 10.1002/chem.201406539] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/29/2022]
Abstract
To explore the influence of nearest neighbors on conformational biases in unfolded peptides, we combined vibrational and 2D NMR spectroscopy to obtain the conformational distributions of selected "GxyG" host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y=A, K, L, V. Large changes of conformational propensities were observed due to nearest-neighbor interactions, at variance with the isolated pair hypothesis. We found that protonated aspartic acid and serine lose their above-the-average preference for turn-like structures in favor of polyproline II (pPII) populations in the presence of neighbors with bulky side chains. Such residues also decrease the above-the-average pPII preference of alanine. These observations suggest that the underlying mechanism involves a disruption of the hydration shell. Thermodynamic analysis of (3) J(H(N) ,H(α) ) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII↔β equilibrium indicating a significant residue dependent temperature dependence of the peptides' conformational ensembles. These results suggest that nearest-neighbor interactions between unlike residues act as conformational randomizers close to the enthalpy-entropy compensation temperature, eliminating intrinsic biases in favor of largely balanced pPII/β dominated ensembles at physiological temperatures.
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Affiliation(s)
- Siobhan E Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 10104 (USA); Present address: Department of Biophysics and Biochemistry, Yale University, New Haven, CT 06250 (USA)
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Toal S, Schweitzer-Stenner R. Local order in the unfolded state: conformational biases and nearest neighbor interactions. Biomolecules 2014; 4:725-73. [PMID: 25062017 PMCID: PMC4192670 DOI: 10.3390/biom4030725] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 06/17/2014] [Accepted: 06/20/2014] [Indexed: 12/23/2022] Open
Abstract
The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.
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Affiliation(s)
- Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19026, USA.
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Schwalbe M, Ozenne V, Bibow S, Jaremko M, Jaremko L, Gajda M, Jensen MR, Biernat J, Becker S, Mandelkow E, Zweckstetter M, Blackledge M. Predictive atomic resolution descriptions of intrinsically disordered hTau40 and α-synuclein in solution from NMR and small angle scattering. Structure 2013; 22:238-49. [PMID: 24361273 DOI: 10.1016/j.str.2013.10.020] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/22/2022]
Abstract
The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and α-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation.
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Affiliation(s)
- Martin Schwalbe
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Valéry Ozenne
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Stefan Bibow
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Mariusz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Lukasz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michal Gajda
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Malene Ringkjøbing Jensen
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Jacek Biernat
- CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Eckhard Mandelkow
- CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany; Center for the Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany.
| | - Martin Blackledge
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France.
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