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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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2
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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] [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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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] [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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4
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Toal S, Meral D, Verbaro D, Urbanc B, Schweitzer-Stenner R. pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study. J Phys Chem B 2013; 117:3689-706. [PMID: 23448349 DOI: 10.1021/jp310466b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.
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Affiliation(s)
- Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, USA
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Byrne A, Kier BL, Williams DV, Scian M, Andersen NH. Circular Permutation of the Trp-cage: Fold Rescue upon Addition of a Hydrophobic Staple. RSC Adv 2013; 2013. [PMID: 24376912 DOI: 10.1039/c3ra43674h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Trp-cage, at 20 residues in length, is generally acknowledged as the smallest fully protein-like folding motif. Linking the termini by a two-residue unit and excising one residue affords circularly permuted sequences that adopt the same structure. This represents the first successful circular permutation of any fold of less than 50-residue length. As was observed for the original topology, a hydrophobic staple near the chain termini is required for enhanced fold stability.
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Affiliation(s)
- Aimee Byrne
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Brandon L Kier
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - D V Williams
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Michele Scian
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
| | - Niels H Andersen
- Department of Chemistry, University of Washington Seattle, Washington, 98195, USA
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Duitch L, Toal S, Measey TJ, Schweitzer-Stenner R. Triaspartate: A Model System for Conformationally Flexible DDD Motifs in Proteins. J Phys Chem B 2012; 116:5160-71. [DOI: 10.1021/jp2121565] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Laura Duitch
- Department of Chemistry, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Siobhan Toal
- Department of Chemistry, Drexel University, 3141 Chestnut Street,
Philadelphia, Pennsylvania 19104, United States
| | - Thomas J. Measey
- Department of Chemistry, University of Pennsylvania, 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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7
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Toal S, Amidi O, Schweitzer-Stenner R. Conformational Changes of Trialanine Induced by Direct Interactions between Alanine Residues and Alcohols in Binary Mixtures of Water with Glycerol and Ethanol. J Am Chem Soc 2011; 133:12728-39. [DOI: 10.1021/ja204123g] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Siobhan Toal
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Omid Amidi
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Departments of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
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Oh KI, Lee KK, Park EK, Yoo DG, Hwang GS, Cho M. Circular dichroism eigenspectra of polyproline II and β-strand conformers of trialanine in water: Singular value decomposition analysis. Chirality 2010; 22 Suppl 1:E186-201. [DOI: 10.1002/chir.20870] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Pizzanelli S, Forte C, Monti S, Schweitzer-Stenner R. Interaction of a tripeptide with cesium perfluorooctanoate micelles. J Phys Chem B 2008; 112:1251-61. [PMID: 18173254 DOI: 10.1021/jp073947x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water was studied in the isotropic phase by means of 1H NMR and by molecular dynamics (MD) simulations. Information on the location of the peptide was experimentally obtained from selective variations in Ala-Phe-Ala chemical shifts and from differential line broadening in the presence of the paramagnetic ion Mn2+. The peptide-micelle association constant was estimated analyzing the chemical shift variations of the most sensitive Ala-Phe-Ala resonances with the peptide concentration. MD simulations of Ala-Phe-Ala in the micellar environment confirmed the experimental observations, identifying the hydrogen bonding interactions of the different peptide moieties with the micelle, yielding a binding constant close to the experimental one. NOESY experiments suggest that the peptide in the micellar environment does not adopt a preferred conformation but is mainly unstructured. Details on the conformational behavior of the peptide in the micellar solution observed through MD were consistent with a different conformational equilibrium in the proximity of the micelle. Information on Ala-Phe-Ala dynamics was obtained from 1H T1 data and compared to MD simulation results on the overall tumbling motion.
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Affiliation(s)
- Silvia Pizzanelli
- Istituto per i Processi Chimico-Fisici (IPCF-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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10
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Doslić N, Kovacević G, Ljubić I. Signature of the Conformational Preferences of Small Peptides: a Theoretical Investigation. J Phys Chem A 2007; 111:8650-8. [PMID: 17691755 DOI: 10.1021/jp072565o] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An extensive computational study of the conformational preferences of N-acetylphenylalaninylamide (NAPA) is reported, including conformational and anharmonic frequency analyses, as well as calculations of excitation energies of the four NAPA conformers lowest in energy. Particular attention is paid to the influence of hydrogen-bonding interactions on the relative stability of the conformers, which was found to be very sensitive to both the level of quantum chemical computations and the anharmonic treatment of molecular vibrations. The assignments of the UV spectral peaks are well supported by the multireference CASSCF/MS-CASPT2 calculations. Upon consideration of the second-order Möller-Plesset (MP2) and density functional theory (DFT) structures, overall energetics, and harmonic and anharmonic corrections, we found no conclusive theoretical evidence for the assumed conformational propensity of small model peptides toward extended beta-strand structures.
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Affiliation(s)
- Nada Doslić
- Department of Physical Chemistry, Ruder Bosković Institute, Bijenicka cesta 54, Post Office Box 180, HR-10002, Zagreb, Republic of Croatia.
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Sebek J, Gyurcsik B, Sebestík J, Kejík Z, Bednarova L, Bour P. Interpretation of synchrotron radiation circular dichroism spectra of anionic, cationic, and zwitterionic dialanine forms. J Phys Chem A 2007; 111:2750-60. [PMID: 17388375 DOI: 10.1021/jp068811y] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Electronic absorption and synchrotron radiation circular dichroism (SRCD) spectra of the anionic, cationic, and zwitterionic forms of L-alanyl-L-alanine (AA) in aqueous solutions were measured and interpreted by molecular dynamics (MD) and ab initio computations. Time-dependent density functional theory (TD DFT) was applied to predict the electronic excited states. The modeling enabled the assessment of the role of molecular conformation, charge, and interaction with the polar environment in the formation of the spectral shapes. Particularly, inclusion of explicit solvent molecules in the computations appeared to be imperative because of the participation of water orbitals in the amide electronic structure. Implicit dielectric continuum solvent models gave inferior results for clusters, especially at low-energy transitions. Because of the dispersion of transition energies, tens of water/AA clusters had to be averaged in order to obtain reasonable spectral shapes with a more realistic inhomogeneous broadening. The modeling explained most of the observed differences, as the anionic and zwitterionic SRCD spectra were similar and significantly different from the cationic spectrum. The greatest deviation between the experimental and theoretical curves observed for the lowest-energy negative anion signal can be explained by the limited precision of the TD DFT method, but also by the complex dynamics of the amine group. The results also indicate that differences in the experimental spectral shapes do not directly correlate with the peptide main-chain conformation. Future peptide and protein conformational studies based on circular dichroic spectroscopy can be reliable only if such effects of molecular dynamics, solvent structure, and polar solvent-solute interactions are taken into account.
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Affiliation(s)
- Jirí Sebek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nAm. 2, 166 10, Prague 6, Czech Republic
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Schweitzer-Stenner R, Measey T, Kakalis L, Jordan F, Pizzanelli S, Forte C, Griebenow K. Conformations of Alanine-Based Peptides in Water Probed by FTIR, Raman, Vibrational Circular Dichroism, Electronic Circular Dichroism, and NMR Spectroscopy. Biochemistry 2007; 46:1587-96. [PMID: 17279623 DOI: 10.1021/bi062224l] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have used a combination of FTIR, VCD, ECD, Raman, and NMR spectroscopies to probe the solution conformations sampled by H-(AAKA)-OH by utilizing an excitonic coupling model and constraints imposed by the 3JCalphaHNH coupling constants of the central residues to simulate the amide I' profile of the IR, isotropic Raman, anisotropic Raman, and VCD spectra in terms of a mixture of three conformations, i.e., polyproline II, beta-strand and right-handed helical. The representative coordinates of the three conformations were obtained from published coil libraries. Alanine was found to exhibit PPII fractions of 0.60 or greater, mixed with smaller fractions of helices and beta-strand conformations. Lysine showed no clear conformational propensity in that it samples polyproline II, beta-strand, and helical conformations with comparable probability. This is at variance with results obtained earlier for ionized polylysine, which suggest a high polyproline II propensity. We reanalyzed previously investigated tetra- and trialanine by combining published vibrational spectroscopy data with 3JCalphaHNH coupling constants and obtained again blends dominated by PPII with smaller admixtures of beta-strand and right-handed helical conformations. The polyproline II propensity of alanine was found to be higher in tetraalanine than in trialanine. For all peptides investigated, our results rule out a substantial population of turn-like conformations. Our results are in excellent agreement with MD simulations on short alanine peptides by Gnanakaran and Garcia [(2003) J. Phys. Chem. B 107, 12555-12557] but at variance with multiple MD simulations particularly for the alanine dipeptide.
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