1
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Schweitzer-Stenner R, Kurbaj R, O'Neill N, Andrews B, Shah R, Urbanc B. Conformational Manifold Sampled by Two Short Linear Motif Segments Probed by Circular Dichroism, Vibrational, and Nuclear Magnetic Resonance Spectroscopy. Biochemistry 2023; 62:2571-2586. [PMID: 37595285 DOI: 10.1021/acs.biochem.3c00212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Disordered protein segments called short linear motifs (SLiM) serve as recognition sites for a variety of biological processes and act as targeting signals, modification, and ligand binding sites. While SLiMs do not adopt one of the known regular secondary structures, the conformational distribution might still reflect the structural propensities of their amino acid residues and possible interactions between them. In the past, conformational analyses of short peptides provided compelling evidence for the notion that individual residues are less conformationally flexible than locally expected for a random coil. Here, we combined various spectroscopies (NMR, IR, vibrational, and UV circular dichroism) to determine the Ramachandran plots of two SLiM motifs, i.e., GRRDSG and GRRTSG. They are two representatives of RxxS motifs that are capable of being phosphorylated by protein kinase A, an enzyme that plays a fundamental role in a variety of biological processes. Our results reveal that the nearest and non-nearest interactions between residues cause redistributions between polyproline II and β-strand basins while concomitantly stabilizing extended relative to turn-forming and helical structures. They also cause shifts in basin positions. With increasing temperature, β-strand populations become more populated at the expense of polyproline II. While molecular dynamics simulations with Amber ff14SB and CHARMM 36m force fields indicate residue-residue interactions, they do not account for the observed structural changes.
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Affiliation(s)
| | - Raghed Kurbaj
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Nichole O'Neill
- Department of Chemistry, Drexel University, Philadelphia, PA19104Pennsylvania,United States
| | - Brian Andrews
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Riya Shah
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
| | - Brigita Urbanc
- Department of Physics, Drexel University, Philadelphia,PA19104Pennsylvania,United States
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2
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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] [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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3
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Hohmann T, Chowdhary S, Ataka K, Er J, Dreyhsig GH, Heberle J, Koksch B. Introducing Aliphatic Fluoropeptides: Perspectives on Folding Properties, Membrane Partition and Proteolytic Stability. Chemistry 2023; 29:e202203860. [PMID: 36722398 DOI: 10.1002/chem.202203860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/02/2023]
Abstract
A de novo designed class of peptide-based fluoropolymers composed of fluorinated aliphatic amino acids as main components is reported. Structural characterization provided insights into fluorine-induced alterations on β-strand to α-helix transition upon an increase in SDS content and revealed the unique formation of PPII structures for trifluorinated fluoropeptides. A combination of circular dichroism, fluorescence-based leaking assays and surface enhanced infrared absorption spectroscopy served to examine the insertion and folding processes into unilamellar vesicles. While partitioning into lipid bilayers, the degree of fluorination conducts a decrease in α-helical content. Furthermore, this study comprises a report on the proteolytic stability of peptides exclusively built up by fluorinated amino acids and proved all sequences to be enzymatically degradable despite the degree of fluorination. Herein presented fluoropeptides as well as the distinctive properties of these artificial and polyfluorinated foldamers with enzyme-degradable features will play a crucial role in the future development of fluorinated peptide-based biomaterials.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Suvrat Chowdhary
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Jasmin Er
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Gesa Heather Dreyhsig
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, 14195, Berlin, Germany
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4
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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] [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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5
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Wei H, Lin S, Liu W, Li Y, Li B, Yang Y. Stereostructure Dependence Phenomenon on the Self-Assembly of Ala-Ala-Ala Lipotripeptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:2248-2256. [PMID: 35133849 DOI: 10.1021/acs.langmuir.1c02813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A series of lipotripeptide stereoisomers based on alanine were synthesized, and their self-assembling behaviors were studied by means of circular dichroism spectra, ATR-IR, temperature-dependent 1H NMR, and X-ray diffraction patterns. In the mixed solvent of hexafluoroisopropanol/H2O (1/9, v/v), eight lipotripeptides were able to self-assembled into nanoflakes or nanoribbons driven by the hydrophobic association of alkyl chains, intermolecular hydrogen bonding among carboxyl groups at C-terminal and amide groups of alanine moieties in the peptide segment. It was found that the stacking chirality of carbonyl groups was determined by the chirality of alanine residue at C-terminal (i.e., "C-terminal determination" rule). Moreover, our research also highlighted the intermolecular hydrogen bonding on amide groups of each alanine residue, terminal carboxyl as well as the molecular packing structures can be subtly manipulated by changing the stereochemical sequence of peptide segment.
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Affiliation(s)
- He Wei
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shuwei Lin
- Key Lab of Advanced Optical Manufacturing Technologies of Jiangsu Province & Key Lab of Modern Optical Technologies of Education Ministry of China, School of Optoelectronics Science and Engineering, Soochow University, Suzhou 215123, China
| | - Wei Liu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yi Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Baozong Li
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Yonggang Yang
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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6
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Zhao J, Dong T, Yu P, Wang J. Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations. J Phys Chem B 2021; 126:161-173. [PMID: 34968072 DOI: 10.1021/acs.jpcb.1c10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na+, Ca2+, Mg2+, and Zn2+) with backbone (amide C═O) and C-terminal carboxylate (COO-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PPII) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH3+ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn2+) can specifically coordinate to the COO- group in bidentate and pseudo-bridging forms simultaneously. For Zn2+, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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7
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Masquelier E, Liang SP, Sepunaru L, Morse DE, Gordon MJ. Reversible electrochemical triggering and optical interrogation of polylysine α-helix formation. Bioelectrochemistry 2021; 144:108007. [PMID: 34871847 DOI: 10.1016/j.bioelechem.2021.108007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Reversible electrochemical triggering of the random coil to α-helix conformational transition of polylysine (Lys10, Lys20, Lys50) was accomplished at a Pt electrode at potentials < |1| V vs. Ag/AgCl. Direct electroreduction of the N-terminus vs ε-amino groups in Lys sidechains, as well as hydronium reduction and electrolysis, could be easily distinguished and deconvolved using differential pulse voltammetry. Electrochemistry was coupled with in situ UV absorbance and circular dichroism spectroscopies to dynamically follow the evolution of α-helix formation at different potentials. Isotope experiments in H2O vs. D2O unequivocally confirm that direct electroreduction of ε-NH3+/ND3+ groups in Lys sidechains, rather than electrochemically generated pH gradient-induced deprotonation, leads to subsequent α-helix formation. The site-selective electrochemistry and optical methodologies presented herein can be generalized and extended to interrogate other protonation-sensitive biomolecular systems, and potentially provide access to early intermediates and control over the dynamic structural evolution of peptides and proteins.
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Affiliation(s)
- Eloise Masquelier
- Materials Department, University of California, Santa Barbara, CA, United States
| | - Sheng-Ping Liang
- Dept. Of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Lior Sepunaru
- Dept. Of Chemistry and Biochemistry, University of California, Santa Barbara, CA, United States
| | - Daniel E Morse
- Dept. Of Molecular, Cellular and Development Biology, University of California, Santa Barbara, CA, United States; Institue for Collaborative Biotechnologies, University of California, Santa Barbara, CA, United States
| | - Michael J Gordon
- Dept. Of Chemical Engineering, University of California, Santa Barbara, CA, United States; Institue for Collaborative Biotechnologies, University of California, Santa Barbara, CA, United States.
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8
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Costales P, Ríos-Lombardía N, Lorenzo-Herrero S, Morís F, González-Sabín J. Novel chiral naphthalimide-cycloalkanediamine conjugates: Design, synthesis and antitumor activity. Bioorg Chem 2021; 112:104859. [PMID: 33836453 DOI: 10.1016/j.bioorg.2021.104859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/18/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
A novel series of enantiopure naphthalimide-cycloalkanediamine conjugates were designed, synthetized and evaluated for in vitro cytotoxicity against human colon adenocarcinoma (LoVo), human lung adenocarcinoma (A549), human cervical carcinoma (Hela) and human promyelocytic leukemia cell lines (HL-60). The cytotoxicity of the compounds was highly dependent on size and relative stereochemistry of the cycloalkyl ring as well as length of the spacer. By contrast, any kind of enantioselection was observed for each pair of enantiomers. Flow cytometric analysis indicated that compounds 22 and 23 could effectively induce G2/M arrest in the four previous cell lines despite a mild apoptotic effect.
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Affiliation(s)
- Paula Costales
- EntreChem SL, Vivero Ciencias de la Salud, Santo Domingo de Guzmán, 33011 Oviedo, Spain
| | | | - Seila Lorenzo-Herrero
- EntreChem SL, Vivero Ciencias de la Salud, Santo Domingo de Guzmán, 33011 Oviedo, Spain
| | - Francisco Morís
- EntreChem SL, Vivero Ciencias de la Salud, Santo Domingo de Guzmán, 33011 Oviedo, Spain
| | - Javier González-Sabín
- EntreChem SL, Vivero Ciencias de la Salud, Santo Domingo de Guzmán, 33011 Oviedo, Spain.
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9
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Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules 2021; 26:molecules26030634. [PMID: 33530506 PMCID: PMC7865441 DOI: 10.3390/molecules26030634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 01/10/2023] Open
Abstract
The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
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10
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Hernández B, Pflüger F, Kruglik SG, Ghomi M. Multiconformational analysis of tripeptides upon consideration of implicit and explicit hydration effects. J Mol Graph Model 2020; 102:107790. [PMID: 33181423 DOI: 10.1016/j.jmgm.2020.107790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/10/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
During the last two decades, numerous observed data obtained by various physical techniques, also supported by molecular modeling approaches, have highlighted the structuring features of tripeptides, as well as their aggregation properties. Herein, we focus on the structural dynamics of four trimers, i.e., Gly-Gly-Gly, Gly-Ala-Gly, Ala-Ala-Ala and Ala-Phe-Ala, in an aqueous environment. Density functional theory calculations (DFT) were carried out to assess the stability of four types of secondary structures, i.e., β-strand, polyproline-II (pP-II), α-helix and γ-turn, of which the formation had been described in these tripeptides. Both implicit and explicit hydration effects were analyzed on the conformational and energetic features of trimers. It has been shown that the use of M062X functional (versus B3LYP) improve the stability of intramolecular H-bonds, especially in inverse γ-turn structures, as well as the energetic and conformational equilibrium in all tripeptides. Explicit hydration reflected by the presence of five water molecules around the backbone polar sites (NH3+, N-H, CO and NH2) considerably changes the conformational landscapes of the trimers. Characteristic intramolecular and intermolecular interactions evidenced by the calculations, were emphasized.
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Affiliation(s)
- Belén Hernández
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Moulin de la Housse, 51687, Reims Cedex 2, France; Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France
| | - Fernando Pflüger
- Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France
| | - Sergei G Kruglik
- Laboratoire Jean-Perrin, Sorbonne Université, CNRS UMR 8237, 4 Place Jussieu, 75005, Paris, France
| | - Mahmoud Ghomi
- Laboratoire Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), UMR 7369, Université de Reims, Faculté des Sciences, Moulin de la Housse, 51687, Reims Cedex 2, France; Université Sorbonne Paris Nord, UFR Santé-Médecine-Biologie Humaine, Groupe de Biophysique Moléculaire, 74 Rue Marcel Cachin, 93017, Bobigny cedex, France.
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11
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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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12
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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13
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Conformational analyses for hydrated oligopeptides by quantum chemical calculation (QCC): effects of intra-molecular hydrogen bonds. Polym Bull (Berl) 2019. [DOI: 10.1007/s00289-018-2540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Koyambo-Konzapa SJ, Dhaouadi Z, Nsangou M. Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method. J Mol Graph Model 2019; 88:194-202. [DOI: 10.1016/j.jmgm.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022]
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15
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Schweitzer-Stenner R, Toal SE. Anticooperative Nearest-Neighbor Interactions between Residues in Unfolded Peptides and Proteins. Biophys J 2019. [PMID: 29539392 DOI: 10.1016/j.bpj.2018.01.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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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16
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Nishimura SN, Higashi N, Koga T. A novel thermo-responsive multiblock architecture composed of a sequential peptide and an amino acid-derived vinyl polymer: toward protein-mimicking single-chain folding. Chem Commun (Camb) 2019; 55:1498-1501. [DOI: 10.1039/c8cc09051c] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel multiblock hybrid copolymer composed of a β-sheet peptide and a glycine-derived vinyl polymer was developed to achieve single-chain folding into well-defined nanoparticles.
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Affiliation(s)
- Shin-nosuke Nishimura
- Department of Molecular Chemistry & Biochemistry
- Faculty of Science & Engineering
- Doshisha University
- Kyotanabe
- Japan
| | - Nobuyuki Higashi
- Department of Molecular Chemistry & Biochemistry
- Faculty of Science & Engineering
- Doshisha University
- Kyotanabe
- Japan
| | - Tomoyuki Koga
- Department of Molecular Chemistry & Biochemistry
- Faculty of Science & Engineering
- Doshisha University
- Kyotanabe
- Japan
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17
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Cheng D, Cai W, Shao X. Understanding the Interaction Between Oligopeptide and Water in Aqueous Solution Using Temperature-Dependent Near-Infrared Spectroscopy. APPLIED SPECTROSCOPY 2018; 72:1354-1361. [PMID: 29664323 DOI: 10.1177/0003702818769410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Investigating the interaction between oligopeptide and water is essential for understanding the structure, dynamics and function of proteins. Temperature-dependent near-infrared (NIR) spectroscopy and independent component analysis (ICA) were employed to study the interaction between oligopeptide and water in aqueous solution. The NIR spectra of two homo-oligopeptides, penta-aspartic acid (D5) and penta-lysine (K5), in aqueous solution of different concentration were measured at different temperature (30-90 ℃). Independent component analysis was performed to extract the spectral information that changes with temperature. The independent components (ICs) representing the spectral information of NH and CH2 groups were obtained. Compared with D5, the two groups in K5 change significantly at higher temperature. The result may suggest that K5 has stronger interaction with water than D5. Moreover, three ICs that contain the spectral information of the water species with no (S0), one (S1), and two (S2) hydrogen-bonds were obtained. It was shown that the spectral intensity of S0 and S1 increases while that of S2 decreases with the temperature, and the changes of oligopeptide solutions are weaker than those of pure water. The results indicate that water structure is sensitive to temperature and the oligopeptide in aqueous solution improves the thermal stability of the water species. When oligopeptide is added, the spectral intensity of S0 and S2 decreases and that of S1 increases for D5 solution, but the intensity of all the three species decreases for K5 solution. Furthermore, the concentration effect of K5 was found to be stronger than D5. The result may reveal that D5 combines with water molecule through forming one hydrogen bond but K5 interacts with water through a different way.
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Affiliation(s)
- Dan Cheng
- 1 Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, China
| | - Wensheng Cai
- 1 Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, China
| | - Xueguang Shao
- 1 Research Center for Analytical Sciences, College of Chemistry, Nankai University, Tianjin, China
- 2 Tianjin Key Laboratory of Biosensing and Molecular Recognition, Tianjin, China
- 3 State Key Laboratory of Medicinal Chemical Biology, Tianjin, China
- 4 Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- 5 Xinjiang Laboratory of Native Medicinal and Edible Plant Resources Chemistry, College of Chemistry and Environmental Science, Kashgar University, Kashgar, China
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18
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Childers MC, Towse CL, Daggett V. Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides. Protein Eng Des Sel 2018; 31:191-204. [PMID: 29992252 PMCID: PMC6205366 DOI: 10.1093/protein/gzy016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/15/2018] [Indexed: 01/06/2023] Open
Abstract
Computational resources have contributed to the design and engineering of novel proteins by integrating genomic, structural and dynamic aspects of proteins. Non-canonical amino acids, such as d-amino acids, expand the available sequence space for designing and engineering proteins; however, the rotamer libraries for d-amino acids are usually constructed as the mirror images of l-amino acid rotamer libraries, an assumption that has not been tested. To this end, we have performed molecular dynamics (MD) simulations of model host-guest peptide systems containing d-amino acids. Our simulations systematically address the applicability of the mirror image convention as well as the effects of neighboring residue chirality. Rotamer libraries derived from these systems provide realistic rotamer distributions suitable for use in both rational and computational design workflows. Our simulations also address the impact of chirality on the intrinsic conformational preferences of amino acids, providing fundamental insights into the relationship between chirality and biomolecular dynamics. While d-amino acids are rare in naturally occurring proteins, they are used in designed proteins to stabilize a desired conformation, increase bioavailability or confer favorable biochemical and physical attributes. Here, we present d-amino acid rotamer libraries derived from MD simulations of alanine-based host-guest pentapeptides and show how certain residues can deviate from mirror image symmetry. Our simulations directly model d-amino acids as guest residues within the chiral l-Ala and d-Ala pentapeptide series to explicitly incorporate any contributions resulting from the chiralities of neighboring residues.
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Affiliation(s)
| | - Clare-Louise Towse
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA, USA
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19
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Lanza G, Chiacchio MA. Quantum Mechanics Study on Hydrophilic and Hydrophobic Interactions in the Trivaline-Water System. J Phys Chem B 2018; 122:4289-4298. [PMID: 29584432 DOI: 10.1021/acs.jpcb.8b00833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the aim to elucidate hydrophobic effects in the unfolded state of peptides, DFT-M062X computations on the Val3H+· nH2O ( n up to 22) clusters have been accomplished. As far as the main chain is concerned, four conformers with β-strand and/or polyproline type II conformations, PPII (indicated as β-β, β-PPII, PPII-β, and PPII-PPII), have been found by changing the ϕ and ψ angles. For bare peptide, the side chain (isopropyl) of each residue can independently take on three different orientations with negligible effects on energetics. The great isopropyl spatial separations in β-β and β-PPII conformers allow for the construction of synergic and extensive water-water and water-peptide H-bonding in the minimal hydration Val3H+·22H2O models without significant steric encumbrance. Conversely, due to the proximity of the isopropyl of the central residue with the other two, some restrictions in the water shell construction around the peptide become evident for the PPII-PPII conformer and the number of energetically accessible structures decreases. This is indicative of correlated motion involving isopropyls and backbone mediated by water molecules, the origin of the nearest neighbor effects. Comparing the thermodynamic data of Ala3H+·22H2O and Val3H+·22H2O, what emerges is that both hydration enthalpy and entropy drive the β-strand stability of the latter.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
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20
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Danish MK, Vozza G, Byrne HJ, Frias JM, Ryan SM. Comparative study of the structural and physicochemical properties of two food derived antihypertensive tri-peptides, Isoleucine-Proline-Proline and Leucine-Lysine-Proline encapsulated into a chitosan based nanoparticle system. INNOV FOOD SCI EMERG 2017. [DOI: 10.1016/j.ifset.2017.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Jurinovich S, Cupellini L, Guido CA, Mennucci B. EXAT: EXcitonic analysis tool. J Comput Chem 2017; 39:279-286. [PMID: 29151259 DOI: 10.1002/jcc.25118] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 01/09/2023]
Abstract
We introduce EXcitonic Analysis Tool (EXAT), a program able to compute optical spectra of large excitonic systems directly from the output of quantum mechanical calculations performed with the popular Gaussian 16 package. The software is able to combine in an excitonic scheme the single-chromophore properties and exciton couplings to simulate energies, coefficients, and excitonic spectra (UV-vis, CD, and LD). The effect of the environment can also be included using a Polarizable Continuum Model. EXAT also presents a simple graphical user interface, which shows on-screen both site and exciton properties. To show the potential of the method, we report two applications on a a chiral perturbed BODIPY system and DNA G-quadruplexes, respectively. The program is available online at http://molecolab.dcci.unipi.it/tools/. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandro Jurinovich
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
| | - Ciro A Guido
- Laboratoire CEISAM - UMR CNRS 6230, Université de Nantes, 2 Rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Benedetta Mennucci
- Dipartimento di Chimica, Università di Pisa, Via G. Moruzzi 13, Pisa, 56124, Italy
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22
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Goyal B, Srivastava KR, Durani S. N-terminal diproline and charge group effects on the stabilization of helical conformation in alanine-based short peptides: CD studies with water and methanol as solvent. J Pept Sci 2017; 23:431-437. [PMID: 28425159 DOI: 10.1002/psc.3005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/25/2022]
Abstract
Protein folding problem remains a formidable challenge as main chain, side chain and solvent interactions remain entangled and have been difficult to resolve. Alanine-based short peptides are promising models to dissect protein folding initiation and propagation structurally as well as energetically. The effect of N-terminal diproline and charged side chains is assessed on the stabilization of helical conformation in alanine-based short peptides using circular dichroism (CD) with water and methanol as solvent. A1 (Ac-Pro-Pro-Ala-Lys-Ala-Lys-Ala-Lys-Ala-NH2 ) is designed to assess the effect of N-terminal homochiral diproline and lysine side chains to induce helical conformation. A2 (Ac-Pro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) and A3 (Ac-dPro-Pro-Glu-Glu-Ala-Ala-Lys-Lys-Ala-NH2 ) with N-terminal homochiral and heterochiral diproline, respectively, are designed to assess the effect of Glu...Lys (i, i + 4) salt bridge interactions on the stabilization of helical conformation. The CD spectra of A1, A2 and A3 in water manifest different amplitudes of the observed polyproline II (PPII) signals, which indicate different conformational distributions of the polypeptide structure. The strong effect of solvent substitution from water to methanol is observed for the peptides, and CD spectra in methanol evidence A2 and A3 as helical folds. Temperature-dependent CD spectra of A1 and A2 in water depict an isodichroic point reflecting coexistence of two conformations, PPII and β-strand conformation, which is consistent with the previous studies. The results illuminate the effect of N-terminal diproline and charged side chains in dictating the preferences for extended-β, semi-extended PPII and helical conformation in alanine-based short peptides. The results of the present study will enhance our understanding on stabilization of helical conformation in short peptides and hence aid in the design of novel peptides with helical structures. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Chemistry, School of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Kinshuk Raj Srivastava
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48105, USA
| | - Susheel Durani
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
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23
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Conformational analyses for alanine oligomer during hydration by quantum chemical calculation (QCC). Polym Bull (Berl) 2017. [DOI: 10.1007/s00289-016-1736-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Lee M, Yoon J, Jang S, Shin S. Conformational sampling of metastable states: Tq-REM as a novel replica exchange method. Phys Chem Chem Phys 2017; 19:5454-5464. [PMID: 28165074 DOI: 10.1039/c6cp05322j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to very large bio-systems is somewhat limited. We propose a new replica exchange scheme (Tq-REM) created by combining the conventional temperature-REM (T-REM) and one of the Hamiltonian-REMs, q-REM, using the effective potential with reduced barriers. In the proposed Tq-REM scheme, high temperature replicas in T-REM are substituted with q-replicas. This combined scheme is expected to exploit advantages of the T-REM and q-REM resulting in improved sampling efficiency while minimizing the drawbacks of both approaches. We investigated the performance of Tq-REM compared with T-REM by performing all-atom MD simulations on Met-enkephalin, (AAQAA)3, and Trpzip2. It was found that convergence of the free energy surfaces was improved by Tq-REM over the conventional T-REM. In particular, the trajectories of Tq-REM were able to sample the relevant conformations for all of the metastable folding intermediates, while some of the local minimum structures are poorly represented by T-REM. The results of the present study suggest that Tq-REM can provide useful tools to investigate systems where metastable states play important roles.
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Affiliation(s)
- MinJun Lee
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
| | - Jeseong Yoon
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
| | - Soonmin Jang
- Department of Chemistry, Sejong University, Seoul 143-747, Korea
| | - Seokmin Shin
- Department of Chemistry, Seoul National University, Seoul 151-747, Korea.
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25
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Chin AF, Toptygin D, Elam WA, Schrank TP, Hilser VJ. Phosphorylation Increases Persistence Length and End-to-End Distance of a Segment of Tau Protein. Biophys J 2016; 110:362-371. [PMID: 26789759 DOI: 10.1016/j.bpj.2015.12.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/24/2015] [Accepted: 12/07/2015] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered regions of proteins, which lack unique tertiary structure under physiological conditions, are enriched in phosphorylation sites and in significant local bias toward the polyproline II conformation. The overrepresented coincidence of this posttranslational regulatory signal and local conformational bias within unstructured regions raises a question: can phosphorylation serve to manipulate the conformational preferences of a disordered protein? In this study, we use time-resolved fluorescence resonance energy transfer and a, to our knowledge, novel data analysis method to directly measure the end-to-end distance distribution of a phosphorylatable peptide derived from the human microtubule associated protein tau. Our results show that phosphorylation at threonine or serine extends the end-to-end distance and increases the effective persistence length of the tested model peptides. Unexpectedly, the extension is independent of salt concentration, suggestive of a nonelectrostatic origin. The phosphorylation extension and stiffening effect provides a peptide-scale physical interpretation for the posttranslational regulation of the highly abundant protein-protein interactions found in disordered proteins, as well as a potential insight into the regulatory mechanism of the tau protein's microtubule binding activity.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - Dmitri Toptygin
- Department of Biology, Johns Hopkins University, Baltimore, Maryland
| | - W Austin Elam
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut
| | - Travis P Schrank
- Department of Otolaryngology, Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland.
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26
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Farrell S, DiGuiseppi D, Alvarez N, Schweitzer-Stenner R. The interplay of aggregation, fibrillization and gelation of an unexpected low molecular weight gelator: glycylalanylglycine in ethanol/water. SOFT MATTER 2016; 12:6096-6110. [PMID: 27363780 DOI: 10.1039/c6sm00879h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hydrogels formed by polypeptides could be much-favored tools for drug delivery because their main ingredients are generally biodegradable. However, the gelation of peptides in aqueous solution generally requires a minimal length of the peptide as well as distinct sequences of hydrophilic and hydrophobic residues. The aggregation of short peptides like tripeptides, which are relatively cheap and offer a high degree of biodegradability, are generally thought to require a high hydrophobicity of their residues. We found that contrary to this expectation cationic glycylalanylglycine in 55 mol% ethanol/45 mol% water forms a gel below a melting temperature of ca. 36 °C. A pure hydrogel state can be obtained after allowing the ethanol component to evaporate. The gel phase consists of crystalline fibrils of several 100 μm, which form a sample-spanning network. Rheological data reveal a soft elastic solid gel. We investigated the kinetics of the various processes that lead to the final gel state of the ternary mixture by a unique combination of UV circular dichroism, infrared, vibrational circular dichroism (VCD) and rheological measurements. A mathematical analysis of our data show that gelation is preceded by the formation of peptide β-sheet like tapes or ribbons, which give rise to a significant enhancement of the amide I' VCD signal, and the subsequent formation of rather thick and long fibrils. The VCD signals indicate that the tapes exhibit a right-handed helicity at temperatures above 16 °C and a left-handed helicity below. The tapes'/ribbons' helicity change occurs at a temperature where the UVCD data reflect a relatively long nucleation process. The kinetics of gel formation probed by the storage and loss moduli are composed of a fast process that follows tape/ribbon/fibril formation and is clearly identifiable in a movie that shows the gelation process and a slow process that causes an additional gel stabilization. The rheological data indicate that left-handed fibrils observed at low temperatures form a more solid-like structure than their right-handed counterparts formed at higher temperatures. Taken together our data reveal GAG as an unexpected gelator, the formation of which is underlied by a set of distinguishable kinetic processes.
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Affiliation(s)
- Stefanie Farrell
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
| | - David DiGuiseppi
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, USA.
| | - Nicolas Alvarez
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, PA 19104, USA
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27
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Milorey B, Farrell S, Toal SE, Schweitzer-Stenner R. Demixing of water and ethanol causes conformational redistribution and gelation of the cationic GAG tripeptide. Chem Commun (Camb) 2016; 51:16498-501. [PMID: 26414527 DOI: 10.1039/c5cc06097d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The cationic tripeptide GAG undergoes three conformational changes in binary mixtures of water and ethanol. At 17 mol% of ethanol conformational sampling is shifted from pPII towards β-strands. A more pronounced shift in the same direction occurs at 40 mol%. At ca. 55 mol% of ethanol and above a peptide concentration of ca. 0.2 M the ternary peptide-water-ethanol mixture forms a hydrogel which is comprised of unusually large crystalline like non-β sheet fibrils forming a sample spanning matrix.
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Affiliation(s)
- Bridget Milorey
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, USA.
| | - Stefanie Farrell
- Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, PA, USA.
| | - Siobhan E Toal
- Department of Chemistry, University of Pennsylvania, 231, South 34th-Street, Philadelphia, PA 19104, USA
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28
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Feng Y, Huang J, Kim S, Shim JH, MacKerell AD, Ge NH. Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation. J Phys Chem B 2016; 120:5325-39. [PMID: 27299801 DOI: 10.1021/acs.jpcb.6b02608] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.
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Affiliation(s)
- Yuan Feng
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
| | - Jing Huang
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Seongheun Kim
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
| | - Ji Hyun Shim
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Science, School of Pharmacy, University of Maryland , Baltimore, Maryland 21201, United States
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
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29
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Mirkin NG, Krimm S. Other species in the aqueous environment of a peptide can invert its intrinsic solvated polyproline II/beta propensity: Implications for amyloid formation. Biopolymers 2016; 105:305-311. [DOI: 10.1002/bip.22812] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/25/2016] [Accepted: 01/26/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Noemi G. Mirkin
- LSA Program in Biophysics; University of Michigan; 930 N. University Ave Ann Arbor MI 48109
| | - Samuel Krimm
- LSA Program in Biophysics; University of Michigan; 930 N. University Ave Ann Arbor MI 48109
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30
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Bastida A, Zúñiga J, Requena A, Miguel B, Candela ME, Soler MA. Conformational Changes of Trialanine in Water Induced by Vibrational Relaxation of the Amide I Mode. J Phys Chem B 2016; 120:348-57. [PMID: 26690744 DOI: 10.1021/acs.jpcb.5b09753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most of the protein-based diseases are caused by anomalies in the functionality and stability of these molecules. Experimental and theoretical studies of the conformational dynamics of proteins are becoming in this respect essential to understand the origin of these anomalies. However, a description of the conformational dynamics of proteins based on mechano-energetic principles still remains elusive because of the intrinsic high flexibility of the peptide chains, the participation of weak noncovalent interactions, and the role of the ubiquitous water solvent. In this work, the conformational dynamics of trialanine dissolved in water (D2O) is investigated through Molecular Dynamics (MD) simulations combined with instantaneous normal modes (INMs) analysis both at equilibrium and after the vibrational excitation of the C-terminal amide I mode. The conformational equilibrium between α and pPII conformers is found to be altered by the intramolecular relaxation of the amide I mode as a consequence of the different relaxation pathways of each conformer which modify the amount of vibrational energy stored in the torsional motions of the tripeptide, so the α → pPII and pPII → α conversion rates are increased differently. The selectivity of the process comes from the shifts of the vibrational frequencies with the conformational changes that modify the resonance conditions driving the intramolecular energy flows.
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Affiliation(s)
- Adolfo Bastida
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - José Zúñiga
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Alberto Requena
- Departamento de Química Física, Universidad de Murcia , 30100 Murcia, Spain
| | - Beatriz Miguel
- Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena , 30203 Cartagena, Spain
| | | | - Miguel Angel Soler
- Department of Medical and Biological Sciences, University of Udine , 33100 Udine, Italy
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31
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Goyal B, Kumar A, Srivastava KR, Durani S. Computational scrutiny of the effect of N-terminal proline and residue stereochemistry in the nucleation of α-helix fold. RSC Adv 2016. [DOI: 10.1039/c6ra10934a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
N-Terminal l- to d-residue mutation nucleate helical fold in Ac–DAla–LAla3–NHMe (Ib, m2), Ac–DPro–LAla3–NHMe (IIb, m1), and Ac–DPro–LPro–LAla2–NHMe (IIIb, m2) peptides.
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Affiliation(s)
- Bhupesh Goyal
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - Anil Kumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | | | - Susheel Durani
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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32
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Salmon L, Blackledge M. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:126601. [PMID: 26517337 DOI: 10.1088/0034-4885/78/12/126601] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented.
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Affiliation(s)
- Loïc Salmon
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France. CEA, DSV, IBS, F-38027 Grenoble, France. CNRS, IBS, F-38027 Grenoble, France
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33
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Aoraha E, Candreva J, Kim JR. Engineering of a peptide probe for β-amyloid aggregates. MOLECULAR BIOSYSTEMS 2015; 11:2281-9. [DOI: 10.1039/c5mb00280j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A non-self-aggregating peptide ligand for β-amyloid aggregates created by simple point mutation of an β-amyloid-derived segment.
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Affiliation(s)
- Edwin Aoraha
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
| | - Jason Candreva
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
| | - Jin Ryoun Kim
- Othmer-Jacobs Department of Chemical and Biomolecular Engineering
- New York University
- Brooklyn
- USA
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34
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Caballero D, Määttä J, Zhou AQ, Sammalkorpi M, O'Hern CS, Regan L. Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine. Protein Sci 2014; 23:970-80. [PMID: 24753338 DOI: 10.1002/pro.2481] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 12/19/2022]
Abstract
A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an α-helix, β-sheet, or other backbone dihedral angle ( ϕ-ψ) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for α-helical structures, while experiments on small peptides observe that β-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model for Ala dipeptide mimetics that includes steric interactions between nonbonded atoms and bond length and angle constraints with the goal of evaluating the role of steric interactions in determining protein backbone conformational preferences. We find four key results. For the hard-sphere MD simulations, we show that (1) β-sheet structures are roughly three and half times more probable than α-helical structures, (2) transitions between α-helix and β-sheet structures only occur when the backbone bond angle τ (NCα C) is greater than 110°, and (3) the probability distribution of τ for Ala conformations in the "bridge" region of ϕ-ψ space is shifted to larger angles compared to other regions. In contrast, (4) the distributions obtained from Amber and CHARMM MD simulations in the bridge regions are broader and have increased τ compared to those for hard sphere simulations and from high-resolution protein crystal structures. Our results emphasize the importance of hard-sphere interactions and local stereochemical constraints that yield strong correlations between ϕ-ψ conformations and τ.
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Affiliation(s)
- Diego Caballero
- Department of Physics, Yale University, New Haven, Connecticut, 06520; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520
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35
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Jensen MR, Zweckstetter M, Huang JR, Blackledge M. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 2014; 114:6632-60. [PMID: 24725176 DOI: 10.1021/cr400688u] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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Toal SE, Verbaro DJ, Schweitzer-Stenner R. Role of Enthalpy–Entropy Compensation Interactions in Determining the Conformational Propensities of Amino Acid Residues in Unfolded Peptides. J Phys Chem B 2014; 118:1309-18. [DOI: 10.1021/jp500181d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Siobhan E. Toal
- Departments of Chemistry and ‡Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United States
| | - Daniel J. Verbaro
- Departments of Chemistry and ‡Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United States
| | - Reinhard Schweitzer-Stenner
- Departments of Chemistry and ‡Biology, Drexel University, 3141 Chestnut
Street, Philadelphia, Pennsylvania 19104, United States
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37
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Xu N, Chingin K, Chen H. Ionic strength of electrospray droplets affects charging of DNA oligonucleotides. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:103-107. [PMID: 24446269 DOI: 10.1002/jms.3311] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/12/2013] [Accepted: 11/14/2013] [Indexed: 06/03/2023]
Abstract
The fundamental aspects of charging in electrospray ionization (ESI) are hotly debated. In the present study, ESI charging of DNA oligonucleotides was explored in both positive (ESI+) and negative (ESI-) polarity using mass spectrometry detection. Single-stranded 12-mer CCCCAATTCCCC in buffer solution (aqueous NH4Ac, 100 mM) produced similar charge state distribution (CSD) in either ESI+ or ESI-. Similarity of CSD in ESI+ and ESI- was also observed for the double-stranded 12-mer CGCGAATTCGCG. By adding typical low-vapor reagents (e.g. m-nitro benzyl alcohol, m-NBA; sulfolane) into the same buffer solution (<0.5% w/v), both CCCCAATTCCCC and CGCGAATTCGCG revealed strong supercharging (SC) effect in ESI-, while very little or no SC effect was observed in ESI+. With either sulfolane or m-NBA, the CGCGAATTCGCG duplex dissociated into single strands in ESI-. No SC was observed in both ESI+ and ESI- for thermally denatured CGCGAATTCGCG duplex in NH4 Ac buffer without the reagents. These findings are difficult to reconcile with the earlier model, which attributes SC in aqueous buffer solution to the conformational changes of analytes. Our observations suggest that the ionic strength of ESI droplets strongly affects the CSD of biopolymers such as DNA oligonucleotides and that SC effect is related to the depletion of ionic strength during the ESI process.
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Affiliation(s)
- Ning Xu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China Institute of Technology, Nanchang, 330013, P.R. China
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38
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Schwalbe M, Ozenne V, Bibow S, Jaremko M, Jaremko L, Gajda M, Jensen MR, Biernat J, Becker S, Mandelkow E, Zweckstetter M, Blackledge M. Predictive atomic resolution descriptions of intrinsically disordered hTau40 and α-synuclein in solution from NMR and small angle scattering. Structure 2013; 22:238-49. [PMID: 24361273 DOI: 10.1016/j.str.2013.10.020] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/22/2022]
Abstract
The development of molecular descriptions of intrinsically disordered proteins (IDPs) is essential for elucidating conformational transitions that characterize common neurodegenerative disorders. We use nuclear magnetic resonance, small angle scattering, and molecular ensemble approaches to characterize the IDPs Tau and α-synuclein. Ensemble descriptions of IDPs are highly underdetermined due to the inherently large number of degrees of conformational freedom compared with available experimental measurements. Using extensive cross-validation we show that five different types of independent experimental parameters are predicted more accurately by selected ensembles than by statistical coil descriptions. The improvement increases in regions whose local sampling deviates from statistical coil, validating the derived conformational description. Using these approaches we identify enhanced polyproline II sampling in aggregation-nucleation sites, supporting suggestions that this region of conformational space is important for aggregation.
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Affiliation(s)
- Martin Schwalbe
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Valéry Ozenne
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Stefan Bibow
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Mariusz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Lukasz Jaremko
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michal Gajda
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Malene Ringkjøbing Jensen
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Jacek Biernat
- CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Eckhard Mandelkow
- CEASAR Research Center, 53175 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany
| | - Markus Zweckstetter
- Department of NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany; Center for the Molecular Physiology of the Brain, University Medical Center, 37073 Göttingen, Germany.
| | - Martin Blackledge
- University Grenoble Alpes, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CNRS, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France; CEA, DSV, Protein Dynamics and Flexibility, Institut de Biologie Structurale, 38000 Grenoble, France.
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39
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Jiang F, Han W, Wu YD. The intrinsic conformational features of amino acids from a protein coil library and their applications in force field development. Phys Chem Chem Phys 2013; 15:3413-28. [PMID: 23385383 DOI: 10.1039/c2cp43633g] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The local conformational (φ, ψ, χ) preferences of amino acid residues remain an active research area, which are important for the development of protein force fields. In this perspective article, we first summarize spectroscopic studies of alanine-based short peptides in aqueous solution. While most studies indicate a preference for the P(II) conformation in the unfolded state over α and β conformations, significant variations are also observed. A statistical analysis from various coil libraries of high-resolution protein structures is then summarized, which gives a more coherent view of the local conformational features. The φ, ψ, χ distributions of the 20 amino acids have been obtained from a protein coil library, considering both backbone and side-chain conformational preferences. The intrinsic side-chain χ(1) rotamer preference and χ(1)-dependent Ramachandran plot can be generally understood by combining the interaction of the side-chain Cγ/Oγ atom with two neighboring backbone peptide groups. Current all-atom force fields such as AMBER ff99sb-ILDN, ff03 and OPLS-AA/L do not reproduce these distributions well. A method has been developed by combining the φ, ψ plot of alanine with the influence of side-chain χ(1) rotamers to derive the local conformational features of various amino acids. It has been further applied to improve the OPLS-AA force field. The modified force field (OPLS-AA/C) reproduces experimental (3)J coupling constants for various short peptides quite well. It also better reproduces the temperature-dependence of the helix-coil transition for alanine-based peptides. The new force field can fold a series of peptides and proteins with various secondary structures to their experimental structures. MD simulations of several globular proteins using the improved force field give significantly less deviation (RMSD) to experimental structures. The results indicate that the local conformational features from coil libraries are valuable for the development of balanced protein force fields.
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Affiliation(s)
- Fan Jiang
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
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40
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Lanza G, Chiacchio MA. Comprehensive and Accurate Ab Initio Energy Surface of Simple Alanine Peptides. Chemphyschem 2013; 14:3284-93. [DOI: 10.1002/cphc.201300445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
| | - Maria A. Chiacchio
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale A. Doria 6, 95125 Catania (Italy)
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41
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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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42
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Rybka K, Toal SE, Verbaro DJ, Mathieu D, Schwalbe H, Schweitzer-Stenner R. Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations. Proteins 2013; 81:968-83. [PMID: 23229867 DOI: 10.1002/prot.24226] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 11/07/2012] [Accepted: 11/21/2012] [Indexed: 11/08/2022]
Abstract
In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides.
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Affiliation(s)
- Karin Rybka
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Goethe-University Frankfurt, Frankfurt/Main, Germany
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43
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Naziga EB, Schweizer F, Wetmore SD. Solvent interactions stabilize the polyproline II conformation of glycosylated oligoprolines. J Phys Chem B 2013; 117:2671-81. [PMID: 23363073 DOI: 10.1021/jp312487v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In nature, proline residues carry several post-translational modifications (PTMs), including 4R hydroxylation and glycosylation. A recent study synthesized contiguously hydroxylated and glycosylated nonaproline peptides and revealed that both PTMs lead to a significant increase in the thermal stability of PPII relative to the unmodified oligoproline. The increased stability of the hydroxylated peptide can be explained by increased stability of the trans isomer due to stereoelectronic effects. However, the effects of glycosylation cannot be completely explained by stereoelectronics since previous experimental results indicate that 4R-glycosylation does not produce observable changes in the trans preference compared to 4R-hydroxylation. We therefore used sophisticated molecular modeling techniques to determine the reason for the further increase in thermal stability upon glycosylation. Free energy estimates obtained from adaptively biased molecular dynamics calculations in implicit (explicit) solvent are -9 kcal mol(-1) (-20 kcal mol(-1)) for the hydroxylated compound and -9 kcal mol(-1) (-46 kcal mol(-1)) for the glycosylated compound, indicating that direct solvent-peptide interactions are vital for explaining the glycosylation effects on PPII stability. Our data reveals for the first time that interactions between the hydroxyl groups in the glycosylated compound and water act in a complementary fashion with stereoelectronic effects to stabilize the PPII conformation in these substituted oligoproline peptides.
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Affiliation(s)
- Emmanuel B Naziga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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44
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Abstract
Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation.
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45
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Mirkin NG, Krimm S. Water interaction differences determine the relative energetic stability of the polyproline II conformation of the alanine dipeptide in aqueous environments. Biopolymers 2012; 97:789-94. [DOI: 10.1002/bip.22064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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46
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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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47
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Schweitzer-Stenner R. Conformational propensities and residual structures in unfolded peptides and proteins. ACTA ACUST UNITED AC 2012; 8:122-33. [DOI: 10.1039/c1mb05225j] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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48
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Carvajal-Rondanelli PA, Marshall SH, Guzman F. Antifreeze glycoprotein agents: structural requirements for activity. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2011; 91:2507-2510. [PMID: 21725975 DOI: 10.1002/jsfa.4473] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 04/07/2011] [Accepted: 04/09/2011] [Indexed: 05/31/2023]
Abstract
Antifreeze glycoproteins (AFGPs) are considered to be the most efficient means to reduce ice damage to cell tissues since they are able to inhibit growth and crystallization of ice. The key element of antifreeze proteins is to act in a non-colligative manner which allows them to function at concentrations 300-500 times lowers than other dissolved solutes. During the past decade, AFGPs have demonstrated tremendous potential for many pharmaceutical and food applications. Presently, the only route to obtain AFGPs involves the time consuming and expensive process of isolation and purification from deep-sea polar fishes. Unfortunately, it is not amenable to mass production and commercial applications. The lack of understanding of the mechanism through which the AFGPs inhibit ice growth has also hampered the realization of industrial and biotechnological applications. Here we report the structural motifs that are essential for antifreeze activity of AFGPs, and propose a unified mechanism based on both recent studies of short alanine peptides and structure activity relationship of synthesized AFGPs.
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49
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Li W, Qin M, Tie Z, Wang W. Effects of solvents on the intrinsic propensity of peptide backbone conformations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:041933. [PMID: 22181201 DOI: 10.1103/physreve.84.041933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 09/16/2011] [Indexed: 05/31/2023]
Abstract
We investigated the effects of solvents on the intrinsic propensity of peptide backbone conformations based on molecular dynamics simulations. The results show that compared with pure water, aqueous urea decreases the helix propensity. In comparison, methanol decreases the polyproline II (PPII) propensity. Such a solvent dependence of the intrinsic propensity of the backbone conformation is correlated with the solvent dependence of the hydration of the backbone groups and the formation probability of the local intrapeptide hydrogen bonds. Aqueous urea which has low ability to stabilize the local intrapeptide hydrogen bonds disfavors the helical conformation. Whereas, methanol which has low ability to hydrate the backbone groups disfavors the polyproline II conformation. In addition, the solvent effects can be further modulated by the side chains of the peptides. The solvent effects of the intrinsic propensity of peptide backbone conformations observed in this work suggest that changing the intrinsic propensity of the protein backbone conformations can partly contribute to the solvent-induced protein structure and dynamics variations. These results will be useful in understanding the solvent dependence of the conformational distributions of the unfolded proteins or peptides (or intrinsically disordered proteins) in which the global tertiary interactions are less important than that in the well-folded proteins.
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Affiliation(s)
- Wenfei Li
- National Laboratory of Solid State Microstructure, and Department of Physics, Nanjing University, Nanjing 210093, China
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50
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Kim SY, Jung Y, Hwang GS, Han H, Cho M. Phosphorylation alters backbone conformational preferences of serine and threonine peptides. Proteins 2011; 79:3155-65. [PMID: 21989936 DOI: 10.1002/prot.23148] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 07/13/2011] [Accepted: 07/14/2011] [Indexed: 11/11/2022]
Abstract
Despite the notion that a control of protein function by phosphorylation works mainly by inducing its conformational changes, the phosphorylation effects on even small peptide conformation have not been fully understood yet. To study its possible effects on serine and threonine peptide conformations, we recently carried out pH- and temperature-dependent circular dichroism (CD) as well as (1)H NMR studies of the phosphorylated serine and threonine peptides and compared them with their unphosphorylated analogs. In the present article, by performing the self-consistent singular value decomposition analysis of the temperature-dependent CD spectra and by analyzing the (3)J(H(N),H(α)) coupling constants extracted from the NMR spectra, the populations of the polyproline II (PPII) and β-strand conformers of the phosphorylated Ser and Thr peptides are determined. As temperature is increased, the β-strand populations of both phosphorylated serine and threonine peptides increase. However, the dependences of PPII/β-strand population ratio on pH are different for these two cases. The phosphorylation of the serine peptide enhances the PPII propensity, whereas that of the threonine peptide has the opposite effect. This suggests that the serine and threonine phosphorylations can alter the backbone conformational propensity via direct but selective intramolecular hydrogen-bonding interactions with the peptide N--H groups. This clearly indicates that the phosphoryl group actively participates in modulating the peptide backbone conformations.
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Affiliation(s)
- Su-Yeon Kim
- Department of Chemistry, Korea University, Seoul 136-701, Korea
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