1
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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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2
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Di Stasi R, De Rosa L, D'Andrea LD. Structure-Based Design of Peptides Targeting VEGF/VEGFRs. Pharmaceuticals (Basel) 2023; 16:851. [PMID: 37375798 DOI: 10.3390/ph16060851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/03/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Vascular endothelial growth factor (VEGF) and its receptors (VEGFRs) play a main role in the regulation of angiogenesis and lymphangiogenesis. Furthermore, they are implicated in the onset of several diseases such as rheumatoid arthritis, degenerative eye conditions, tumor growth, ulcers and ischemia. Therefore, molecules able to target the VEGF and its receptors are of great pharmaceutical interest. Several types of molecules have been reported so far. In this review, we focus on the structure-based design of peptides mimicking VEGF/VEGFR binding epitopes. The binding interface of the complex has been dissected and the different regions challenged for peptide design. All these trials furnished a better understanding of the molecular recognition process and provide us with a wealth of molecules that could be optimized to be exploited for pharmaceutical applications.
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Affiliation(s)
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, 80131 Napoli, Italy
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3
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Carrera-Aubesart A, Defaus S, Pérez-Peinado C, Sandín D, Torrent M, Jiménez MÁ, Andreu D. Examining Topoisomers of a Snake-Venom-Derived Peptide for Improved Antimicrobial and Antitumoral Properties. Biomedicines 2022; 10:2110. [PMID: 36140211 PMCID: PMC9495681 DOI: 10.3390/biomedicines10092110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 11/30/2022] Open
Abstract
Ctn[15-34], the C-terminal section of crotalicidin (Ctn), a cathelicidin from a South American pit viper, is an antimicrobial and antitumoral peptide with remarkably longer stability in human serum than the parent Ctn. In this work, a set of topoisomers of both Ctn and Ctn[15-34], including the retro, enantio, and retroenantio versions, were synthesized and tested to investigate the structural requirements for activity. All topoisomers were as active as the cognate sequences against Gram-negative bacteria and tumor cells while slightly more toxic towards normal cells. More importantly, the enhanced serum stability of the D-amino-acid-containing versions suggests that such topoisomers must be preferentially considered as future antimicrobial and anticancer peptide leads.
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Affiliation(s)
- Adam Carrera-Aubesart
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Sira Defaus
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Clara Pérez-Peinado
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
| | - Daniel Sandín
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marc Torrent
- Systems Biology of Infection Lab, Department of Biochemistry and Molecular Biology, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Ángeles Jiménez
- Institute of Physical Chemistry “Rocasolano” (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - David Andreu
- Proteomics and Protein Chemistry Unit, Department of Medicine and Life Sciences, Pompeu Fabra University, 08003 Barcelona, Spain
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4
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Zhang J, Liu S, Li H, Tian X, Li X. Tryptophan-Based Self-Assembling Peptides with Bacterial Flocculation and Antimicrobial Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:11316-11323. [PMID: 32907333 DOI: 10.1021/acs.langmuir.0c01957] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tryptophan as an aromatic amino acid with a hydrophobic indole group plays important roles in stabilizing protein structures and enhancing molecular bindings in nature, but was rarely used in the molecular design of self-assembling peptides or gelators. Therefore, we prepared a series of short peptides from Trp amino acids and examined the potential roles of Trp residues for regulating peptide self-assembly and gelation. The introduced Trp amino acids not only diversify the molecular structures of peptide gelators, but also promote aromatic and hydrogen-bonding interactions for supramolecular self-assembling and gelation, which generates self-assembled nanostructures with twisted helical morphologies and supramolecular hydrogels with low minimal gelation concentrations. More importantly, the self-assembling peptides with Trp residues displayed strong preference for interacting with the lipidic membranes of bacteria, which resulted in bacterial flocculation and the death of E. coli and S. aureus.
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Affiliation(s)
- Jikun Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Shengnan Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Hang Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
| | - Xin Tian
- School for Radiological and Interdisciplinary Sciences (RAD-X), Soochow University, Suzhou 215123, China
| | - Xinming Li
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, China
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5
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Migliore M, Bonvicini A, Tognetti V, Guilhaudis L, Baaden M, Oulyadi H, Joubert L, Ségalas-Milazzo I. Characterization of β-turns by electronic circular dichroism spectroscopy: a coupled molecular dynamics and time-dependent density functional theory computational study. Phys Chem Chem Phys 2020; 22:1611-1623. [PMID: 31894790 DOI: 10.1039/c9cp05776e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electronic circular dichroism is one of the most used spectroscopic techniques for peptide and protein structural characterization. However, while valuable experimental spectra exist for α-helix, β-sheet and random coil secondary structures, previous studies showed important discrepancies for β-turns, limiting their use as a reference for structural studies. In this paper, we simulated circular dichroism spectra for the best-characterized β-turns in peptides, namely types I, II, I' and II'. In particular, by combining classical molecular dynamics simulations and state-of-the-art quantum time-dependent density functional theory (with the polarizable embedding multiscale model) computations, two common electronic circular dichroism patterns were found for couples of β-turn types (namely, type I/type II' and type II/type I'), at first for a minimal di-peptide model (Ace-Ala-Ala-NHMe), but also for all sequences tested with non-aromatic residues in the central positions. On the other hand, as expected, aromatic substitution causes important perturbations to the previously found ECD patterns. Finally, by applying suitable approximations, these patterns were subsequently rationalized based on the exciton chirality rule. All these results provide useful predictions and pave the way for a possible experimental characterization of β-turns based on circular dichroism spectroscopy.
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Affiliation(s)
- Mattia Migliore
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Andrea Bonvicini
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Vincent Tognetti
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Laure Guilhaudis
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, PSL Research University, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Hassan Oulyadi
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Laurent Joubert
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
| | - Isabelle Ségalas-Milazzo
- Normandy Univ., COBRA UMR 6014 & FR 3038, Université de Rouen, INSA Rouen, CNRS, 1 rue Tesnière, 76821 Mont St Aignan, Cedex, France.
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6
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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7
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Zamora-Carreras H, Maestro B, Strandberg E, Ulrich AS, Sanz JM, Jiménez MÁ. Roles of Amphipathicity and Hydrophobicity in the Micelle-Driven Structural Switch of a 14-mer Peptide Core from a Choline-Binding Repeat. Chemistry 2018; 24:5825-5839. [PMID: 29369425 DOI: 10.1002/chem.201704802] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 01/16/2023]
Abstract
Choline-binding repeats (CBRs) are ubiquitous sequences with a β-hairpin core that are found in the surface proteins of several microorganisms such as S. pneumoniae (pneumococcus). Previous studies on a 14-mer CBR sequence derived from the pneumoccal LytA autolysin (LytA239-252 peptide) have demonstrated a switch behaviour for this peptide, so that it acquires a stable, native-like β-hairpin conformation in aqueous solution but is reversibly transformed into an amphipathic α-helix in the presence of detergent micelles. With the aim of understanding the factors responsible for this unusual β-hairpin to α-helix transition, and to specifically assess the role of peptide hydrophobicity and helical amphipathicity in the process, we designed a series of LytA239-252 variants affecting these two parameters and studied their interaction with dodecylphosphocholine (DPC) micelles by solution NMR, circular dichroism and fluorescence spectroscopies. Our results indicate that stabilising cross-strand interactions become essential for β-hairpin stability in the absence of optimal turn sequences. Moreover, both amphipathicity and hydrophobicity display comparable importance for helix stabilisation of CBR-derived peptides in micelles, indicating that these sequences represent a novel class of micelle/membrane-interacting peptides.
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Affiliation(s)
- Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
| | - Beatriz Maestro
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain
| | - Erik Strandberg
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O. Box 3640, 76021, Karlsruhe, Germany.,Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Jesús M Sanz
- Instituto de Biología MolecularyCelular, Universidad Miguel Hernández, Elche, 03202, Alicante, Spain.,Biological Research Centre (CIB), Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006, Madrid, Spain
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8
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Morais M, Zamora-Carreras H, Raposinho PD, Oliveira MC, Pantoja-Uceda D, Correia JDG, Jiménez MA. NMR Insights into the Structure-Function Relationships in the Binding of Melanocortin Analogues to the MC1R Receptor. Molecules 2017; 22:molecules22071189. [PMID: 28714883 PMCID: PMC6152105 DOI: 10.3390/molecules22071189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 01/25/2023] Open
Abstract
Linear and cyclic analogues of the α-melanocyte stimulating hormone (α-MSH) targeting the human melanocortin receptor 1 (MC1R) are of pharmacological interest for detecting and treating melanoma. The central sequence of α-MSH (His-Phe-Arg-Trp) has been identified as being essential for receptor binding. To deepen current knowledge on the molecular basis for α-MSH bioactivity, we aimed to understand the effect of cycle size on receptor binding. To that end, we synthesised two macrocyclic isomeric α-MSH analogues, c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys]-Lys-NH2 (CycN-K6) and c[NH-NO2-C6H3-CO-His-DPhe-Arg-Trp-Lys-Lys]-NH2 (CycN-K7). Their affinities to MC1R receptor were determined by competitive binding assays, and their structures were analysed by 1H and 13C NMR. These results were compared to those of the previously reported analogue c[S-NO2-C6H3-CO-His-DPhe-Arg-Trp-Cys]-Lys-NH2 (CycS-C6). The MC1R binding affinity of the 22-membered macrocyclic peptide CycN-K6 (IC50 = 155 ± 16 nM) is higher than that found for the 25-membered macrocyclic analogue CycN-K7 (IC50 = 495 ± 101 nM), which, in turn, is higher than that observed for the 19-membered cyclic analogue CycS-C6 (IC50 = 1770 ± 480 nM). NMR structural study indicated that macrocycle size leads to changes in the relative dispositions of the side chains, particularly in the packing of the Arg side chain relative to the aromatic rings. In contrast to the other analogues, the 22-membered cycle’s side chains are favorably positioned for receptor interaction.
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Affiliation(s)
- Maurício Morais
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela LRS, Portugal.
- Division of Imaging Sciences and Biomedical Engineering, King's College London, 4th Floor Lambeth Wing, St Thomas' Hospital, London SE1 7EH, UK.
| | - Héctor Zamora-Carreras
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain.
| | - Paula D Raposinho
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela LRS, Portugal.
| | - Maria Cristina Oliveira
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela LRS, Portugal.
| | - David Pantoja-Uceda
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain.
| | - João D G Correia
- Centro de Ciências e Tecnologias Nucleares, Instituto Superior Técnico, Universidade de Lisboa, Estrada Nacional 10 (km 139.7), 2695-066 Bobadela LRS, Portugal.
| | - M Angeles Jiménez
- Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain.
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9
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Makwana KM, Mahalakshmi R. Capping β-hairpin with N-terminal d-amino acid stabilizes peptide scaffold. Biopolymers 2017; 106:260-6. [PMID: 26999275 DOI: 10.1002/bip.22837] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/25/2022]
Abstract
Various strategies exist to stabilize de novo designed synthetic peptide β-hairpins or β-sheets structures, especially at the non-hydrogen bonding position. However, strategies to stabilize strand termini, which are affected by fraying, are highly limited. Here, by substituting N-terminal aliphatic amino acid with its mirror image counterpart, we achieve a significant increase in scaffold stabilization, resulting from the formation of a terminal aliphatic-aromatic hydrophobic CH…pi cluster. Our extensive solution NMR studies support the incorporation of an N-terminal d-aliphatic amino acid in the design of short β-hairpins, while successfully retaining the overall structural scaffold. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 260-266, 2016.
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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, 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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10
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Anderson JM, Jurban B, Huggins KNL, Shcherbakov AA, Shu I, Kier B, Andersen NH. Nascent Hairpins in Proteins: Identifying Turn Loci and Quantitating Turn Contributions to Hairpin Stability. Biochemistry 2016; 55:5537-5553. [DOI: 10.1021/acs.biochem.6b00732] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jordan M. Anderson
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brice Jurban
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Kelly N. L. Huggins
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | | | - Irene Shu
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Brandon Kier
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
| | - Niels H. Andersen
- Department of Chemistry, University of Washington, Seattle, Washington 98105, United States
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11
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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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12
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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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13
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Falcao CB, Pérez-Peinado C, de la Torre BG, Mayol X, Zamora-Carreras H, Jiménez MÁ, Rádis-Baptista G, Andreu D. Structural Dissection of Crotalicidin, a Rattlesnake Venom Cathelicidin, Retrieves a Fragment with Antimicrobial and Antitumor Activity. J Med Chem 2015; 58:8553-63. [PMID: 26465972 DOI: 10.1021/acs.jmedchem.5b01142] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In silico dissection of crotalicidin (Ctn), a cathelicidin from a South American pit viper, yielded fragments Ctn[1-14] and Ctn[15-34], which were tested to ascertain to what extent they reproduced the structure and activity of the parent peptide. NMR data showing Ctn to be α-helical at the N-terminus and unstructured at the C-terminus were matched by similar data from the fragments. The peptides were tested against Gram-positive and -negative bacteria and for toxicity against both tumor and healthy cells. Despite its amphipathic α-helical structure, Ctn[1-14] was totally inert toward bacteria or eukaryotic cells. In contrast, unstructured Ctn[15-34] replicated the activity of parent Ctn against Gram-negative bacteria and tumor cells while being significantly less toxic toward eukaryotic cells. This selectivity for bacteria and tumor cells, plus a stability to serum well above that of Ctn, portrays Ctn[15-34] as an appealing candidate for further development as an anti-infective or antitumor lead.
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Affiliation(s)
- Claudio Borges Falcao
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , 08003 Barcelona, Spain.,Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará , 60455-760 Fortaleza, CE, Brazil
| | - Clara Pérez-Peinado
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , 08003 Barcelona, Spain
| | - Beatriz G de la Torre
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , 08003 Barcelona, Spain
| | - Xavier Mayol
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques , 08003 Barcelona, Spain
| | - Héctor Zamora-Carreras
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - M Ángeles Jiménez
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
| | - Gandhi Rádis-Baptista
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , 08003 Barcelona, Spain.,Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceará , 60455-760 Fortaleza, CE, Brazil
| | - David Andreu
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra , 08003 Barcelona, Spain
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14
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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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15
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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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16
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Kier BL, Anderson JM, Andersen NH. Disulfide-Mediated β-Strand Dimers: Hyperstable β-Sheets Lacking Tertiary Interactions and Turns. J Am Chem Soc 2015; 137:5363-71. [PMID: 25835058 PMCID: PMC7450586 DOI: 10.1021/ja5117809] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Disulfide bonds between cysteine residues are essential to the structure and folding of many proteins. Yet their role in the design of structured peptides and proteins has frequently been limited to use as intrachain covalent staples that reinforce existing structure or induce knot-like conformations. In β-hairpins, their placement at non-H-bonding positions across antiparallel strands has proven useful for achieving fully folded positive controls. Here we report a new class of designed β-sheet peptide dimers with strand-central disulfides as a key element. We have found that the mere presence of a disulfide bond near the middle of a short peptide chain is sufficient to nucleate some antiparallel β-sheet structure; addition of β-capping units and other favorable cross-strand interactions yield hyperstable sheets. Strand-central cystines were found to be superior to the best designed reversing turns in terms of nucleating β-sheet structure formation. We have explored the limitations and possibilities of this technique (the use of disulfides as sheet nucleators), and we provide a set of rules and rationales for the application and further design of disulfide-tethered "turnless" β-sheets.
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Affiliation(s)
- Brandon L Kier
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Jordan M Anderson
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
| | - Niels H Andersen
- Chemistry Department, University of Washington, Seattle, Washington 98195, United States
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17
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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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18
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Apellániz B, Rujas E, Serrano S, Morante K, Tsumoto K, Caaveiro JMM, Jiménez MÁ, Nieva JL. The Atomic Structure of the HIV-1 gp41 Transmembrane Domain and Its Connection to the Immunogenic Membrane-proximal External Region. J Biol Chem 2015; 290:12999-3015. [PMID: 25787074 DOI: 10.1074/jbc.m115.644351] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Indexed: 11/06/2022] Open
Abstract
The membrane-proximal external region (MPER) C-terminal segment and the transmembrane domain (TMD) of gp41 are involved in HIV-1 envelope glycoprotein-mediated fusion and modulation of immune responses during viral infection. However, the atomic structure of this functional region remains unsolved. Here, based on the high resolution NMR data obtained for peptides spanning the C-terminal segment of MPER and the TMD, we report two main findings: (i) the conformational variability of the TMD helix at a membrane-buried position; and (ii) the existence of an uninterrupted α-helix spanning MPER and the N-terminal region of the TMD. Thus, our structural data provide evidence for the bipartite organization of TMD predicted by previous molecular dynamics simulations and functional studies, but they do not support the breaking of the helix at Lys-683, as was suggested by some models to mark the initiation of the TMD anchor. Antibody binding energetics examined with isothermal titration calorimetry and humoral responses elicited in rabbits by peptide-based vaccines further support the relevance of a continuous MPER-TMD helix for immune recognition. We conclude that the transmembrane anchor of HIV-1 envelope is composed of two distinct subdomains: 1) an immunogenic helix at the N terminus also involved in promoting membrane fusion; and 2) an immunosuppressive helix at the C terminus, which might also contribute to the late stages of the fusion process. The unprecedented high resolution structural data reported here may guide future vaccine and inhibitor developments.
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Affiliation(s)
- Beatriz Apellániz
- From the Biophysics Unit (Consejo Superior de Investigaciones Científicas, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Edurne Rujas
- From the Biophysics Unit (Consejo Superior de Investigaciones Científicas, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain, the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, 113-8656 Tokyo, Japan, and
| | - Soraya Serrano
- the Institute of Physical Chemistry "Rocasolano" (Consejo Superior de Investigaciones Científicas), Serrano 119, E-28006 Madrid, Spain
| | - Koldo Morante
- the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, 113-8656 Tokyo, Japan, and
| | - Kouhei Tsumoto
- the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, 113-8656 Tokyo, Japan, and
| | - Jose M M Caaveiro
- the Department of Bioengineering, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, 113-8656 Tokyo, Japan, and
| | - M Ángeles Jiménez
- the Institute of Physical Chemistry "Rocasolano" (Consejo Superior de Investigaciones Científicas), Serrano 119, E-28006 Madrid, Spain
| | - José L Nieva
- From the Biophysics Unit (Consejo Superior de Investigaciones Científicas, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain,
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Markiewicz BN, Culik RM, Gai F. Tightening up the structure, lighting up the pathway: Application of molecular constraints and light to manipulate protein folding, self-assembly and function. Sci China Chem 2014; 57:1615-1624. [PMID: 25722715 PMCID: PMC4337807 DOI: 10.1007/s11426-014-5225-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins. Recently, other types of molecular constraints, especially photoresponsive linkers and functional groups, have also found increased use in a wide variety of applications. Herein, we provide a concise review of using various forms of molecular strategies to constrain proteins, thereby stabilizing their native states, gaining insight into their folding mechanisms, and/or providing a handle to trigger a conformational process of interest with light. The applications discussed here cover a wide range of topics, ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.
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Affiliation(s)
| | - Robert M. Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, PA, 19104, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, PA, 19104, USA
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20
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Makwana KM, Mahalakshmi R. Asymmetric contribution of aromatic interactions stems from spatial positioning of the interacting aryl pairs in β-hairpins. Chembiochem 2014; 15:2357-60. [PMID: 25196944 DOI: 10.1002/cbic.201402340] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Indexed: 11/11/2022]
Abstract
Isolated aromatic interactions in designed octapeptide β-hairpin scaffolds display a near-universal T-shaped face-to-edge geometry in all positional permutations, with the exception of aryl-Trp interactions. The heterogeneous asymmetric indole ring of Trp competes for a "shielding" face geometry, which lowers the scaffold stability in FtE aryl-Trp pairs. Assessment of the contributions of aryl pairs (in the absence of solvent-driven interactions) to the overall β-hairpin structure reveals the superiority of Trp-Phe and Trp-Tyr contributions over the well-established scaffold stabilization by Trp-Trp.
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Affiliation(s)
- Kamlesh Madhusudan Makwana
- Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh 462023 (India)
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21
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Koukos PI, Glykos NM. Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide. J Phys Chem B 2014; 118:10076-84. [DOI: 10.1021/jp5046113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Panagiotis I. Koukos
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
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22
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Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [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: 01/09/2023]
Abstract
![]()
Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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23
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De Rosa L, Diana D, Basile A, Russomanno A, Isernia C, Turco MC, Fattorusso R, D'Andrea LD. Design, structural and biological characterization of a VEGF inhibitor β-hairpin-constrained peptide. Eur J Med Chem 2014; 73:210-6. [DOI: 10.1016/j.ejmech.2013.12.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 11/19/2013] [Accepted: 12/13/2013] [Indexed: 01/01/2023]
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Serrano S, Araujo A, Apellániz B, Bryson S, Carravilla P, de la Arada I, Huarte N, Rujas E, Pai EF, Arrondo JLR, Domene C, Jiménez MA, Nieva JL. Structure and immunogenicity of a peptide vaccine, including the complete HIV-1 gp41 2F5 epitope: implications for antibody recognition mechanism and immunogen design. J Biol Chem 2014; 289:6565-6580. [PMID: 24429284 DOI: 10.1074/jbc.m113.527747] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The membrane-proximal external region (MPER) of gp41 harbors the epitope recognized by the broadly neutralizing anti-HIV 2F5 antibody, a research focus in HIV-1 vaccine development. In this work, we analyze the structure and immunogenic properties of MPERp, a peptide vaccine that includes the following: (i) the complete sequence protected from proteolysis by the 2F5 paratope; (ii) downstream residues postulated to establish weak contacts with the CDR-H3 loop of the antibody, which are believed to be crucial for neutralization; and (iii) an aromatic rich anchor to the membrane interface. MPERp structures solved in dodecylphosphocholine micelles and 25% 1,1,1,3,3,3-hexafluoro-2-propanol (v/v) confirmed folding of the complete 2F5 epitope within continuous kinked helices. Infrared spectroscopy (IR) measurements demonstrated the retention of main helical conformations in immunogenic formulations based on alum, Freund's adjuvant, or two different types of liposomes. Binding to membrane-inserted MPERp, IR, molecular dynamics simulations, and characterization of the immune responses further suggested that packed helical bundles partially inserted into the lipid bilayer, rather than monomeric helices adsorbed to the membrane interface, could encompass effective MPER peptide vaccines. Together, our data constitute a proof-of-concept to support MPER-based peptides in combination with liposomes as stand-alone immunogens and suggest new approaches for structure-aided MPER vaccine development.
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Affiliation(s)
- Soraya Serrano
- Institute of Physical Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain
| | - Aitziber Araujo
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Beatriz Apellániz
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Steve Bryson
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; The Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - Pablo Carravilla
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Igor de la Arada
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Nerea Huarte
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Edurne Rujas
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Emil F Pai
- Departments of Biochemistry, Medical Biophysics, and Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; The Campbell Family Institute for Cancer Research, Ontario Cancer Institute/University Health Network, Toronto, Ontario M5G 1L7, Canada
| | - José L R Arrondo
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain
| | - Carmen Domene
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom; Department of Chemistry, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, United Kingdom
| | - María Angeles Jiménez
- Institute of Physical Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Serrano 119, E-28006 Madrid, Spain.
| | - José L Nieva
- Biophysics Unit, Consejo Superior de Investigaciones Científicas and University of the Basque Country (CSIC-UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), P. O. Box 644, 48080 Bilbao, Spain.
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25
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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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26
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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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27
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Morais M, Oliveira BL, Correia JDG, Oliveira MC, Jiménez MA, Santos I, Raposinho PD. Influence of the Bifunctional Chelator on the Pharmacokinetic Properties of 99mTc(CO)3-Labeled Cyclic α-Melanocyte Stimulating Hormone Analog. J Med Chem 2013; 56:1961-73. [DOI: 10.1021/jm301647t] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maurício Morais
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
| | - Bruno L. Oliveira
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
| | - João D. G. Correia
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
| | - Maria Cristina Oliveira
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
| | - Maria Angeles Jiménez
- Instituto de Química
Física Rocasolano, Consejo Superior de Investigaciones Científicas
(CSIC), Serrano 119, 28006 Madrid, Spain
| | - Isabel Santos
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
| | - Paula D. Raposinho
- Unidade de Ciências Químicas
e Radiofarmacêuticas, IST/ITN, Instituto Superior Técnico,
Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953,
Sacavém, Portugal
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Morais M, Raposinho PD, Oliveira MC, Pantoja-Uceda D, Jiménez MA, Santos I, Correia JDG. NMR Structural Analysis of MC1R-Targeted Rhenium(I) Metallopeptides and Biological Evaluation of 99mTc(I) Congeners. Organometallics 2012. [DOI: 10.1021/om300502n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Maurício Morais
- Unidade de Ciências Quı́micas
e Radiofarmacêuticas, ITN, Instituto Superior
Técnico, Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953, Sacavém, Portugal
| | - Paula D. Raposinho
- Unidade de Ciências Quı́micas
e Radiofarmacêuticas, ITN, Instituto Superior
Técnico, Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953, Sacavém, Portugal
| | - Maria Cristina Oliveira
- Unidade de Ciências Quı́micas
e Radiofarmacêuticas, ITN, Instituto Superior
Técnico, Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953, Sacavém, Portugal
| | - David Pantoja-Uceda
- Instituto de Quı́mica Fı́sica Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Maria Angeles Jiménez
- Instituto de Quı́mica Fı́sica Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Serrano 119, 28006 Madrid, Spain
| | - Isabel Santos
- Unidade de Ciências Quı́micas
e Radiofarmacêuticas, ITN, Instituto Superior
Técnico, Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953, Sacavém, Portugal
| | - João D. G. Correia
- Unidade de Ciências Quı́micas
e Radiofarmacêuticas, ITN, Instituto Superior
Técnico, Universidade Técnica de Lisboa, Estrada Nacional 10, 2686-953, Sacavém, Portugal
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29
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Almeida AM, Li R, Gellman SH. Parallel β-sheet secondary structure is stabilized and terminated by interstrand disulfide cross-linking. J Am Chem Soc 2012; 134:75-8. [PMID: 22148521 PMCID: PMC3266109 DOI: 10.1021/ja208856c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Disulfide bonds between Cys residues in adjacent strands of parallel β-sheets are rare among proteins, which suggests that parallel β-sheet structure is not stabilized by such disulfide cross-links. We report experimental results that show, surprisingly, that an interstrand disulfide bond can stabilize parallel β-sheets formed by an autonomously folding peptide in aqueous solution. NMR analysis reveals that parallel β-sheet structure is terminated beyond the disulfide bond, which causes deviation from the extended backbone conformation at one of the Cys residues.
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Affiliation(s)
- Aaron M. Almeida
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
| | - Rebecca Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wi, 53706 (USA)
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30
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Disulfide and amide-bridged cyclic peptide analogues of the VEGF81–91 fragment: Synthesis, conformational analysis and biological evaluation. Bioorg Med Chem 2011; 19:7526-33. [DOI: 10.1016/j.bmc.2011.10.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 01/17/2023]
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31
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Diana D, Basile A, De Rosa L, Di Stasi R, Auriemma S, Arra C, Pedone C, Turco MC, Fattorusso R, D'Andrea LD. β-hairpin peptide that targets vascular endothelial growth factor (VEGF) receptors: design, NMR characterization, and biological activity. J Biol Chem 2011; 286:41680-41691. [PMID: 21969375 DOI: 10.1074/jbc.m111.257402] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
VEGF receptors have been the target of intense research aimed to develop molecules able to inhibit or stimulate angiogenesis. Based on the x-ray structure of the complex placental growth factor-VEGF receptor 1(D2), we designed a VEGF receptor-binding peptide reproducing the placental growth factor β-hairpin region Gln(87)-Val(100) that is involved in receptor recognition. A conformational analysis showed that the designed peptide adopts the expected fold in pure water. Moreover, a combination of NMR interaction analysis and cell binding studies were used to demonstrate that the peptide targets VEGF receptors. The VEGF receptor 1(D2)-interacting residues were characterized at the molecular level, and they correspond to the residues recognizing the placental growth factor sequence Gln(87)-Val(100). Finally, the peptide biological activity was characterized in vitro and in vivo, and it showed a VEGF-like behavior. Indeed, the peptide activated VEGF-dependent intracellular pathways, induced endothelial cell proliferation and rescue from apoptosis, and promoted angiogenesis in vivo. This compound is one of the few peptides known with proangiogenic activity, which makes it a candidate for the development of a novel peptide-based drug for medical applications in therapeutic angiogenesis.
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Affiliation(s)
- Donatella Diana
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Anna Basile
- Dipartimento di Scienze Farmaceutiche e Biomediche, Università di Salerno, via Ponte don Melillo, 84084 Fisciano (Salerno), Italy
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy
| | - Sara Auriemma
- Dipartimento delle Scienze Biologiche, Università di Napoli "Federico II," via Mezzocannone 16, 80134 Napoli, Italy
| | - Claudio Arra
- Istituto Nazionale Tumori "Fondazione G. Pascale," via Mariano Semmola 49, 80131 Napoli, Italy
| | - Carlo Pedone
- Dipartimento delle Scienze Biologiche, Università di Napoli "Federico II," via Mezzocannone 16, 80134 Napoli, Italy
| | - Maria Caterina Turco
- Dipartimento di Scienze Farmaceutiche e Biomediche, Università di Salerno, via Ponte don Melillo, 84084 Fisciano (Salerno), Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Antonio Vivaldi 43, 81100 Caserta, Italy
| | - Luca Domenico D'Andrea
- Istituto di Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, via Mezzocannone 16, 80134 Napoli, Italy.
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32
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Bandyopadhyay A, Mali SM, Lunawat P, Raja KMP, Gopi HN. Synthesis and Structural Investigations of Functionalizable Hybrid β-Hairpin. Org Lett 2011; 13:4482-5. [DOI: 10.1021/ol201840p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anupam Bandyopadhyay
- Department of Chemistry, Indian Institute of Science Education and Research, Garware Circle, Pashan, Pune-411 021, India, and Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625 021, India
| | - Sachitanand M. Mali
- Department of Chemistry, Indian Institute of Science Education and Research, Garware Circle, Pashan, Pune-411 021, India, and Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625 021, India
| | - Pooja Lunawat
- Department of Chemistry, Indian Institute of Science Education and Research, Garware Circle, Pashan, Pune-411 021, India, and Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625 021, India
| | - K. Muruga Poopathi Raja
- Department of Chemistry, Indian Institute of Science Education and Research, Garware Circle, Pashan, Pune-411 021, India, and Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625 021, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Garware Circle, Pashan, Pune-411 021, India, and Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai-625 021, India
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33
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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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34
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Basile A, Del Gatto A, Diana D, Di Stasi R, Falco A, Festa M, Rosati A, Barbieri A, Franco R, Arra C, Pedone C, Fattorusso R, Turco MC, D’Andrea LD. Characterization of a Designed Vascular Endothelial Growth Factor Receptor Antagonist Helical Peptide with Antiangiogenic Activity in Vivo. J Med Chem 2011; 54:1391-400. [DOI: 10.1021/jm101435r] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Anna Basile
- Dipartimento di Scienze Farmaceutiche, Università di Salerno and BioUniverSA SRL, Salerno, Italy
| | - Annarita Del Gatto
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Antonia Falco
- Dipartimento di Scienze Farmaceutiche, Università di Salerno and BioUniverSA SRL, Salerno, Italy
| | - Michelina Festa
- Dipartimento di Scienze Farmaceutiche, Università di Salerno and BioUniverSA SRL, Salerno, Italy
| | - Alessandra Rosati
- Dipartimento di Scienze Farmaceutiche, Università di Salerno and BioUniverSA SRL, Salerno, Italy
| | - Antonio Barbieri
- Istituto Nazionale Tumori “Fondazione G. Pascale”, Napoli, Italy
| | - Renato Franco
- Istituto Nazionale Tumori “Fondazione G. Pascale”, Napoli, Italy
| | - Claudio Arra
- Istituto Nazionale Tumori “Fondazione G. Pascale”, Napoli, Italy
| | - Carlo Pedone
- Dipartimento delle Scienze Biologiche, Università di Napoli “Federico II”, Napoli, Italy
| | - Roberto Fattorusso
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy
| | - Maria Caterina Turco
- Dipartimento di Scienze Farmaceutiche, Università di Salerno and BioUniverSA SRL, Salerno, Italy
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35
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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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36
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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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