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O'Neill N, Lima TA, Furlan Ferreira F, Alvarez NJ, Schweitzer-Stenner R. Determining the nanostructure and main axis of gly-his-gly fibrils using the amide I' bands in FTIR, VCD, and Raman spectra. Spectrochim Acta A Mol Biomol Spectrosc 2024; 306:123584. [PMID: 37956526 DOI: 10.1016/j.saa.2023.123584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/29/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
The zwitterionic tripeptide glycyl-histidine-glycine (GHG) has been shown to self-assemble into visible crystalline fibrils that form a gel-supporting network with a very high storage modulus. Here we elaborate on the theory and experimental setup behind our novel approach employed to determining the main fibril axis for these gel-forming fibrils by simulating the amide I band profile for infrared absorption (IR), vibrational circular dichroism (VCD), and visible Raman scattering. We also highlight that combining these three vibrational spectroscopies can help in validating structures that are solved using powder x-ray diffraction analysis (PXRD). The PXRD analysis yielded a GHG fibril unit cell with P21 symmetry containing two peptide monomers and two water molecules. The monomers adopt a conformation reminiscent of the distorted polyproline II conformation obtained for tri-lysine in aqueous solution. Stabilization occurs primarily through peptide-peptide intermolecular hydrogen bond interactions, while the role of water in peptide hydration is minimal. The comparison of simulated and experimental amide I' band profiles suggests that the xz plane of the crystal unit cell is being predominantly probed in the experimental IR and VCD spectra, with the x axis of the unit cell pointing in the direction of the main fibril axis. The monomer peptide in the unit cell interacts with six adjacent peptides forming hydrophobic channels by edge-to-face and parallel-displaced ππstacking in the y direction. These cores are further stabilized by a plethora of intermolecular interactions in the x and z directions. Our result suggests that the hydrophobic xz-surfaces would be a good target for the adsorption of hydrophobic drugs.
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Affiliation(s)
- Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA; Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP 09210-580, Brazil
| | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Schweitzer-Stenner R. The relevance of short peptides for an understanding of unfolded and intrinsically disordered proteins. Phys Chem Chem Phys 2023; 25:11908-11933. [PMID: 37096579 DOI: 10.1039/d3cp00483j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Over the last thirty years the unfolded state of proteins has attracted considerable interest owing to the discovery of intrinsically disordered proteins which perform a plethora of functions despite resembling unfolded proteins to a significant extent. Research on both, unfolded and disordered proteins has revealed that their conformational properties can deviate locally from random coil behavior. In this context results from work on short oligopeptides suggest that individual amino acid residues sample the sterically allowed fraction of the Ramachandran plot to a different extent. Alanine has been found to exhibit a peculiarity in that it has a very high propensity for adopting polyproline II like conformations. This Perspectives article reviews work on short peptides aimed at exploring the Ramachandran distributions of amino acid residues in different contexts with experimental and computational means. Based on the thus provided overview the article discussed to what extent short peptides can serve as tools for exploring unfolded and disordered proteins and as benchmarks for the development of a molecular dynamics force field.
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Thursch LJ, Lima TA, O'Neill N, Ferreira FF, Schweitzer-Stenner R, Alvarez NJ. Influence of central sidechain on self-assembly of glycine-x-glycine peptides. Soft Matter 2023; 19:394-409. [PMID: 36454226 DOI: 10.1039/d2sm01082h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Low molecular weight gelators (LMWGs) are the subject of intense research for a range of biomedical and engineering applications. Peptides are a special class of LMWG, which offer infinite sequence possibilities and, therefore, engineered properties. This work examines the propensity of the GxG peptide family, where x denotes a guest residue, to self-assemble into fibril networks via changes in pH and ethanol concentration. These triggers for gelation are motivated by recent work on GHG and GAG, which unexpectedly self-assemble into centimeter long fibril networks with unique rheological properties. The propensity of GxG peptides to self-assemble, and the physical and chemical properties of the self-assembled structures are characterized by microscopy, spectroscopy, rheology, and X-ray diffraction. Interestingly, we show that the number, length, size, and morphology of the crystalline self-assembled aggregates depend significantly on the x-residue chemistry and the solution conditions, i.e. pH, temperature, peptide concentration, etc. The different x-residues allow us to probe the importance of different peptide interactions, e.g. π-π stacking, hydrogen bonding, and hydrophobicity, on the formation of fibrils. We conclude that fibril formation requires π-π stacking interactions in pure water, while hydrogen bonding can form fibrils in the presence of ethanol-water solutions. These results validate and support theoretical arguments on the propensity for self-assembly and leads to a better understanding of the relationship between peptide chemistry and fibril self-assembly. Overall, GxG peptides constitute a unique family of peptides, whose characterization will aid in advancing our understanding of self-assembly driving forces for fibril formation in peptide systems.
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Affiliation(s)
- Lavenia J Thursch
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
| | - Nichole O'Neill
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
| | - Fabio F Ferreira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, Brazil
| | | | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA.
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Schweitzer-Stenner R. Heme-Protein Interactions and Functional Relevant Heme Deformations: The Cytochrome c Case. Molecules 2022; 27:molecules27248751. [PMID: 36557884 PMCID: PMC9781506 DOI: 10.3390/molecules27248751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
Heme proteins are known to perform a plethora of biologically important functions. This article reviews work that has been conducted on various class I cytochrome c proteins over a period of nearly 50 years. The article focuses on the relevance of symmetry-lowering heme-protein interactions that affect the function of the electron transfer protein cytochrome c. The article provides an overview of various, mostly spectroscopic studies that explored the electronic structure of the heme group in these proteins and how it is affected by symmetry-lowering deformations. In addition to discussing a large variety of spectroscopic studies, the article provides a theoretical framework that should enable a comprehensive understanding of the physical chemistry that underlies the function not only of cytochrome c but of all heme proteins.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Schweitzer-Stenner R. Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides. Int J Mol Sci 2022; 23:ijms23105643. [PMID: 35628453 PMCID: PMC9147007 DOI: 10.3390/ijms23105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Flory isolated pair hypothesis (IPH) is one of the corner stones of the random coil model, which is generally invoked to describe the conformational dynamics of unfolded and intrinsically disordered proteins (IDPs). It stipulates, that individual residues sample the entire sterically allowed space of the Ramachandran plot without exhibiting any correlations with the conformational dynamics of its neighbors. However, multiple lines of computational, bioinformatic and experimental evidence suggest that nearest neighbors have a significant influence on the conformational sampling of amino acid residues. This implies that the conformational entropy of unfolded polypeptides and proteins is much less than one would expect based on the Ramachandran plots of individual residues. A further implication is that the Gibbs energies of residues in unfolded proteins or polypeptides are not additive. This review provides an overview of what is currently known and what has yet to be explored regarding nearest neighbor interactions in unfolded proteins.
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Andrews B, Guerra J, Schweitzer-Stenner R, Urbanc B. Do molecular dynamics force fields accurately model Ramachandran distributions of amino acid residues in water? Phys Chem Chem Phys 2022; 24:3259-3279. [PMID: 35048087 DOI: 10.1039/d1cp05069a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Molecular dynamics (MD) is a powerful tool for studying intrinsically disordered proteins, however, its reliability depends on the accuracy of the force field. We assess Amber ff19SB, Amber ff14SB, OPLS-AA/M, and CHARMM36m with respect to their capacity to capture intrinsic conformational dynamics of 14 guest residues x (=G, A, L, V, I, F, Y, DP, EP, R, C, N, S, T) in GxG peptides in water. The MD-derived Ramachandran distribution of each guest residue is used to calculate 5 J-coupling constants and amide I' band profiles to facilitate a comparison to spectroscopic data through reduced χ2 functions. We show that the Gaussian model, optimized to best fit the experimental data, outperforms all MD force fields by an order of magnitude. The weaknesses of the MD force fields are: (i) insufficient variability of the polyproline II (pPII) population among the guest residues; (ii) oversampling of antiparallel at the expense of transitional β-strand region; (iii) inadequate sampling of turn-forming conformations for ionizable and polar residues; and (iv) insufficient guest residue-specificity of the Ramachandran distributions. Whereas Amber ff19SB performs worse than the other three force fields with respect to χ2 values, it accounts for residue-specific pPII content better than the other three force fields. Additional testing of residue-specific RSFF1 and Amber ff14SB combined with TIP4P/2005 on six guest residues x (=A, I, F, DP, R, S) reveals that residue specificity derived from protein coil libraries or an improved water model alone do not result in significantly lower χ2 values.
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Affiliation(s)
- Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
| | - Jose Guerra
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | | | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania, USA.
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9
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Hughes EF, O'Neill N, Schweitzer-Stenner R. Self-assembly of Fmoc-diphenylalanine in water above the critical pH for gelation. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.2865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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10
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Milorey B, Schwalbe H, O'Neill N, Schweitzer-Stenner R. Repeating Aspartic Acid Residues Prefer Turn-like Conformations in the Unfolded State: Implications for Early Protein Folding. J Phys Chem B 2021; 125:11392-11407. [PMID: 34619031 DOI: 10.1021/acs.jpcb.1c06472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding can be described as a motion of the polypeptide chain in a potential energy funnel, where the conformational manifold is narrowed as the chain traverses from a completely unfolded state until it reaches the folded (native) state. The initial folding stages set the tone for this process by substantially narrowing the manifold of accessible conformations. In an ideally unfolded state with no long-range stabilizing forces, local conformations (i.e., residual structures) are likely to drive the folding process. While most amino acid residues tend to predominantly adopt extended structures in unfolded proteins and peptides, aspartic acid exhibits a relatively high intrinsic preference for turn-forming conformations. Regions in an unfolded polypeptide or protein that are rich in aspartic acid residues may therefore be crucial sites for protein folding steps. By combining NMR and vibrational spectroscopies, we observed that the conformational sampling of multiple sequentially neighbored aspartic acid residues in the model peptides GDDG and GDDDG even show an on average higher propensity for turn-forming structures than the intrinsic reference system D in GDG, which suggests that nearest neighbor interactions between adjacent aspartic acid residues stabilize local turn-forming structures. In the presence of the unlike neighbor phenylalanine, nearest neighbor interactions are of a totally different nature in that it they decrease the turn-forming propensities and mutually increase the sampling of polyproline II (pPII) conformations. We hypothesize the structural role of aspartic residues in intrinsically disordered proteins in general, and particularly in small linear motifs, that are very much determined by their respective neighbors.
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Affiliation(s)
- Bridget Milorey
- Deparment of Chemistry, Drexel University, Philadelphia, Pennsylvania 19026, United States
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universität, Max von Laue Strasse 7, 60438 Frankfurt, Germany
| | - Nichole O'Neill
- Deparment of Chemistry, Drexel University, Philadelphia, Pennsylvania 19026, United States
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11
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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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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Thursch LJ, Lima TA, Schweitzer-Stenner R, Alvarez NJ. The impact of thermal history on the structure of glycylalanylglycine ethanol/water gels. J Pept Sci 2021; 27:e3305. [PMID: 33619869 DOI: 10.1002/psc.3305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 12/30/2022]
Abstract
This work revisits several open questions regarding the mechanisms of GAG fibril formation and structure as a function of temperature. The authors recently hypothesized that there is a solubility limit of GAG in ethanol/water that induces self-assembly. In other words, not all peptides can participate in fibrillization and some fraction is still soluble in solution. We show via FTIR spectroscopy that, indeed, free peptides are still present in solution after fibril formation, strongly supporting the solubility model. Furthermore, previous work showed GAG self-assembled into right-handed (phase I) or left-handed (phase II) chiral structures depending on temperature. In this study, we analyze the crystalline structure of phase I and II gels via WAXS and SAXS to compare their crystalline structures and order. Rheological measurements were used to investigate the response of the fibrillar network to temperature. They reveal that the ability of the peptide to self-assemble depends on the solubility at a given temperature and not on thermal history. Furthermore, the gel softening point, the linear viscoelastic gel microstructure, and relaxation spectrum are very similar between phase I and phase II. Overall, the temperature only affects the chirality of the fibrils and the formation kinetics.
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Affiliation(s)
- Lavenia J Thursch
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, USA
| | - Thamires A Lima
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, USA
| | | | - Nicolas J Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA, USA
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14
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Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short peptides as predictors for the structure of polyarginine sequences in disordered proteins. Biophys J 2021; 120:662-676. [PMID: 33453267 PMCID: PMC7896027 DOI: 10.1016/j.bpj.2020.12.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/08/2020] [Accepted: 12/30/2020] [Indexed: 12/12/2022] Open
Abstract
Intrinsically disordered proteins and intrinsically disordered regions are frequently enriched in charged amino acids. Intrinsically disordered regions are regularly involved in important biological processes in which one or more charged residues is the driving force behind a protein-biomolecule interaction. Several lines of experimental and computational evidence suggest that polypeptides and proteins that carry high net charges have a high preference for extended conformations with average end-to-end distances exceeding expectations for self-avoiding random coils. Here, we show that charged arginine residues even in short glycine-capped model peptides (GRRG and GRRRG) significantly affect the conformational propensities of each other when compared with the intrinsic propensities of a mostly unperturbed arginine in the tripeptide GRG. A conformational analysis based on experimentally determined J-coupling constants from heteronuclear NMR spectroscopy and amide I' band profiles from vibrational spectroscopy reveals that nearest-neighbor interactions stabilize extended β-strand conformations at the expense of polyproline II and turn conformations. The results from molecular dynamics simulations with a CHARMM36m force field and TIP3P water reproduce our results only to a limited extent. The use of the Ramachandran distribution of the central residue of GRRRG in a calculation of end-to-end distances of polyarginines of different length yielded the expected power law behavior. The scaling coefficient of 0.66 suggests that such peptides would be more extended than predicted by a self-avoiding random walk. Our findings thus support in principle theoretical predictions.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania
| | | | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
| | - Harald Schwalbe
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universität, Frankfurt, Germany
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania
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15
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Milorey B, Schweitzer-Stenner R, Andrews B, Schwalbe H, Urbanc B. Short Arginine-Based Peptides As Predictors for the Extended Structure of Polyarginine Sequences in Intrinsically Disordered Proteins. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Zhang S, Andrews B, Schweitzer-Stenner R, Urbanc B. Intrinsic Conformational Dynamics of Alanine in Water/Ethanol Mixtures: An Experiment-Driven Molecular Dynamics Study. J Phys Chem B 2020; 124:11600-11616. [PMID: 33300341 DOI: 10.1021/acs.jpcb.0c08245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In vitro, cationic glycylalanylglycine (GAG) forms a hydrogel in binary mixtures of water and ethanol. In water, alanine residue is known for its high polyproline II (pPII) content. Spectroscopic data, including three J-coupling constants and amide I' profiles, indicate that addition of 42% ethanol to water significantly reduces the pPII content of alanine residue in GAG. Here, experiment-based Gaussian Ramachandran distributions of alanine in GAG at different ethanol fractions are examined and three MD force fields are evaluated with respect to their ability to capture these ethanol-induced conformational changes. MD simulations on monomeric GAG in eight different water/ethanol mixtures within Amber ff14SB, OPLS-AA/M, and CHARMM36m reveal that only Amber ff14SB partially captures the ethanol-induced conformational changes of alanine residue in monomeric GAG when 42% ethanol is added to water. MD simulations of 200 mM GAG ensembles in pure water and in the aqueous solution with 42% ethanol showcase the ability of CHARMM36m to capture the effect of ethanol on the average pPII content of alanine in GAG and provide a plausible explanation for this effect, which may stem from an increased propensity of GAG to form oligomers in the presence of ethanol.
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Affiliation(s)
- Shuting Zhang
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | | | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia, Pennsylvania 19104, United States
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Zhang S, Schweitzer-Stenner R, Urbanc B. Corrections to “Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water?”. J Chem Theory Comput 2020; 16:5982. [DOI: 10.1021/acs.jctc.0c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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19
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DiGuiseppi DM, Thursch L, Alvarez NJ, Schweitzer-Stenner R. Exploring the gel phase of cationic glycylalanylglycine in ethanol/water. II. Spectroscopic, kinetic and thermodynamic studies. J Colloid Interface Sci 2020; 573:123-134. [DOI: 10.1016/j.jcis.2020.03.108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/24/2022]
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Kumar A, Toal SE, DiGuiseppi D, Schweitzer-Stenner R, Wong BM. Water-Mediated Electronic Structure of Oligopeptides Probed by Their UV Circular Dichroism, Absorption Spectra, and Time-Dependent DFT Calculations. J Phys Chem B 2020; 124:2579-2590. [PMID: 32207305 DOI: 10.1021/acs.jpcb.0c00657] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We investigate the UV absorption spectra of a series of cationic GxG peptides (where x denotes a guest residue) in aqueous solution and find that only a subset of these spectra show a strong dependence with temperature. To explore whether or not this observation reflects conformational dependencies, we carry out time-dependent density functional calculations for the polyproline II (pPII) and β-strand conformations in implicit and explicit water. We find that the calculated CD spectra for pPII can qualitatively account for the experimental spectra irrespective of the water model. The β-strand UV-CD spectra, however, require the explicit consideration of water. Contrary to conventional wisdom, we find that both the NV1 and NV2 band are the envelopes of contributions from multiple transitions that involve more than just the HOMOs and LUMOs of the peptide groups. A natural transition orbital analysis reveals that some of the transitions have a charge-transfer character. The overall manifold of transitions depends on the peptide's backbone conformation, peptide hydration, and side chain of the guest residue. Our results reveal that peptide groups, side chains, and hydration shells must be considered as an entity for a physically valid characterization of UV absorbance and circular dichroism.
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Affiliation(s)
- Anshuman Kumar
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California, Riverside, Riverside, California 92521, United States
| | - Siobhan E Toal
- Department of Chemistry and Biochemistry, Rowan University, Glassboro, New Jersey 08028, United States
| | - David DiGuiseppi
- Department of Chemistry, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | | | - Bryan M Wong
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, Department of Chemistry, and Department of Physics & Astronomy, University of California, Riverside, Riverside, California 92521, United States
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22
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Hesser M, Thursch L, DiGuiseppi D, Lewis T, Alvarez N, Schweitzer-Stenner R. Tuning the Aggregation of GHG by Changing Sample Concentration and pH. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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23
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Milorey B, Schwalbe H, Schweitzer-Stenner R. Nearest Neighbor Effects in Homopeptide Segments of Short Peptides Explored by Circular Dichroism and NMR Spectroscopy. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Zhang S, Schweitzer-Stenner R, Urbanc B. Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water? J Chem Theory Comput 2019; 16:510-527. [PMID: 31751129 DOI: 10.1021/acs.jctc.9b00588] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We examine the ability of six molecular dynamics (MD) force fields (Amber ff14SB, Amber ff99SBnmr1, Amber ff03ws, OPLS-AA/L, OPLS-AA/M, and CHARMM36) to reproduce conformational ensembles of the central alanine in GAG and AAA in a way that is consistent with five (GAG) or six (AAA) J coupling constants and amide I' profiles. MD-derived Ramachandran plots for all six force fields under study differ from those obtained by the Gaussian fit to experimental data in three major ways: (i) the polyproline II (pPII) basin in the Ramachandran plot is too concentrated, (ii) the antiparallel β (aβ) basin is overpopulated, and (iii) the transitional β (βt) basin is underpopulated. Amber ff14SB outperforms the other five MD force fields and yields the highest pPII populations of the central alanine residue in GAG (55%) and AAA (63%), in good agreement with the predictions of the Gaussian model (59 and 76%). The analysis of the hydration layer around the central alanine residue reveals considerable reorientation of water molecules and reduction in both the average number of water molecules and the average number of water-water hydrogen bonds when glycines (in GAG) are replaced by alanines (in AAA), elucidating water-mediated nearest neighbor effects on alanine's conformational dynamics.
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Kumar A, Schweitzer-Stenner R, Wong BM. A new interpretation of the structure and solvent dependence of the far UV circular dichroism spectrum of short oligopeptides. Chem Commun (Camb) 2019; 55:5701-5704. [PMID: 31032831 DOI: 10.1039/c9cc01513b] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
UV circular dichroism (UVCD) spectroscopy is a prominent tool for exploring secondary structures of polypeptides and proteins. In the unfolded state of these biomolecules, most of the individual residues primarily sample a conformation called polyproline II. Its CD spectrum contains a negatively biased positive couplet with a pronounced negative maximum below and a weak positive maximum above 200 nm. It is traditionally rationalized in terms of an excitonic coupling mechanism augmented by polarization effects. In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory's isolated pair hypothesis.
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Affiliation(s)
- Anshuman Kumar
- Department of Chemical & Environmental Engineering, Materials Science & Engineering Program, University of California-Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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27
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DiGuiseppi D, Thursch L, Alvarez NJ, Schweitzer-Stenner R. Exploring the thermal reversibility and tunability of a low molecular weight gelator using vibrational and electronic spectroscopy and rheology. Soft Matter 2019; 15:3418-3431. [PMID: 30938745 DOI: 10.1039/c9sm00104b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cationic glycylalanylglycine (GAG) self-assembles into a gel in a 55 mol% ethanol/45 mol% water mixture. The gel exhibits a network of crystalline fibrils grown to lengths on a 10-4-10-5 m scale (Farrel et al., Soft Matter, 2016, 12, 6096-6110). Rheological data are indicative of a rather strong gel with storage moduli in the 10 kPa regime. Spectroscopic data revealed the existence of two gel phases; one forms below T = 15 °C (phase I) while the other one forms in a temperature range between 15 °C and the melting temperature of ca. 35 °C (phase II). We explored the reformation of the cationic GAG gel in 55 mol% ethanol/45 mol% water after thermal annealing by spectroscopic and rheological means. Our data reveal that even a short residence time of 5 minutes in the sol phase at 50 °C produced a delay of the gelation process and a gel of lesser strength. These observations suggest that the residence time at the annealing temperature can be used to adjust the strength of both gel phases. Our spectroscopic data show that the annealing process does not change the chirality of peptide fibrils in the two gel phases and that the initial aggregation state of the reformation process is by far more ordered for phase I than it is for phase II. In the gel phases of GAG/ethanol/water mixtures, ethanol seems to function as a sort of catalyst that enables the self-assembly of the peptide in spite of its low intrinsic propensity for aggregation.
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Affiliation(s)
- David DiGuiseppi
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
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28
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Ilawe NV, Schweitzer-Stenner R, DiGuiseppi D, Wong BM. Is a cross-β-sheet structure of low molecular weight peptides necessary for the formation of fibrils and peptide hydrogels? Phys Chem Chem Phys 2019; 20:18158-18168. [PMID: 29696249 DOI: 10.1039/c8cp00691a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Short peptides have emerged as versatile building blocks for supramolecular structures and hydrogels. In particular, the presence of aromatic amino acid residues and/or aromatic end groups is generally considered to be a prerequisite for initiating aggregation of short peptides into nanotubes or cross β-sheet type fibrils. However, the cationic GAG tripeptide surprisingly violates these rules. Specifically, in water/ethanol mixtures, GAG peptides aggregate into very long crystalline fibrils at temperatures below 35 °C where they eventually form a spanning network structure and, thus, a hydrogel. Two gel phases are formed in this network, and they differ substantially in chirality and thickness of the underlying fibrils, their rheological parameters, and the kinetics of oligomerization, fibrilization, and gel formation. The spectroscopic data strongly suggests that the observed fibrils do not exhibit canonical cross β-sheet structures and are indicative of a yet unknown secondary conformation. To complement our unusual experimental observations in this perspective article, we performed large-scale DFT calculations to probe the geometry and spectroscopic properties of these GAG oligomers. Most importantly, our experimental and computational results yield rather unconventional structures that are not reminiscent of classical cross-β-sheet structures, and we give two extremely likely candidates for oligomer structures that are consistent with experimental amide I' profiles in IR and vibrational circular dichroism (VCD) spectra of the two gel phases.
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Affiliation(s)
- Niranjan V Ilawe
- Department of Chemical & Environmental Engineering, and Materials Science & Engineering Program, University of California-Riverside, Riverside, CA 92521, USA.
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29
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Abstract
Growing evidence suggests that the conformational distributions of amino acid residues in unfolded peptides and proteins depend on the nature of the nearest neighbors. To explore whether the underlying interactions would lead to a breakdown of the isolated pair hypothesis of the classical random coil model, we further analyzed the conformational propensities that were recently obtained for the two guest residues (x,y) of GxyG tetrapeptides. We constructed a statistical thermodynamics model that allows for cooperative as well as for anticooperative interactions between adjacent residues adopting either a polyproline II or a β-strand conformation. Our analysis reveals that the nearest-neighbor interactions between most of the central residues in the investigated GxyG peptides are anticooperative. Interaction Gibbs energies are rather large at high temperatures (350 K), at which point many proteins undergo thermal unfolding. At room temperature, these interaction energies are less pronounced. We used the obtained interaction parameter in a Zimm-Bragg/Ising-type approach to calculate the temperature dependence of the ultraviolet circular dichroism (CD) of the MAX3 peptide, which is predominantly built by KV repeats. The agreement between simulation and experimental data was found to be satisfactory. Finally, we analyzed the temperature dependence of the CD and 3J(HNHα) parameters of the amyloid β1-9 fragment. The results of this analysis and a more qualitative consideration of the temperature dependence of denatured proteins probed by CD spectroscopy further corroborate the dominance of anticooperative nearest-neighbor interactions. Generally, our results show that unfolded peptides-and most likely also proteins-exhibit some similarity with antiferromagnetic systems.
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Affiliation(s)
| | - Siobhan E Toal
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania
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30
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Hesser M, DiGuiseppi D, Thursch L, Alvarez N, Schweitzer-Stenner R. Exploring the Unexpected pH Triggered Self-Assembly and Gelation of the GHG Tripeptide in Water. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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31
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Milorey B, Schweitzer-Stenner R. pH Induced Switch between Different Modes of Cytochrome C Binding to Cardiolipin Containing Liposomes. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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32
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Lavenia T, Alvarez NJ, DiGuiseppi D, Schweitzer-Stenner R. Exploring the Tunability of the Aggregation and Gelation Process of the Tripeptide Gag. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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33
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Kurbaj R, Milorey B, Schweitzer-Stenner R. Substrate Inducedconformational Changes of Liposomebound Cytochrome C. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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34
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DiGuiseppi DM, Thursch L, Alvarez N, Schweitzer-Stenner R. Tuning and Exploring the Reformation Process of a Cationic Tripeptide Hydrogel. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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35
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Hennessy NJ, Levine M, DiGuiseppi D, Abramovich L, Schweitzer-Stenner R. Exploring the Initial Phase of FmocFF Dipeptides Gelation in Mixture of Water and Dimethylsulphoxide. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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36
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Milorey B, Schweitzer-Stenner R, Kurbaj R, Malyshka D. pH-Induced Switch between Different Modes of Cytochrome c Binding to Cardiolipin-Containing Liposomes. ACS Omega 2019; 4:1386-1400. [PMID: 31459406 PMCID: PMC6647999 DOI: 10.1021/acsomega.8b02574] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/02/2019] [Indexed: 05/28/2023]
Abstract
Fluorescence, visible circular dichroism (CD), absorption, and resonance Raman spectroscopy techniques were combined to explore structural changes of ferricytochrome c upon its binding to cardiolipin-containing liposomes (20% 1,1',1,2'-tetraoleyolcardiolipin and 1,2-deoleyol-sn-glycero-3-phosphocholine) at acidic pH (6.5). According to the earlier work of Kawai [J. Biol. Chem.2005, 280, 34709-347171],cytochrome c binding at this pH is governed by interactions between the phosphate head groups of cardiolipin and amino acid side chains of the so-called L-site, which contains the charged residues K22, K25, K27, and potentially H26 and H33. We found that L-site binding causes a conformational transition that involves a change of the protein's ligation and spin state. In this paper, we report spectroscopic responses to an increasing number of cardiolipin-containing liposomes at pH 6.5 in the absence and presence of NaCl. The latter was found to mostly inhibit protein binding already with 50 mM concentration. The inhibition effect can be quantitatively reproduced by applying the electrostatic theory of Heimburg [Biophys. J.1995, 68, 536-546]. A comparison with corresponding spectroscopic response data obtained at pH 7.4 reveals major differences in that the latter indicates hydrophobic binding, followed by an electrostatically driven conformational change. Visible CD data suggest that structural changes in the heme pocket of liposome-bound ferricytochrome c resemble to some extent those in the denatured protein in urea at neutral and acidic pH. The measured noncoincidence between absorption and CD Soret band of cytochrome c in the presence of a large access of cardiolipin is caused by the electric field at the membrane surface. The very fact that its contribution to the internal electric field in the heme pocket is detectable by spectroscopic means suggests some penetration of the protein into membrane surface.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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38
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Schweitzer-Stenner R. Relating the multi-functionality of cytochrome c to membrane binding and structural conversion. Biophys Rev 2018; 10:1151-1185. [PMID: 29574621 PMCID: PMC6082307 DOI: 10.1007/s12551-018-0409-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/23/2018] [Indexed: 12/16/2022] Open
Abstract
Cytochrome c is known as an electron-carrying protein in the respiratory chain of mitochondria. Over the last 20 years, however, alternative functions of this very versatile protein have become the focus of research interests. Upon binding to anionic lipids such as cardiolipin, the protein acquires peroxidase activity. Multiple lines of evidence suggest that this requires a conformational change of the protein which involves partial unfolding of its tertiary structure. This review summarizes the current state of knowledge of how cytochrome c interacts with cardiolipin-containing surfaces and how this affects its structure and function. In this context, we delineate partially conflicting results regarding the affinity of cytochrome c binding to cardiolipin-containing liposomes of different size and its influence on the structure of the protein and the morphology of the membrane.
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39
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Schweitzer-Stenner R, Toal SE. Anti-cooperative Nearest Neighbor Coupling Determines the Statistical Coil State of Peptides and Proteins at High Temperatures. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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40
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Lewis G, Milorey B, Schweitzer-Stenner R. Correlating Structure and Function of Non-Native Cytochrome C: The Relationship Between Iron Spin State and Peroxidase Activity. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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41
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Milorey B, Schweitzer-Stenner R. Implementing a Statistical Thermodynamic Model to Describe Functionally Relevant Cytochrome C - Cardiolipin L-Site Binding. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.3766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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42
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Abstract
Ferricytochrome c has been previously shown to photoreduce in the presence of ferrocyanide anions, but the process has been poorly understood.
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Toal SE, Kubatova N, Richter C, Linhard V, Schwalbe H, Schweitzer-Stenner R. Corrigendum: Randomizing the Unfolded State of Peptides (and Proteins) by Nearest Neighbor Interactions between Unlike Residues. Chemistry 2017; 23:18084-18087. [PMID: 29265638 DOI: 10.1002/chem.201705353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schweitzer-Stenner R, Toal SE. Construction and comparison of the statistical coil states of unfolded and intrinsically disordered proteins from nearest-neighbor corrected conformational propensities of short peptides. Mol Biosyst 2017; 12:3294-3306. [PMID: 27545097 DOI: 10.1039/c6mb00489j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Assessing the influence of nearest neighbors on the conformational ensemble of amino acid residues in unfolded and intrinsically disordered proteins and peptides is pivotal for a thorough understanding of the statistical coil state of unfolded proteins as well as of the energetics of the folding process. Research aimed at exploring nearest neighbor interactions has mostly focused on the analysis of restricted coil libraries that reflect conformational distributions in loops connecting more regular secondary structure segments. Recently, however, Toal et al. reported an experimentally based structural analysis of selected xy-pairs in GxyG tetrapeptides, which revealed quantitative information about conformational changes induced by nearest-neighbor interactions (Eur. J. Chem., 2015, 21, 5173-5192). Here, we perform analyses of Ramachandran plots of xy-pairs in GxyG and in coil libraries (Ting et al., PLOS CompBiol, 2010, 6, e1000763) using Hellinger distances as a quantitative measure of dissimilarities between Ramachandran distributions. Our analysis reveals that nearest-neighbor effects inferred from the above coil library are much less pronounced than corresponding structural changes observed for GxyG peptides. To determine whether nearest-neighbor induced conformational changes observed for GxyG can be utilized for the analysis of unfolded proteins, we analyzed sets of 3J(HHHα) coupling constants of three different unfolded proteins, namely the 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein (FnBPc), denatured hen lysozyme, and the htau40 protein. For the first two proteins we found statistically meaningful correlations between predicted nearest-neighbor induced changes of 3J(HHHα) and experimentally observed deviations from corresponding coupling constants of GxG peptides in water, which we used as reference system with minimal nearest-neighbor interactions. This observation is in line with the NMR based understanding of these proteins being predominantly statistical coils. For htau40, however, which is known to exhibit residual structure and large deviations form statistical coil expectations, these correlations are weak or absent. Our results thus underscore the importance of nearest-neighbor interactions for a complete physical description of an ideal statistical coil state of a protein.
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Affiliation(s)
| | - Siobhan E Toal
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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DiGuiseppi D, Milorey B, Lewis G, Kubatova N, Farrell S, Schwalbe H, Schweitzer-Stenner R. Probing the Conformation-Dependent Preferential Binding of Ethanol to Cationic Glycylalanylglycine in Water/Ethanol by Vibrational and NMR Spectroscopy. J Phys Chem B 2017; 121:5744-5758. [DOI: 10.1021/acs.jpcb.7b02899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Nina Kubatova
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
| | | | - Harald Schwalbe
- Institut
für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität, 60438 Frankfurt am Main, Germany
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Milorey B, Malyshka D, Schweitzer-Stenner R. pH Dependence of Ferricytochrome c Conformational Transitions during Binding to Cardiolipin Membranes: Evidence for Histidine as the Distal Ligand at Neutral pH. J Phys Chem Lett 2017; 8:1993-1998. [PMID: 28418677 DOI: 10.1021/acs.jpclett.7b00597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conformational changes of ferricytochrome c upon binding to cardiolipin-containing small unilamellar vesicles were studied at slightly acidic pH using fluorescence, visible circular dichroism, UV-visible absorption, and resonance Raman spectroscopy. The obtained spectroscopic response data suggest a mode of interaction, which is clearly distinct from the binding process observed at neutral pH. Evidence of a reversible and electrostatic binding mechanism under these conditions is provided through binding inhibition in the presence of 150 mM NaCl. Moreover, UV-visible absorption and resonance Raman spectra reveal that the conformational ensemble of membrane bound cytochrome c is dominated by a mixture of conformers with pentacoordinated and hexacoordinated high-spin heme irons, which contrast with the dominance of low-spin species at neutral pH. While our results confirm the L-site binding proposed by Kawai et al., they point to the protonation of a histidine ligand (H33) as conformational trigger.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Dmitry Malyshka
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
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DiGuiseppi D, Kubatova N, Lewis G, Schwalbe H, Schweitzer-Stenner R. Exploring the Effects on the Conformational Propensity of Alanine in the Unblocked Tripeptide Glycyl-Analyl-Glycine in Water/Ethanol Mixtures. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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DiGuiseppi D, Farrell S, Alvarez N, Schweitzer-Stenner R. Exploring the Unexpected Gelation of Tripeptides in a Binary Mixture of Water and Ethanol. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.2767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Malyshka D, Schweitzer-Stenner R. Ferrocyanide-Mediated Photoreduction of Ferricytochrome C Utilized to Selectively Probe Non-native Conformations Induced by Binding to Cardiolipin-Containing Liposomes. Chemistry 2016; 23:1151-1156. [PMID: 27859757 DOI: 10.1002/chem.201604992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Indexed: 01/29/2023]
Abstract
Ferricytochrome c binding to cardiolipin-containing liposomes produces a heterogeneous distribution of conformations comprising native-like and non-native misfolded proteins. We utilized the photoreduction of native ferricytochrome c in the presence of potassium ferrocyanide and resonance Raman spectroscopy to probe the population of native and misfolded cytochrome c on liposomes with 20 % tetraoleylcardiolipin (TOCL)/80 % dioleylphosphocholine (DOPC) and with 100 % TOCL as a function of TOCL concentration. Our data provided strong support for an earlier model, which predicts that the equilibrium between native and non-native conformations is shifted to the latter with decreasing protein occupation of liposomes.
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Affiliation(s)
- Dmitry Malyshka
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
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Serpas L, Milorey B, Pandiscia LA, Addison AW, Schweitzer-Stenner R. Autoxidation of Reduced Horse Heart Cytochrome c Catalyzed by Cardiolipin-Containing Membranes. J Phys Chem B 2016; 120:12219-12231. [PMID: 27934230 DOI: 10.1021/acs.jpcb.6b05620] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Visible circular dichroism, absorption, and fluorescence spectroscopy were used to probe the binding of horse heart ferrocytochrome c to anionic cardiolipin (CL) head groups on the surface of 1,1',2,2'-tetraoleoyl cardiolipin (TOCL)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) (20%:80%) liposomes in an aerobic environment. We found that ferrocytochrome c undergoes a conformational transition upon binding that leads to complete oxidation of the protein at intermediate and high CL concentrations. At low lipid concentrations, the protein maintains a structure that is only slightly different from its native one, whereas an ensemble of misligated predominantly hexacoordinated low-spin states become increasingly populated at high lipid concentrations. A minor fraction of conformations with either high- or quantum-mixed-spin states were detected at a CL to protein ratio of 200 (the largest one investigated). The population of the non-native state is less pronounced than that found for cytochrome c-CL interactions initiated with oxidized cytochrome c. Under anaerobic conditions, the protein maintains its reduced state but still undergoes some conformational change upon binding to CL head groups on the liposome surface. Our data suggest that CL-containing liposomes function as catalysts by reducing the activation barrier for a Fe2+ → O2 electron transfer. Adding NaCl to the existing cytochrome-liposome mixtures under aerobic conditions inhibits protein autoxidation of ferrocytochrome c and stabilizes the reduced state of the membrane-bound protein.
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Affiliation(s)
- Lee Serpas
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Bridget Milorey
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Leah A Pandiscia
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Anthony W Addison
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Department of Chemistry, Drexel University , 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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