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Pham TL, Thomas F. Design of Functional Globular β-Sheet Miniproteins. Chembiochem 2024; 25:e202300745. [PMID: 38275210 DOI: 10.1002/cbic.202300745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
The design of discrete β-sheet peptides is far less advanced than e. g. the design of α-helical peptides. The reputation of β-sheet peptides as being poorly soluble and aggregation-prone often hinders active design efforts. Here, we show that this reputation is unfounded. We demonstrate this by looking at the β-hairpin and WW domain. Their structure and folding have been extensively studied and they have long served as model systems to investigate protein folding and folding kinetics. The resulting fundamental understanding has led to the development of hyperstable β-sheet scaffolds that fold at temperatures of 100 °C or high concentrations of denaturants. These have been used to design functional miniproteins with protein or nucleic acid binding properties, in some cases with such success that medical applications are conceivable. The β-sheet scaffolds are not always completely rigid, but can be specifically designed to respond to changes in pH, redox potential or presence of metal ions. Some engineered β-sheet peptides also exhibit catalytic properties, although not comparable to those of natural proteins. Previous reviews have focused on the design of stably folded and non-aggregating β-sheet sequences. In our review, we now also address design strategies to obtain functional miniproteins from β-sheet folding motifs.
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Affiliation(s)
- Truc Lam Pham
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Truc Lam Pham, Prof. Dr. Franziska Thomas, Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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2
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Marshall LK, Fahrenbach AC, Thordarson P. RNA-Binding Peptides Inspired by the RNA Recognition Motif. ACS Chem Biol 2024; 19:243-248. [PMID: 38314708 DOI: 10.1021/acschembio.3c00694] [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: 02/07/2024]
Abstract
β-Hairpin peptides with RNA-binding sequences mimicking the central two β-strands of the RNA recognition motif (RRM) protein domain have been observed to bind in a 2:1 fashion to a series of RNA homooligonucleotides in aqueous solution (PBS buffer, pH 7.40) with binding energies (-27 to -35 kJ mol-1) similar to those of full-size protein RRMs. The peptides display mild selectivities with respect to the binding of the different homooligomers. Binding studies in 500 mM magnesium chloride suggest that the complex formation is not predominantly driven by Coulombic attraction. These peptides represent a starting point for further studies of non-Coulombic binding of RNA by peptides and proteins, which is important in the context of contemporary biology, potential therapeutic applications, and prebiotic peptide-RNA interactions.
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3
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Richaud AD, Mandal S, Das A, Roche SP. Tunable CH/π Interactions within a Tryptophan Zipper Motif to Stabilize the Fold of Long β-Hairpin Peptides. ACS Chem Biol 2023; 18:2555-2563. [PMID: 37976523 DOI: 10.1021/acschembio.3c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The tryptophan zipper (Trpzip) is an iconic folding motif of β-hairpin peptides capitalizing on two pairs of cross-strand tryptophans, each stabilized by an aromatic-aromatic stacking in an edge-to-face (EtF) geometry. Yet, the origins and the contribution of this EtF packing to the unique Trpzip stability remain poorly understood. To address this question of structure-stability relationship, a library of Trpzip hairpins was developed by incorporating readily accessible nonproteinogenic tryptophans of varying electron densities. We found that each EtF geometry was, in fact, stabilized by an intricate combination of XH/π interactions. By tuning the π-electron density of Trpface rings, CH/π interactions are strengthened to gain additional stability. On the contrary, our DFT calculations support the notion that Trpedge modulations are challenging due to their simultaneous paradoxical engagement as H-bond donors in CH/π and acceptors in NH/π interactions.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Pashan, Pune 411008, India
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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4
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Wang Q, Xu Q, Wang H, Han B, Xia D, Wang D, Zhang W. Molecular mechanisms of interaction between enzymes and Maillard reaction products formed from thermal hydrolysis pretreatment of waste activated sludge. WATER RESEARCH 2021; 206:117777. [PMID: 34688093 DOI: 10.1016/j.watres.2021.117777] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Thermal hydrolysis pretreatment (THP) is often used to improve the anaerobic digestion performance of waste activated sludge (WAS) in wastewater treatment plants (WWTPs). During the THP process, the proteins and polysaccharides in the biomass will undergo hydrolysis and Maillard reaction, producing biorefractory organic substances, such as recalcitrant dissolved organic nitrogen (rDON) and melanoidins. In this study, a series of spectroscopy methods were used to quantitatively analyze the Maillard reaction of glucose and lysine, and the interaction mechanisms of the Maillard reaction products (MRPs) and lysozyme were investigated. Results showed that the typical aromatic heterocyclic structures in MRPs, such as pyrazine and furan, were found to quench molecular fluorescence of lysozyme, resulting in an unfolding of standard protein structure and increase in lysozyme hydrophobicity. Significant loss of enzyme activity was detected during this process. Thermodynamic parameters obtained from isothermal titration calorimetry (ITC) confirmed that the interaction between MRPs and lysozyme occurred both exothermically and spontaneously. Density functional theory (DFT) calculations suggested that the molecular interactions of MRPs and protein included parallel dislocation aromatic stacking, T-shaped vertical aromatic stacking, H-bond and H-bond coupled to aromatic stacking.
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Affiliation(s)
- Qiandi Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qiongying Xu
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Huidi Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Bo Han
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 430074, Hubei, China
| | - Dasha Xia
- Hangzhou Yanqu Information Technology Co., Ltd., Hangzhou, 310012, China
| | - Dongsheng Wang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China; Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Weijun Zhang
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, Hubei, China.
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5
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Richaud AD, Zhao G, Hobloss S, Roche SP. Folding in Place: Design of β-Strap Motifs to Stabilize the Folding of Hairpins with Long Loops. J Org Chem 2021; 86:13535-13547. [PMID: 34499510 PMCID: PMC8576641 DOI: 10.1021/acs.joc.1c01442] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite their pivotal role in defining antibody affinity and protein function, β-hairpins harboring long noncanonical loops remain synthetically challenging because of the large entropic penalty associated with their conformational folding. Little is known about the contribution and impact of stabilizing motifs on the folding of β-hairpins with loops of variable length and plasticity. Here, we report a design of minimalist β-straps (strap = strand + cap) that offset the entropic cost of long-loop folding. The judicious positioning of noncovalent interactions (hydrophobic cluster and salt-bridge) within the novel 8-mer β-strap design RW(V/H)W···WVWE stabilizes hairpins with up to 10-residue loops of varying degrees of plasticity (Tm up to 52 °C; 88 ± 1% folded at 18 °C). This "hyper" thermostable β-strap outperforms the previous gold-standard technology of β-strand-β-cap (16-mer) and provides a foundation for producing new classes of long hairpins as a viable and practical alternative to macrocyclic peptides.
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Affiliation(s)
- Alexis D Richaud
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Guangkuan Zhao
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Samir Hobloss
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
| | - Stéphane P Roche
- Department of Chemistry and Biochemistry, Florida Atlantic University, Boca Raton, Florida 33431, United States
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6
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Debnath S, Ghosh S, Pandit G, Satpati P, Chatterjee S. Effect of Differential Geminal Substitution of γ Amino Acid Residues at the ( i + 2) Position of αγ Turn Segments on the Conformation of Template β-Hairpin Peptides. J Org Chem 2021; 86:11310-11323. [PMID: 34479402 DOI: 10.1021/acs.joc.1c00351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The effect of insertion of three geminally dimethyl substituted γ amino acid residues [γ2,2 (4-amino-2,2-dimethylbutanoic acid), γ3,3 (4-amino-3,3-dimethylbutanoic acid), and γ4,4 (4-amino-4,4-dimethylbutanoic acid)] at the (i + 2) position of a two-residue αγ C12 turn segment in a model octapeptide sequence Leu-Phe-Val-Aib-Xxx-Leu-Phe-Val (where Xxx = γ amino acid residues) has been investigated in this study. Solution conformational studies (NMR, CD, and IR) and ab initio calculations indicated that γ3,3 and γ4,4 residues were well accommodated in the β-hairpin nucleating αγ C12 turns, which gave rise to well-registered hairpins, in contrast to γ2,2, which was unable to form a tight C12 β-hairpin nucleating turn and promote a well-registered β-hairpin. Geminal disubstitution at the Cα carbon in γ2,2 led to unfavorable steric contacts, disabling its accommodation in the αγ C12 hairpin nucleating turn unlike the γ3,3 and γ4,4 residues. Geminal substitutions at different carbons along the backbone constrained backbone torsion angles for the three γ amino acid residues differently, generating diverse conformational preferences in them. Folded hairpins were energetically more stable (∼8 to 9 kcal/mol) than the unfolded peptides. Conformational preference of the peptides was independent of the N-terminal protecting group. Such fundamental understanding will instrumentalize the future directed design of foldamers.
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Affiliation(s)
- Swapna Debnath
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Suvankar Ghosh
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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7
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Krumm ZA, Lloyd GM, Francis CP, Nasif LH, Mitchell DA, Golde TE, Giasson BI, Xia Y. Precision therapeutic targets for COVID-19. Virol J 2021; 18:66. [PMID: 33781287 PMCID: PMC8006140 DOI: 10.1186/s12985-021-01526-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/04/2021] [Indexed: 01/18/2023] Open
Abstract
Beginning in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a novel pathogen that causes coronavirus disease 2019 (COVID-19). SARS-CoV-2 has infected more than 111 million people worldwide and caused over 2.47 million deaths. Individuals infected with SARS-CoV-2 show symptoms of fever, cough, dyspnea, and fatigue with severe cases that can develop into pneumonia, myocarditis, acute respiratory distress syndrome, hypercoagulability, and even multi-organ failure. Current clinical management consists largely of supportive care as commonly administered treatments, including convalescent plasma, remdesivir, and high-dose glucocorticoids. These have demonstrated modest benefits in a small subset of hospitalized patients, with only dexamethasone showing demonstrable efficacy in reducing mortality and length of hospitalization. At this time, no SARS-CoV-2-specific antiviral drugs are available, although several vaccines have been approved for use in recent months. In this review, we will evaluate the efficacy of preclinical and clinical drugs that precisely target three different, essential steps of the SARS-CoV-2 replication cycle: the spike protein during entry, main protease (MPro) during proteolytic activation, and RNA-dependent RNA polymerase (RdRp) during transcription. We will assess the advantages and limitations of drugs that precisely target evolutionarily well-conserved domains, which are less likely to mutate, and therefore less likely to escape the effects of these drugs. We propose that a multi-drug cocktail targeting precise proteins, critical to the viral replication cycle, such as spike protein, MPro, and RdRp, will be the most effective strategy of inhibiting SARS-CoV-2 replication and limiting its spread in the general population.
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Affiliation(s)
- Zachary A Krumm
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Grace M Lloyd
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Connor P Francis
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32610, USA
- UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Lith H Nasif
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Duane A Mitchell
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, FL, 32610, USA
- UF Clinical and Translational Science Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Todd E Golde
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Benoit I Giasson
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
- College of Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Yuxing Xia
- Department of Neuroscience, College of Medicine, University of Florida, 1275 Center Drive, Gainesville, FL, 32610, USA.
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, 32610, USA.
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8
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Surfactant-like peptides: From molecular design to controllable self-assembly with applications. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213418] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Bureau HR, Quirk S, Hernandez R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv 2020; 10:6520-6535. [PMID: 35495997 PMCID: PMC9049704 DOI: 10.1039/d0ra00920b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 11/21/2022] Open
Abstract
The single-point mutations of tprzip1 are indicated at left, and their relative energetics are compared at right.
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10
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Structural changes of a simple peptide—Trpzip-1—in aqueous solutions and the corresponding hydration phenomena under the influence of temperature. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Mahalakshmi R. Aromatic interactions in β-hairpin scaffold stability: A historical perspective. Arch Biochem Biophys 2018; 661:39-49. [PMID: 30395808 DOI: 10.1016/j.abb.2018.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/31/2018] [Accepted: 11/01/2018] [Indexed: 01/21/2023]
Abstract
Non-covalent interactions between naturally occurring aromatic residues have been widely exploited as scaffold stabilizing agents in de novo designed peptides and in Nature - inspired structures. Our understanding of the factors driving aromatic interactions and their observed interaction geometries have advanced remarkably with improvements in conventional structural studies, availability of novel molecular methods and in silico studies, which have together provided atomistic information on aromatic interactions and interaction strengths. This review attempts to recapitulate the early advances in our understanding of aromatic interactions as stabilizing agents of peptide β-hairpins.
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Affiliation(s)
- Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462066, India.
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12
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Roussel G, Caudano Y, Matagne A, Sansom MS, Perpète EA, Michaux C. Peptide-surfactant interactions: A combined spectroscopic and molecular dynamics simulation approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:464-470. [PMID: 28961531 DOI: 10.1016/j.saa.2017.09.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 06/07/2023]
Abstract
In the present contribution, we report a combined spectroscopic and computational approach aiming to unravel at atomic resolution the effect of the anionic SDS detergent on the structure of two model peptides, the α-helix TrpCage and the β-stranded TrpZip. A detailed characterization of the specific amino acids involved is performed. Monomeric (single molecules) and micellar SDS species differently interact with the α-helix and β-stranded peptides, emphasizing the different mechanisms occurring below and above the critical aggregation concentration (CAC). Below the CAC, the α-helix peptide is fully unfolded, losing its hydrophobic core and its Asp-Arg salt bridge, while the β-stranded peptide keeps its native structure with its four Trp well oriented. Above the CAC, the SDS micelles have the same effect on both peptides, that is, destabilizing the tertiary structure while keeping their secondary structure. Our studies will be helpful to deepen our understanding of the action of the denaturant SDS on peptides and proteins.
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Affiliation(s)
- Guillaume Roussel
- Department of Physiology and Biophysics, University of California, D340 Medical Sciences I, Irvine, CA 92697-4560, USA
| | - Yves Caudano
- Research Centre in Physics of Matter and Radiation (PMR), University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium
| | - André Matagne
- Laboratory of Enzymology and Protein Folding, Centre for Protein Engineering, Institut de Chimie B6, University of Liège, Belgium
| | - Mark S Sansom
- Department of Biochemistry, University of Oxford, South Park Road, OX13QU Oxford, United Kingdom
| | - Eric A Perpète
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium
| | - Catherine Michaux
- Laboratory of Physical Chemistry of Biomolecules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, 61, Rue de Bruxelles, 5000 Namur, Belgium.
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13
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Vaissière A, Aldrian G, Konate K, Lindberg MF, Jourdan C, Telmar A, Seisel Q, Fernandez F, Viguier V, Genevois C, Couillaud F, Boisguerin P, Deshayes S. A retro-inverso cell-penetrating peptide for siRNA delivery. J Nanobiotechnology 2017; 15:34. [PMID: 28454579 PMCID: PMC5410048 DOI: 10.1186/s12951-017-0269-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/17/2017] [Indexed: 01/28/2023] Open
Abstract
Background Small interfering RNAs (siRNAs) are powerful tools to control gene expression. However, due to their poor cellular permeability and stability, their therapeutic development requires a specific delivery system. Among them, cell-penetrating peptides (CPP) have been shown to transfer efficiently siRNA inside the cells. Recently we developed amphipathic peptides able to self-assemble with siRNAs as peptide-based nanoparticles and to transfect them into cells. However, despite the great potential of these drug delivery systems, most of them display a low resistance to proteases. Results Here, we report the development and characterization of a new CPP named RICK corresponding to the retro-inverso form of the CADY-K peptide. We show that RICK conserves the main biophysical features of its L-parental homologue and keeps the ability to associate with siRNA in stable peptide-based nanoparticles. Moreover the RICK:siRNA self-assembly prevents siRNA degradation and induces inhibition of gene expression. Conclusions This new approach consists in a promising strategy for future in vivo application, especially for targeted anticancer treatment (e.g. knock-down of cell cycle proteins).RICK-based nanoparticles: RICK peptides and siRNA self-assemble in peptide-based nanoparticles to penetrate into the cells and to induce target protein knock-down. ![]() Electronic supplementary material The online version of this article (doi:10.1186/s12951-017-0269-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anaïs Vaissière
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Gudrun Aldrian
- Sys2Diag, UMR 9005-CNRS/ALCEDIAG, 1682 Rue de la Valsiere, 34184, Montpellier, France
| | - Karidia Konate
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Mattias F Lindberg
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Carole Jourdan
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Anthony Telmar
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Quentin Seisel
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Frédéric Fernandez
- Microscopie Électronique et Analytique, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Véronique Viguier
- Microscopie Électronique et Analytique, Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Coralie Genevois
- EA 7435 IMOTION (Imagerie moléculaire et thérapies innovantes en oncologie), Université de Bordeaux, 146 rue Leo Saignat, 33076, Bordeaux, France
| | - Franck Couillaud
- EA 7435 IMOTION (Imagerie moléculaire et thérapies innovantes en oncologie), Université de Bordeaux, 146 rue Leo Saignat, 33076, Bordeaux, France
| | - Prisca Boisguerin
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France
| | - Sébastien Deshayes
- Centre de Recherche de Biologie cellulaire de Montpellier, UMR 5237 CNRS, 1919 Route de Mende, 34293, Montpellier, France.
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Chi H, Keiderling TA. Structural Rearrangement from Oligomer to Fibril Detected with FRET in a Designed Amphiphilic Peptide. Chembiochem 2016; 18:195-205. [DOI: 10.1002/cbic.201600436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Heng Chi
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
- Department of Pharmacy; Jiangsu Food and Pharmaceutical Science College; 4 E. Meicheng Rd. Huai'an Jiangsu Province 223005 China
| | - Timothy A. Keiderling
- Department of Chemistry (M/C 111); University of Illinois at Chicago; 845 W. Taylor Street Chicago IL 60607 USA
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15
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Anderson JM, Kier BL, Jurban B, Byrne A, Shu I, Eidenschink LA, Shcherbakov AA, Hudson M, Fesinmeyer RM, Andersen NH. Aryl-aryl interactions in designed peptide folds: Spectroscopic characteristics and optimal placement for structure stabilization. Biopolymers 2016; 105:337-356. [PMID: 26850220 PMCID: PMC5638712 DOI: 10.1002/bip.22821] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 01/27/2023]
Abstract
We have extended our studies of Trp/Trp to other Aryl/Aryl through-space interactions that stabilize hairpins and other small polypeptide folds. Herein we detail the NMR and CD spectroscopic features of these types of interactions. NMR data remains the best diagnostic for characterizing the common T-shape orientation. Designated as an edge-to-face (EtF or FtE) interaction, large ring current shifts are produced at the edge aryl ring hydrogens and, in most cases, large exciton couplets appear in the far UV circular dichroic (CD) spectrum. The preference for the face aryl in FtE clusters is W ≫ Y ≥ F (there are some exceptions in the Y/F order); this sequence corresponds to the order of fold stability enhancement and always predicts the amplitude of the lower energy feature of the exciton couplet in the CD spectrum. The CD spectra for FtE W/W, W/Y, Y/W, and Y/Y pairs all include an intense feature at 225-232 nm. An additional couplet feature seen for W/Y, W/F, Y/Y, and F/Y clusters, is a negative feature at 197-200 nm. Tyr/Tyr (as well as F/Y and F/F) interactions produce much smaller exciton couplet amplitudes. The Trp-cage fold was employed to search for the CD effects of other Trp/Trp and Trp/Tyr cluster geometries: several were identified. In this account, we provide additional examples of the application of cross-strand aryl/aryl clusters for the design of stable β-sheet models and a scale of fold stability increments associated with all possible FtE Ar/Ar clusters in several structural contexts. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 337-356, 2016.
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Affiliation(s)
- Jordan M Anderson
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Brandon L Kier
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Aimee Byrne
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | | | | | - Mike Hudson
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - R M Fesinmeyer
- Department of Chemistry, University of Washington, Seattle, WA, 98195
| | - Niels H Andersen
- Department of Chemistry, University of Washington, Seattle, WA, 98195
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16
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Makwana KM, Mahalakshmi R. Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed β-Hairpins. Chemistry 2016; 22:4147-56. [DOI: 10.1002/chem.201504428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/15/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory; Department of Biological Sciences; Indian Institute of Science Education and Research, Bhopal; 462023 Madhya Pradesh India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory; Department of Biological Sciences; Indian Institute of Science Education and Research, Bhopal; 462023 Madhya Pradesh India
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17
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Popp A, Scheerer D, Chi H, Keiderling TA, Hauser K. Site‐Specific Dynamics of β‐Sheet Peptides with
D
Pro–Gly Turns Probed by Laser‐Excited Temperature‐Jump Infrared Spectroscopy. Chemphyschem 2016; 17:1273-80. [DOI: 10.1002/cphc.201501089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Popp
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
| | - David Scheerer
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
| | - Heng Chi
- Department of Pharmacy and Health Management Jiangsu Food and Pharmaceutical Science College 4 E. Meicheng Rd. Huai'an Jiangsu Province 223003 P. R. China
| | - Timothy A. Keiderling
- Department of Chemistry University of Illinois at Chicago 845 W. Taylor St. Chicago Illinois 60607-7061 USA
| | - Karin Hauser
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
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18
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Madhusudan Makwana K, Mahalakshmi R. Implications of aromatic-aromatic interactions: From protein structures to peptide models. Protein Sci 2015; 24:1920-33. [PMID: 26402741 DOI: 10.1002/pro.2814] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 09/17/2015] [Accepted: 09/18/2015] [Indexed: 12/11/2022]
Abstract
With increasing structural information on proteins, the opportunity to understand physical forces governing protein folding is also expanding. One of the significant non-covalent forces between the protein side chains is aromatic-aromatic interactions. Aromatic interactions have been widely exploited and thoroughly investigated in the context of folding, stability, molecular recognition, and self-assembly processes. Through this review, we discuss the contribution of aromatic interactions to the activity and stability of thermophilic, mesophilic, and psychrophilic proteins. Being hydrophobic, aromatic amino acids tend to reside in the protein hydrophobic interior or transmembrane segments of proteins. In such positions, it can play a diverse role in soluble and membrane proteins, and in α-helix and β-sheet stabilization. We also highlight here some excellent investigations made using peptide models and several approaches involving aryl-aryl interactions, as an increasingly popular strategy in protein and peptide engineering. A recent survey described the existence of aromatic clusters (trimer, tetramer, pentamer, and higher order assemblies), revealing the self-associating property of aryl groups, even in folded protein structures. The application of this self-assembly of aromatics in the generation of modern bionanomaterials is also discussed.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, 462023, India
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19
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Xu L, Chou S, Wang J, Shao C, Li W, Zhu X, Shan A. Antimicrobial activity and membrane-active mechanism of tryptophan zipper-like β-hairpin antimicrobial peptides. Amino Acids 2015; 47:2385-97. [PMID: 26088720 DOI: 10.1007/s00726-015-2029-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/10/2015] [Indexed: 11/24/2022]
Abstract
Antimicrobial peptides (AMPs) with amphipathic β-hairpin structures have been demonstrated to possess potent antimicrobial activities and great cell selectivities. However, our understanding of β-hairpin antimicrobial peptides lags behind that of α-helices, mainly because it is difficult for short peptides to form robust β-hairpin structures. Tryptophan zipper (trpzip) peptides are among the most stable β-hairpin peptides known to fold spontaneously without requiring covalent disulfide constraint or metal binding. To develop model β-hairpin AMPs with small size and remarkable stability, a series of amphiphilic linear peptides were designed based on the trpzip motif. The sequence of designed peptides is (WK) n (D) PG(KW) n -NH2 (n = 1, 2, 3, 4, 5), and the antimicrobial activity and membrane interaction mechanism of the peptides were evaluated. The results showed that these peptides readily fold into β-hairpin structures in aqueous and membrane-mimicking environments and exhibit broad-spectrum antimicrobial activities against both gram-positive and gram-negative bacteria. The antibacterial potency of the peptides initially increased and then decreased with increasing chain length. WK3, a 14-residue peptide, displayed excellent antimicrobial activity with minimal hemolytic activity and cytotoxicity, suggesting that it possesses great cell selectivity. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), fluorescence spectroscopy, and flow cytometry indicated that representative peptides WK3 and WK4 exert their activities by permeabilizing the microbial membrane and damaging cell membrane integrity. This study reveals the application potential of the designed peptides as promising antimicrobial agents for the control of infectious diseases, and it also provides new insights into the design and optimization of highly stable β-hairpin AMPs with great antimicrobial activities and cell selectivities.
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Affiliation(s)
- Lin Xu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.,Heilongjiang Polytechnic, 5 Xuefu Road, Harbin, 150080, China
| | - Shuli Chou
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Jiajun Wang
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Changxuan Shao
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Weizhong Li
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Xin Zhu
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, 59 Mucai Street, Harbin, 150030, China.
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20
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Martínez L, Martorell G, Sampedro Á, Ballester P, Costa A, Rotger C. Hydrogen Bonded Squaramide-Based Foldable Module Induces Both β- and α-Turns in Hairpin Structures of α-Peptides in Water. Org Lett 2015; 17:2980-3. [DOI: 10.1021/acs.orglett.5b01268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | - Pablo Ballester
- Institut of Chemical Research of Catalonia (ICIQ), Avda. Països Catalans 16, 43007 Tarragona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig Lluís Compays 23, 08010 Barcelona, Spain
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21
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Pachahara SK, Nagaraj R. Probing the role of aromatic residues in the self-assembly of Aβ(16-22) in fluorinated alcohols and their aqueous mixtures. Biochem Biophys Rep 2015; 2:1-13. [PMID: 29124140 PMCID: PMC5668628 DOI: 10.1016/j.bbrep.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 11/19/2022] Open
Abstract
The Aβ(16–22) sequence KLVFFAE spans the hydrophobic core of the Aβ peptide and plays an important role in its self-assembly. Apart from forming amyloid fibrils, Aβ(16–22) can self-associate into highly ordered nanotubes and ribbon-like structures depending on the composition of solvent used for dissolution. The Aβ(16–22) sequence which has FF at the 19th and 20th positions would be a good model to investigate peptide self-assembly in the context of aromatic interactions. In this study, self-assembly of Aβ(16–22) and its aromatic analogs obtained by replacement of F19, F20 or both by Y or W was examined after dissolution in fluorinated alcohols and their aqueous mixtures in solvent cluster forming conditions. The results indicate that the presence of aromatic residues Y and W and their position in the sequence plays an important role in self-assembly. We observe the formation of amyloid fibrils and other self-assembled structures such as spheres, rings and beads. Our results indicate that 20% HFIP is more favourable for amyloid fibril formation as compared to 20% TFE, when F is replaced with Y or W. The dissolution of peptides in DMSO followed by evaporation of solvent and dissolution in water appears to greatly influence peptide conformation, morphology and cross-β content of self-assembled structures. Our study shows that positioning of aromatic residues F, Y and W have an important role in directing self-assembly of the peptides. Effect of fluorinated alcohols on the aggregation of Aβ(16–22) and analogs was investigated. Replacement of F by Y and W in the Aβ(16–22) sequence modulates self-assembly. Positions of F, Y, W in Aβ(16–22) plays an important role in self-assembly.
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22
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Makwana KM, Mahalakshmi R. NMR Analysis of Tuning Cross-Strand Phe/Tyr/Trp-Trp Interactions in Designed β-Hairpin Peptides: Terminal Switch from L to D Amino Acid as a Strategy for β-Hairpin Capping. J Phys Chem B 2015; 119:5376-85. [PMID: 25849307 DOI: 10.1021/acs.jpcb.5b00554] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Interaction among the side chains of aromatic amino acids is a well-known mechanism of protein and peptide structure stabilization, particularly in β sheets. Using short β-hairpin models bearing the sequence Ac-Leu-Xxx-Val-DPro-Gly-Leu-Trp-Val-NH2, we report the surprising observation of significant destabilization in aryl–tryptophan interactions, which results in poorly folded peptide populations accompanied by lowering of stability. We find that such destabilization arises from forced occupancy of the indole ring in the shielded Edge position, in T-shaped aryl geometries. We demonstrate that this destabilizing effect can be efficiently salvaged by replacing the N-terminal LLeu with DLeu, which causes an increase in the folded hairpin population, while retaining Trp in the Edge position. Our observation of unique cross strand NOEs and data from temperature-dependent NMR and CD measurements reveals the formation of a locally stabilized aliphatic–aromatic network, leading to an overall increase in ΔGF° by ∼ −0.6 to −1.2 kcal/mol. Our results suggest that a contextual evaluation of stabilization by tryptophan is necessary in β hairpins. Furthermore, we report for the first time that the use of D isomers of aliphatic amino acids at the terminus is stabilizing, which can serve as a new strategy for increasing β-hairpin stability.
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Affiliation(s)
- Kamlesh M Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal 462023, India
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23
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Nicholas S. The peptide NCbz-Val-Tyr-OMe and aromatic π-π interactions. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2015; 71:211-5. [PMID: 25734852 DOI: 10.1107/s2053229615002739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/09/2015] [Indexed: 11/10/2022]
Abstract
The peptide N-benzyloxycarbonyl-L-valyl-L-tyrosine methyl ester or NCbz-Val-Tyr-OMe (where NCbz is N-benzyloxycarbonyl and OMe indicates the methyl ester), C(23)H(28)N(2)O(6), has an extended backbone conformation. The aromatic rings of the Tyr residue and the NCbz group are involved in various attractive intra- and intermolecular aromatic π-π interactions which stabilize the conformation and packing in the crystal structure, in addition to N-H...O and O-H...O hydrogen bonds. The aromatic π-π interactions include parallel-displaced, perpendicular T-shaped, perpendicular L-shaped and inclined orientations.
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Affiliation(s)
- Sumesh Nicholas
- Department of Physics, Indian Institute of Science, Bangalore, Karnataka 560 012, India
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24
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Gasymov OK, Abduragimov AR, Glasgow BJ. Double tryptophan exciton probe to gauge proximal side chains in proteins: augmentation at low temperature. J Phys Chem B 2015; 119:3962-8. [PMID: 25693116 DOI: 10.1021/jp512864s] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The circular dichroic (CD) exciton couplet between tryptophans and/or tyrosines offers the potential to probe distances within 10 Å in proteins. The exciton effect has been used with native chromophores in critical positions in a few proteins. Here, site-directed mutagenesis created double tryptophan probes for key sites of a protein (tear lipocalin). For tear lipocalin, the crystal and solution structures are concordant in both apo- and holo-forms. Double tryptophan substitutions were performed at sites that could probe conformation and were likely within 10 Å. Far-UV CD spectra of double Trp mutants were performed with controls that had noninteracting substituted tryptophans. Low temperature (77 K) was tested for augmentation of the exciton signal. Exciton coupling appeared with tryptophan substitutions at positions within loop A-B (28 and 31, 33), between loop A-B (28) and strand G (103 and 105), as well as between the strands B (35) and C (56). The CD exciton couplet signals were amplified 3-5-fold at 77 K. The results were concordant with close distances in crystal and solution structures. The exciton couplets had functional significance and correctly assigned the holo-conformation. The methodology creates an effective probe to identify proximal amino acids in a variety of motifs.
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Affiliation(s)
- Oktay K Gasymov
- Departments of Pathology and Ophthalmology and Jules Stein Eye Institute, University California at Los Angeles , Los Angeles, California 90095, United States
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25
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Popp A, Wu L, Keiderling TA, Hauser K. Effect of hydrophobic interactions on the folding mechanism of β-hairpins. J Phys Chem B 2014; 118:14234-42. [PMID: 25393957 DOI: 10.1021/jp506658x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrophobic interactions are essential in stabilizing protein structures. How they affect the folding pathway and kinetics, however, is less clear. We used time-resolved infrared spectroscopy to study the dynamics of hydrophobic interactions of β-hairpin variants of the sequence Trpzip2 (SWTWENGKWTWK-NH2) that is stabilized by two cross-strand Trp-Trp pairs. The hydrophobicity strength was varied by substituting the tryptophans pairwise by either tyrosines or valines. Relaxation dynamics were induced by a laser-excited temperature jump, which separately probed for the loss of the cross-strand β-hairpin interaction and the rise of the disordered structure. All substitutions tested result in reduced thermal stability, lower transition temperatures, and faster dynamics compared to Trpzip2. However, the changes in folding dynamics depend on the amino acid substituted for Trp. The aromatic substitution of Tyr for Trp results in the same kinetics for the unfolding of sheet and growth of disorder, with similar activation energies, independent of the substitution position. Substitution of Trp with a solely hydrophobic Val results in even faster kinetics than substitution with Tyr but is additionally site-dependent. If the hairpin has a Val pair close to its termini, the rate constants for loss of sheet and gain of disorder are the same, but if the pair is close to the turn, the sheet and disorder components show different relaxation kinetics. The Trp → Val substitutions reveal that hydrophobic interactions alone weakly stabilize the hairpin structure, but adding edge-to-face aromatic interaction strengthens it, and both modify the complex folding process.
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Affiliation(s)
- Alexander Popp
- Biophysical Chemistry, Department of Chemistry, University of Konstanz , 78457 Konstanz, Germany
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26
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Singh PK, Solanki V, Sharma S, Thakur KG, Krishnan B, Korpole S. The intramolecular disulfide-stapled structure of laterosporulin, a class IId bacteriocin, conceals a human defensin-like structural module. FEBS J 2014; 282:203-14. [PMID: 25345978 DOI: 10.1111/febs.13129] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/16/2014] [Accepted: 10/21/2014] [Indexed: 11/27/2022]
Abstract
The growing emergence of antibiotic-resistant bacteria has led to the exploration of naturally occurring defense peptides as antimicrobials. In this study, we found that laterosporulin (LS), a class IId bacteriocin, effectively kills active and nonmultiplying cells of both Gram-positive and Gram-negative bacteria. Fluorescence and electron microscopy suggest that growth inhibition occurs because of increased membrane permeability. The crystal structure of LS at 2.0 Å resolution reveals an all-β conformation of this peptide, with four β-strands forming a twisted β-sheet. All six intrinsic cysteines are intramolecularly disulfide-bonded, with two disulfides constraining the N terminus of the peptide and the third disulfide crosslinking the extreme C terminus, resulting in the formation of a closed structure. The significance of disulfides in maintaining the in-solution peptide structure was confirmed by CD and fluorescence analyses. Despite a low overall sequence similarity, LS has disulfide connectivity [C(I)-C(V), C(II)-C(IV), and C(III)-C(VI)] like that of β-defensins and a striking architectural similarity with α-defensins. Therefore LS presents a missing link between bacteriocins and mammalian defensins, and is also a potential antimicrobial lead, in particular against nonmultiplying bacteria.
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Affiliation(s)
- Pradip Kumar Singh
- Microbial Type Culture Collection & Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
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27
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Markiewicz BN, Oyola R, Du D, Gai F. Aggregation gatekeeper and controlled assembly of Trpzip β-hairpins. Biochemistry 2014; 53:1146-54. [PMID: 24498924 PMCID: PMC3985754 DOI: 10.1021/bi401568a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein and peptide aggregation is an important issue both in vivo and in vitro. Herein, we examine the aggregation behaviors of two well-studied β-hairpins, Trpzip1 and Trpzip2. Previous studies suggested that Trpzip2 remains monomeric up to a concentration of ~15 mM whereas Trpzip1 readily aggregates at micromolar concentrations at acidic or neutral pH. This disparity is puzzling considering that these two peptides differ only in their turn sequences (i.e., GN vs NG). We hypothesize that these peptides can aggregate from their folded states via native edge-to-edge interactions and that the Lys8 residue in Trpzip2 is a more effective aggregation gatekeeper, because of a more favorable orientation. In support of this hypothesis, we find that increasing the pH to 13 or replacing Lys8 with a hydrophobic and photolabile Lys analogue, Lys(nvoc), leads to a significant increase in the aggregation propensity of Trpzip2, and that the aggregation of this Trpzip2 mutant can be reversed upon restoring the native Lys side chain via photocleavage of the nvoc moiety. In addition, we find that while both Trpzip1 and Trpzip2 form parallel β-sheet aggregates, the Lys(nvoc) Trpzip2 mutant forms antiparallel β-sheets and more stable fibrils. Taken together, these findings provide another example showing how sensitive peptide and protein aggregation is to minor sequence variation and that it is possible to use a photolabile non-natural amino acid, such as Lys(nvoc), to tune the rate of peptide aggregation and to control fibrillar structure.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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28
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Makwana KM, Mahalakshmi R. Comparative analysis of cross strand aromatic–Phe interactions in designed peptide β-hairpins. Org Biomol Chem 2014; 12:2053-61. [DOI: 10.1039/c3ob42247j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Examination of the preferential interaction geometries of the aromatic amino acids Phe, Tyr and Trp with the benzyl ring of Phe in designed octapeptide hairpin scaffolds reveals stabilizing contributions of a Trp–Phe pair, even in amphipathic solvents.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory
- Department of Biological Sciences
- Indian Institute of Science Education and Research
- Bhopal, India
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29
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Abstract
Since the first report in 1993 (JACS 115, 5887-5888) of a peptide able to form a monomeric β-hairpin structure in aqueous solution, the design of peptides forming either β-hairpins (two-stranded antiparallel β-sheets) or three-stranded antiparallel β-sheets has become a field of growing interest and activity. These studies have yielded great insights into the principles governing the stability and folding of β-hairpins and antiparallel β-sheets. This chapter provides an overview of the reported β-hairpin/β-sheet peptides focussed on the applied design criteria, reviews briefly the factors contributing to β-hairpin/β-sheet stability, and describes a protocol for the de novo design of β-sheet-forming peptides based on them. Guidelines to select appropriate turn and strand residues and to avoid self-association are provided. The methods employed to check the success of new designed peptides are also summarized. Since NMR is the best technique to that end, NOEs and chemical shifts characteristic of β-hairpins and three-stranded antiparallel β-sheets are given.
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Affiliation(s)
- M Angeles Jiménez
- Consejo Superior de Investigaciones Científicas (CSIC), Instituto de Química Física Rocasolano (IQFR), Serrano 119, 28006, Madrid, Spain,
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30
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Diez-García F, Pantoja-Uceda D, Jiménez MÁ, Chakrabartty A, Laurents DV. Structure of a simplified β-hairpin and its ATP complex. Arch Biochem Biophys 2013; 537:62-71. [PMID: 23811197 DOI: 10.1016/j.abb.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/13/2013] [Accepted: 06/16/2013] [Indexed: 11/29/2022]
Abstract
The capacity of three designed duodecamer peptides with the low diversity sequence: H1ϕ2I3K4I5D6G7K8ϕ9I10K11H12 where ϕ is His, Phe or Trp, to adopt a β-hairpin conformation was studied using NMR spectroscopy. Whereas KIAβH, the variant with His at positions two and nine, is disordered, KIAβF, the peptide with Phe at these positions, adopts a small population of β-hairpin. A high population of β-hairpin structure was detected for KIAβW, the variant with Trp. Utilizing NMR data, the structure of KIAβW was solved and it reveals a β-hairpin stabilized by hydrophobic interactions between Ile residues on one face and Trp-Trp and cation-π interactions on the opposite face. Upon adding ATP, these peptides show chemical shift changes indicative of ATP binding. The binding of ATP to KIAβW shows a KD ≈ 20 μM at pH 5, 5 °C and has a 1:1 stoichiometry. The KIAβW-ATP complex was determined using NMR spectroscopy and reveals the adenine ring sandwiched between the two Trp indole rings and that ATP binding induces important conformational changes in His1, Trp2, Lys4, Trp9 and Lys11 in the β-hairpin. The implications of these results for the hypothetic presence of β-hairpins and amyloids alongside RNAs on the prebiotic Earth are discussed.
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31
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Mendes YS, Alves NS, Souza TLF, Sousa IP, Bianconi ML, Bernardi RC, Pascutti PG, Silva JL, Gomes AMO, Oliveira AC. The structural dynamics of the flavivirus fusion peptide-membrane interaction. PLoS One 2012; 7:e47596. [PMID: 23094066 PMCID: PMC3477123 DOI: 10.1371/journal.pone.0047596] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 09/18/2012] [Indexed: 11/18/2022] Open
Abstract
Membrane fusion is a crucial step in flavivirus infections and a potential target for antiviral strategies. Lipids and proteins play cooperative roles in the fusion process, which is triggered by the acidic pH inside the endosome. This acidic environment induces many changes in glycoprotein conformation and allows the action of a highly conserved hydrophobic sequence, the fusion peptide (FP). Despite the large volume of information available on the virus-triggered fusion process, little is known regarding the mechanisms behind flavivirus-cell membrane fusion. Here, we evaluated the contribution of a natural single amino acid difference on two flavivirus FPs, FLA(G) ((98)DRGWGNGCGLFGK(110)) and FLA(H) ((98)DRGWGNHCGLFGK(110)), and investigated the role of the charge of the target membrane on the fusion process. We used an in silico approach to simulate the interaction of the FPs with a lipid bilayer in a complementary way and used spectroscopic approaches to collect conformation information. We found that both peptides interact with neutral and anionic micelles, and molecular dynamics (MD) simulations showed the interaction of the FPs with the lipid bilayer. The participation of the indole ring of Trp appeared to be important for the anchoring of both peptides in the membrane model, as indicated by MD simulations and spectroscopic analyses. Mild differences between FLA(G) and FLA(H) were observed according to the pH and the charge of the target membrane model. The MD simulations of the membrane showed that both peptides adopted a bend structure, and an interaction between the aromatic residues was strongly suggested, which was also observed by circular dichroism in the presence of micelles. As the FPs of viral fusion proteins play a key role in the mechanism of viral fusion, understanding the interactions between peptides and membranes is crucial for medical science and biology and may contribute to the design of new antiviral drugs.
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Affiliation(s)
- Ygara S. Mendes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Nathalia S. Alves
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Theo L. F. Souza
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ivanildo P. Sousa
- Programa de Vacinas Virais, Instituto de Tecnologia em Imunobiológicos, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - M. Lucia Bianconi
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael C. Bernardi
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro G. Pascutti
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jerson L. Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andre M. O. Gomes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andréa C. Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica, and Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
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32
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Schlamadinger DE, Leigh BS, Kim JE. UV resonance Raman study of TrpZip2 and related peptides: π-π interactions of tryptophan. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2012; 43:1459-1464. [PMID: 25525290 PMCID: PMC4267580 DOI: 10.1002/jrs.4061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high-resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β-hairpin peptide that is stabilized by edge-to-face and face-to-face tryptophan π-π interactions. The vibrational markers of isolated edge-to-face π-π interactions are investigated in the related β-hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the Bb absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross-sections of Bb-coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π-π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces.
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Affiliation(s)
- Diana E. Schlamadinger
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Brian S. Leigh
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Judy E. Kim
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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33
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Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc 2012; 134:8026-9. [PMID: 22540162 PMCID: PMC3354031 DOI: 10.1021/ja301681v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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34
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Impact ofβ-Turn Sequence onβ-Hairpin Dynamics Studied with Infrared-Detected Temperature Jump. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/102423] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Folding dynamics forβ-structure loss and disordered structure gain were studied in a modelβ-hairpin peptide based on Cochran’s tryptophan zipper peptide Trpzip2, but with an altered Thr-Gly (TG) turn sequence, that is, SWTWETGKWTWK, using laser-induced temperature-jump (T-jump) kinetics with IR detection. As has been shown previously, the TG turn sequence reduces the thermodynamicβ-hairpin stability as compared to the Asn-Gly sequence used in Trpzip2 (TZ2-NG). In this study, we found that the TG-turn slows down the overall relaxation dynamics as compared to TZ2-NG, which were studied at higher temperatures where the time constants show little difference between relaxation of theβ-strand and the disordered conformation. These time constants become equivalent at lower temperatures for TZ2-TG than was seen for TZ2-NG. The correlation of thermodynamic stability and rates of relaxation suggests that the change from NG to TG turn results in a slowing of folding, lowerkf, with less change of the unfolding rate,ku, assuming two state behavior at higher temperatures.
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35
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Hwang S, Hilty C. Folding of a tryptophan zipper peptide investigated on the basis of the nuclear Overhauser effect and thermal denaturation. J Phys Chem B 2011; 115:15355-61. [PMID: 22040105 DOI: 10.1021/jp206405b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Short, secondary-structure-containing peptides are suitable models for the study of protein folding due to their relative simplicity. Here, we investigate thermal denaturation of the tryptophan zipper peptide, trpzip4, a peptide that forms a β-hairpin in solution. In order to monitor the thermal denaturation of peptides or small proteins, chemical shift values of H(α) or H(N) may be used. However, various factors other than secondary structure can influence chemical shift values, such as side-chain orientation of nearby aromatic residues. Nuclear Overhauser effect (NOE) intensity from backbone interproton cross peaks is an alternative way to study thermal denaturation, as long as various factors that give rise to a change in NOE intensity upon changing the temperature are considered. As a relative indicator for denaturation, we define a cutoff temperature, where half of the initial NOE intensity is lost for each backbone interproton cross peak. For trpzip4, this cutoff temperature is highest for residues in the central part of the structure and lowest for residues near the termini. These observations support the notion that the structure of the trpzip4 peptide is stabilized by a hydrophobic cluster formed by tryptophan residues located in the central region of the β-hairpin.
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Affiliation(s)
- Soyoun Hwang
- Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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36
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Xu Y, Du D, Oyola R. Infrared study of the stability and folding kinetics of a series of β-hairpin peptides with a common NPDG turn. J Phys Chem B 2011; 115:15332-8. [PMID: 22136248 DOI: 10.1021/jp2046867] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The thermal stability and folding kinetics of a series of 15-residue β-hairpins with a common Type I [3:5] NPDG turn were studied using Fourier transform infrared spectroscopy (FTIR) and laser-induced temperature jump (T-jump) with infrared detection, respectively. Mutations at positions 3, 5, or 13 in the peptide sequence SEXYXNPDGTWTXTE, where X represents the position of mutation, were performed to study the roles of hydrophobic interactions in determining the thermodynamic and kinetic properties of β-hairpin folding. The thermal stability studies show a broad thermal folding/unfolding transition for all the peptides. T-jump studies indicate that these β-hairpin peptides fold in less than 2 μs. In addition, both folding and unfolding rate constants decrease with increasing strength of hydrophobic interactions. Kinetically, the hydrophobic interactions have more significant influence on the unfolding rate than the folding rate. Φ-value analysis indicates that the hydrophobic interactions between the side chains are mainly formed at the latter part of the transition-state region during the folding process. In summary, the results suggest that the formation of the native structure of these β-hairpins depends on the correct topology of the hydrophobic cluster. Besides the formation of the turn region as a key process for folding as suggested by previous studies, a hydrophobic collapse process may also play a crucial role during β-hairpin folding.
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Affiliation(s)
- Yao Xu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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37
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Wu L, McElheny D, Setnicka V, Hilario J, Keiderling TA. Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy. Proteins 2011; 80:44-60. [DOI: 10.1002/prot.23140] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/28/2011] [Accepted: 07/21/2011] [Indexed: 12/28/2022]
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38
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Hatfield MPD, Murphy RF, Lovas S. The CLN025 decapeptide retains a β-hairpin conformation in urea and guanidinium chloride. J Phys Chem B 2011; 115:4971-81. [PMID: 21480621 DOI: 10.1021/jp111076j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The conformational stability of the β-hairpin miniprotein, CLN025, a variant of chignolin in which the N- and C-terminal glycines are replaced by tyrosines, in various concentrations of guanidinium chloride (GdmCl) and urea was examined by molecular dynamics simulations and electronic circular dichroism (ECD) spectropolarimetry. The peptide maintains its β-hairpin conformation in GdmCl and urea solutions. In GdmCl, Gly7 influences the turn to reduce the number of Asp3-Gly7 H-bonds and the Tyr1-Trp9 H-bond is lost. The structure of the peptide is less stable in 3 M GdmCl than in water or 6 M GdmCl, because the number of Asp3-Thr8 and Tyr1-Tyr10 H-bonds are reduced and the Tyr2 side chain moves away from the Pro4 and Trp9 side chains and toward the Tyr10 side chain. This reduces the number of Tyr2-Pro4 CH-π interactions and Tyr2-Trp9 and Tyr1-Tyr10 aromatic-aromatic (Ar-Ar) interactions and increases the number of Tyr2-Tyr10 Ar-Ar interactions. In 6 M GdmCl at 300 and 333 K, the number of Tyr1-Tyr10 and Asp3-Thr8 H-bonds increases, but fewer structures have Tyr2-Pro4 CH-π and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In urea, Gly7 is in a mixture of β-turn and random meander structures and the number of Asp3-Thr6 and Tyr1-Tyr10 H-bonds are reduced as are the number of Tyr2-Pro4 CH-π interactions and Tyr1-Tyr10 and Tyr2-Trp9 Ar-Ar interactions. In 4 M urea, a shorter turn places Gly7 into the β-sheet region and Tyr10 is pushed out into the solvent. In 8 M urea, the number of Asp3-Glu5 H-bonds is increased and the β-sheet is lost, but the electrostatic interaction between the charged termini is restored and a cation-π interaction between the indolyl ring of Trp9 and the positively charged N-terminus is formed. In 8 M urea at 333 K, the β-hairpin conformation is almost lost. The structure of CLN025 is stable, because the weakly polar interactions and H-bonds maintain the β-hairpin conformation in the various environments. CLN025 should not be considered a miniprotein, because it lacks a well-defined tertiary structure, it is resistant to denaturation, it does not have an increased heat capacity near its melting temperature, and the structures near and above the melting temperature retain a β-hairpin conformation.
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Affiliation(s)
- Marcus P D Hatfield
- Department of Biomedical Sciences, Criss II, Room 313, Creighton University, 2500 California Plaza, Omaha, Nebraska 68178, USA
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39
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Chen L, Shao Q, Gao YQ, Russell DH. Molecular Dynamics and Ion Mobility Spectrometry Study of Model β-Hairpin Peptide, Trpzip1. J Phys Chem A 2011; 115:4427-35. [DOI: 10.1021/jp110014j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Liuxi Chen
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Qiang Shao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yi-Qin Gao
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H. Russell
- The Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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40
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Santiveri CM, Jiménez MA. Tryptophan residues: scarce in proteins but strong stabilizers of β-hairpin peptides. Biopolymers 2011; 94:779-90. [PMID: 20564027 DOI: 10.1002/bip.21436] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Tryptophan plays important roles in protein stability and recognition despite its scarcity in proteins. Except as fluorescent groups, they have been used rarely in peptide design. Nevertheless, Trp residues were crucial for the stability of some designed minimal proteins. In 2000, Trp-Trp pairs were shown to contribute more than any other hydrophobic interaction to the stability of β-hairpin peptides. Since then, Trp-Trp pairs have emerged as a paradigm for the design of stable β-hairpins, such as the Trpzip peptides. Here, we analyze the nature of the stabilizing capacity of Trp-Trp pairs by reviewing the β-hairpin peptides containing Trp-Trp pairs described up to now, the spectroscopic features and geometry of the Trp-Trp pairs, and their use as binding sites in β-hairpin peptides. To complete the overview, we briefly go through the other relevant β-hairpin stabilizing Trp-non-Trp interactions and illustrate the use of Trp in the design of short peptides adopting α-helical and mixed α/β motifs. This review is of interest in the field of rational design of proteins, peptides, peptidomimetics, and biomaterials.
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Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid 28006, Spain
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41
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Santiveri CM, Pérez de Vega MJ, González-Muñiz R, Jiménez MA. Trp-Trp pairs as β-hairpin stabilisers: Hydrogen-bonded versus non-hydrogen-bonded sites. Org Biomol Chem 2011; 9:5487-92. [DOI: 10.1039/c1ob05353a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Hauser K, Ridderbusch O, Roy A, Hellerbach A, Huang R, Keiderling TA. Comparison of Isotopic Substitution Methods for Equilibrium and T-Jump Infrared Studies of β-Hairpin Peptide Conformation. J Phys Chem B 2010; 114:11628-37. [DOI: 10.1021/jp1028245] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Karin Hauser
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Oliver Ridderbusch
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Anjan Roy
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Alexandra Hellerbach
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Rong Huang
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Institute of Physics, RWTH Aachen University, Sommerfeldstr. 14, 52074 Aachen, Germany, Institute of Biophysics, Goethe-University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt, Germany, and Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
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43
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Kim J, Keiderling TA. All-Atom Molecular Dynamics Simulations of β-Hairpins Stabilized by a Tight Turn: Pronounced Heterogeneous Folding Pathways. J Phys Chem B 2010; 114:8494-504. [DOI: 10.1021/jp912159t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joohyun Kim
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street (M/C 111), Chicago, Illinois 60607-7061
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44
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Roy A, Bour P, Keiderling TA. TD-DFT modeling of the circular dichroism for a tryptophan zipper peptide with coupled aromatic residues. Chirality 2010; 21 Suppl 1:E163-71. [PMID: 19899143 DOI: 10.1002/chir.20792] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this work, time dependent density functional theory (TD-DFT) is used to provide a reliable basis for interpretation of the electronic spectra of coupled tryptophan (Trp) residues, particularly those in a model Trpzip beta-hairpin peptide. Pairs of isolated indoles form chiral coupled chromophores whose computed electronic ultraviolet circular dichroism (CD) is in excellent agreement with observed transition wavelengths and intensities. The calculations were compared to experimental data for pairwise coupling in mutant Trpzip peptides that are recently available. A study of variation of the basis set, geometry optimization, and the solvent environment on the spectra showed limited impact on bandshapes. An alternative simplified computational scheme, dependent on the transition dipole coupling (TDC) mechanism, is shown to give a representation of qualitative aspects of the intense CD for the (1)B bands at 228 and 213 nm. The results confirm the origin of the Trpzip diagnostic CD as primarily a dipolar interaction between Trp sidechains, and show that quantum computations of electronic CD can provide a reliable basis for interpretation of these chirally coupled aromatic spectral phenomena.
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Affiliation(s)
- Anjan Roy
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
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45
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Wu L, McElheny D, Takekiyo T, Keiderling TA. Geometry and Efficacy of Cross-Strand Trp/Trp, Trp/Tyr, and Tyr/Tyr Aromatic Interaction in a β-Hairpin Peptide. Biochemistry 2010; 49:4705-14. [DOI: 10.1021/bi100491s] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Takahiro Takekiyo
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061
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46
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Lewandowska A, Ołdziej S, Liwo A, Scheraga HA. beta-hairpin-forming peptides; models of early stages of protein folding. Biophys Chem 2010; 151:1-9. [PMID: 20494507 DOI: 10.1016/j.bpc.2010.05.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 05/01/2010] [Accepted: 05/01/2010] [Indexed: 11/19/2022]
Abstract
Formation of beta-hairpins is considered the initial step of folding of many proteins and, consequently, peptides constituting the beta-hairpin sequence of proteins (the beta-hairpin-forming peptides) are considered as models of early stages of protein folding. In this article, we discuss the results of experimental studies (circular-dichroism, infrared and nuclear magnetic resonance spectroscopy, and differential scanning calorimetry) of the structure of beta-hairpin-forming peptides excised from the B1 domain of protein G, which are known to fold on their own. We demonstrate that local interactions at the turn sequence and hydrophobic interactions between nonpolar residues are the dominant structure-determining factors, while there is no convincing evidence that stable backbone hydrogen bonds are formed in these peptides in aqueous solution. Consequently, the most plausible mechanism for folding of the beta-hairpin sequence appears to be the broken-zipper mechanism consisting of the following three steps: (i) bending the chain at the turn sequence owing to favorable local interactions, (ii) formation of loose hydrophobic contacts between nonpolar residues, which occur close to the contacts in the native structure of the protein but not exactly in the same position and, finally, (iii) formation of backbone hydrogen bonds and locking the hydrophobic contacts in the native positions as a hydrophobic core develops, sufficient to dehydrate the backbone peptide groups. This mechanism provides sufficient uniqueness (contacts form between residues that become close together because the chain is bent at the turn position) and robustness (contacts need not occur at once in the native positions) for folding a beta-hairpin sequence.
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47
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Hatfield MPD, Murphy RF, Lovas S. VCD spectroscopic properties of the beta-hairpin forming miniprotein CLN025 in various solvents. Biopolymers 2010; 93:442-50. [PMID: 19937759 PMCID: PMC4499852 DOI: 10.1002/bip.21356] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. Little is known about the vibrational circular dichroic spectroscopic features of the beta-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable beta-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a beta-hairpin in water, TFE, MeOH, and DMSO and to examine differences in the secondary structure, hydrogen bonds, and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with N(alpha)-Fmoc protected amino acids. The VCD spectra displayed a (-,+,-) pattern with bands at 1640 to 1656 cm(-1), 1667 to 1687 cm(-1), and 1679 to 1686 cm(-1) formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm(-1) with component bands at 1630 cm(-1), 1646 cm(-1), 1658 cm(-1), and 1675 to 1680 cm(-1) that are indicative of the beta-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of beta-hairpins formed by (D)Pro-Xxx turns and indicated that observed pattern is typical of beta-hairpins.
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Affiliation(s)
| | - Richard. F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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48
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Hatfield MPD, Murphy RF, Lovas S. Molecular dynamics analysis of the conformations of a beta-hairpin miniprotein. J Phys Chem B 2010; 114:3028-37. [PMID: 20148510 PMCID: PMC2848447 DOI: 10.1021/jp910465e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations of a beta-hairpin miniprotein, CLN025, were performed to examine the conformational stability of the peptide in H(2)O at 278, 300, 333, and 363 K, as well as in TFE, MeOH, and DMSO at 300 K. CLN025 is a variant of the Chignolin miniprotein, in which the terminal Gly residues of Chignolin are replaced with Tyr residues, which leads to a 29.7 K increase in melting temperature. The energy of the intramolecular interactions was calculated using DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. CLN025 maintained a beta-hairpin conformation in all environments. The beta-hairpin is stabilized by hydrogen bonds, an electrostatic interaction between the charged termini of the peptide, and weakly polar interactions. The interaction between the backbones of the N and C-terminal strands accounts for -97.32 to -120.87 kcal mol(-1) of the stabilization energy. The energies of the CH-pi interactions between Tyr2 and Pro4 were between -1.80 and -8.9 kcal mol(-1), and the energy of the Tyr2-Trp9 Ar-Ar interaction was between -0.43 and -8.11 kcal mol(-1). Increasing temperature caused the Tyr2-Pro4 CH-pi and the Tyr2-Trp9 and Tyr2-Tyr10 Ar-Ar interactions to become less favorable, but the Tyr1-Trp9 interaction became more favorable and played an important role in stabilizing the beta-hairpin of CLN025 that resulted in the increased melting temperature. Weakly polar interactions play an important role in the structure and stability of CLN025 and other proteins.
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Affiliation(s)
| | - Richard F. Murphy
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, U.S.A
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Wu L, McElheny D, Huang R, Keiderling TA. Role of Tryptophan−Tryptophan Interactions in Trpzip β-Hairpin Formation, Structure, and Stability. Biochemistry 2009; 48:10362-71. [PMID: 19788311 DOI: 10.1021/bi901249d] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ling Wu
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Rong Huang
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
| | - Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607-7061
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