1
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Takeuchi N, Taniguchi M, Kato Y, Takata R, Osaka I, Nakajima N, Hamada M, Koyama Y. Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units. Macromol Rapid Commun 2023; 44:e2300323. [PMID: 37668077 DOI: 10.1002/marc.202300323] [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: 06/02/2023] [Revised: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.
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Affiliation(s)
- Nanami Takeuchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masataka Taniguchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yuki Kato
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Riko Takata
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Noriyuki Nakajima
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masahiro Hamada
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhito Koyama
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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2
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Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
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Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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3
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Wegener KL, McGrath AE, Dixon NE, Oakley AJ, Scanlon DB, Abell AD, Bruning JB. Rational Design of a 3 10 -Helical PIP-Box Mimetic Targeting PCNA, the Human Sliding Clamp. Chemistry 2018; 24:11325-11331. [PMID: 29917264 DOI: 10.1002/chem.201801734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/17/2018] [Indexed: 12/29/2022]
Abstract
The human sliding clamp (PCNA) controls access to DNA for many proteins involved in DNA replication and repair. Proteins are recruited to the PCNA surface by means of a short, conserved peptide motif known as the PCNA-interacting protein box (PIP-box). Inhibitors of these essential protein-protein interactions may be useful as cancer therapeutics by disrupting DNA replication and repair in these highly proliferative cells. PIP-box peptide mimetics have been identified as a potentially rapid route to potent PCNA inhibitors. Here we describe the rational design and synthesis of the first PCNA peptidomimetic ligands, based on the high affinity PIP-box sequence from the natural PCNA inhibitor p21. These mimetics incorporate covalent i,i+4 side-chain/side-chain lactam linkages of different lengths, designed to constrain the peptides into the 310 -helical structure required for PCNA binding. NMR studies confirmed that while the unmodified p21 peptide had little defined structure in solution, mimetic ACR2 pre-organized into 310 -helical structure prior to interaction with PCNA. ACR2 displayed higher affinity binding than most known PIP-box peptides, and retains the native PCNA binding mode, as observed in the co-crystal structure of ACR2 bound to PCNA. This study offers a promising new strategy for PCNA inhibitor design for use as anti-cancer therapeutics.
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Affiliation(s)
- Kate L Wegener
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
| | - Amy E McGrath
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Nicholas E Dixon
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Aaron J Oakley
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, NSW, 2522, Australia
| | - Denis B Scanlon
- Department of Chemistry, The University of Adelaide, South Australia, 5005, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing (IPAS), Department of Chemistry, and the Centre for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing (IPAS), School of Biological Sciences, The University of Adelaide, South Australia, 5005, Australia
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4
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Pal S, Prabhakaran EN. Hydrogen bond surrogate stabilized water soluble 310-helix from a disordered pentapeptide containing coded α-amino acids. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.05.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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5
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Lin H, Jiang Y, Hu K, Zhang Q, He C, Wang T, Li Z. An in-tether sulfilimine chiral center induces β-turn conformation in short peptides. Org Biomol Chem 2018; 14:9993-9999. [PMID: 27722542 DOI: 10.1039/c6ob01805j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A sulfilimine chiral center in the tether at i, i + 3 positions of short peptides was systematically studied to elucidate the chirality-driven conformational changes. A rare and unexpected type III β-turn structure was induced in short peptides by an in-tether chiral center, supported by circular dichroism spectroscopy, NMR and X-ray crystallography.
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Affiliation(s)
- Huacan Lin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Yixiang Jiang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Kuan Hu
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Qingzhou Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
| | - Chuanxin He
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China.
| | - Tao Wang
- Department of Biology, South University of Science and Technology, Shenzhen, 518055, China.
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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6
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Mesterházy E, Lebrun C, Jancsó A, Delangle P. A Constrained Tetrapeptide as a Model of Cu(I) Binding Sites Involving Cu4S6 Clusters in Proteins. Inorg Chem 2018; 57:5723-5731. [DOI: 10.1021/acs.inorgchem.7b02735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Edit Mesterházy
- INAC, SYMMES, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
| | - Colette Lebrun
- INAC, SYMMES, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged H-6720, Hungary
| | - Pascale Delangle
- INAC, SYMMES, Université Grenoble Alpes, CEA, CNRS, F-38000 Grenoble, France
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7
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Yoshisada R, van Gijzel L, Jongkees SAK. Towards Tuneable Retaining Glycosidase-Inhibiting Peptides by Mimicry of a Plant Flavonol Warhead. Chembiochem 2017; 18:2333-2339. [PMID: 28984404 DOI: 10.1002/cbic.201700457] [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: 08/26/2017] [Indexed: 11/06/2022]
Abstract
Retaining glycosidases are an important class of enzymes involved in glycan degradation. To study better the role of specific enzymes in deglycosylation processes, and thereby the importance of particular glycosylation patterns, a set of potent inhibitors, each specific to a particular glycosidase, would be an invaluable toolkit. Towards this goal, we detail here a more in-depth study of a prototypical macrocyclic peptide inhibitor of the model retaining glycosidase human pancreatic α-amylase (HPA). Notably, incorporation of l-DOPA into this peptide affords an inhibitor of HPA with potency that is tenfold higher (Ki =480 pm) than that of the previously found consensus sequence. This represents a first successful step in converting a recently discovered natural-product-derived motif, already specific for the catalytic side-chain arrangement conserved in the active sites of retaining glycosidases, into a tuneable retaining glycosidase inhibition warhead.
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Affiliation(s)
- Ryoji Yoshisada
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Lieke van Gijzel
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
| | - Seino A K Jongkees
- Department of Chemical Biology and Drug Discovery, Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, Utrecht, 3584CG, The Netherlands
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8
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Peptides as Bio-inspired Molecular Electronic Materials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017. [PMID: 29081052 DOI: 10.1007/978-3-319-66095-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Understanding the electronic properties of single peptides is not only of fundamental importance to biology, but it is also pivotal to the realization of bio-inspired molecular electronic materials. Natural proteins have evolved to promote electron transfer in many crucial biological processes. However, their complex conformational nature inhibits a thorough investigation, so in order to study electron transfer in proteins, simple peptide models containing redox active moieties present as ideal candidates. Here we highlight the importance of secondary structure characteristic to proteins/peptides, and its relevance to electron transfer. The proposed mechanisms responsible for such transfer are discussed, as are details of the electrochemical techniques used to investigate their electronic properties. Several factors that have been shown to influence electron transfer in peptides are also considered. Finally, a comprehensive experimental and theoretical study demonstrates that the electron transfer kinetics of peptides can be successfully fine tuned through manipulation of chemical composition and backbone rigidity. The methods used to characterize the conformation of all peptides synthesized throughout the study are outlined, along with the various approaches used to further constrain the peptides into their geometric conformations. The aforementioned sheds light on the potential of peptides to one day play an important role in the fledgling field of molecular electronics.
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9
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10
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Wang FL, Guo Y, Li SJ, Guo QX, Shi J, Li YM. Diaminodiacid-based solid-phase synthesis of all-hydrocarbon stapled α-helical peptides. Org Biomol Chem 2015; 13:6286-90. [PMID: 25966031 DOI: 10.1039/c5ob00741k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An alternative stapling strategy is described herein using Fmoc-solid phase peptide synthesis (SPPS) that employed pre-prepared diaminodiacid building blocks to introduce all-hydrocarbon staples into peptides by on-resin cyclization. Compared to unstapled native peptides, diaminodiacid-based stapled peptides exhibited an increased α-helicity ratio and stability toward protease. Moreover, the linkage length was found to affect the bioactivity of the peptides and their ability to inhibit the Wnt pathway. Therefore, the new stapling method provides an alternative way to obtain stapled peptides with tunable linkers of diaminodiacids.
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Affiliation(s)
- Feng-Liang Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
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11
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Grubišić S, Brancato G, Barone V. An improved AMBER force field for α,α-dialkylated peptides: intrinsic and solvent-induced conformational preferences of model systems. Phys Chem Chem Phys 2013; 15:17395-407. [DOI: 10.1039/c3cp52721b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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12
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Yin H. Constrained peptides as miniature protein structures. ISRN BIOCHEMISTRY 2012; 2012:692190. [PMID: 25969758 PMCID: PMC4392992 DOI: 10.5402/2012/692190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022]
Abstract
This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.
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Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, 596 University of Colorado at Boulder, Boulder, CO 80309-0596, USA
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13
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Pujol AM, Lebrun C, Gateau C, Manceau A, Delangle P. Mercury-Sequestering Pseudopeptides with a Tris(cysteine) Environment in Water. Eur J Inorg Chem 2012. [DOI: 10.1002/ejic.201200484] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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14
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Grubišić S, Brancato G, Pedone A, Barone V. Extension of the AMBER force field to cyclic α,α dialkylated peptides. Phys Chem Chem Phys 2012; 14:15308-20. [DOI: 10.1039/c2cp42713c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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15
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Estieu-Gionnet K, Guichard G. Stabilized helical peptides: overview of the technologies and therapeutic promises. Expert Opin Drug Discov 2011; 6:937-63. [PMID: 22646216 DOI: 10.1517/17460441.2011.603723] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Helical structures in proteins and naturally occurring peptides play a major role in a variety of biological processes by mediating interactions with proteins and other macromolecules such as nucleic acids and lipid membranes. The use of short synthetic peptides encompassing helical segments to modulate or disrupt such interactions, when associated with human diseases, represents great pharmacological interest. AREAS COVERED Multiple chemical approaches have been developed to increase the conformational and metabolic stabilities of helical peptides and to improve their biomedical potential. After a brief overview of these technologies and the most recent developments, this review will focus on the main therapeutic areas and targets and will discuss their promise. EXPERT OPINION Potential benefits associated with increased helix stability extend beyond simple affinity enhancement. Some peptidomimetic helices are being endowed with features desirable for cellular activity such as increased resistance to proteolysis and/or cell permeability. Recent advances in the field of peptide and related peptidomimetic helices are not just conceptual, but are likely to be of practical utility in the process of optimizing peptides as clinical candidates, and developing medium-size therapeutics.
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Affiliation(s)
- Karine Estieu-Gionnet
- Institut Européen de Chimie et Biologie , Université de Bordeaux, CNRS UMR 5248, CBMN, 2 rue R. Escarpit, 33607 Pessac , France
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16
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Pujol AM, Gateau C, Lebrun C, Delangle P. A Series of Tripodal Cysteine Derivatives as Water‐Soluble Chelators that are Highly Selective for Copper(I). Chemistry 2011; 17:4418-28. [DOI: 10.1002/chem.201003613] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Anaïs M. Pujol
- INAC, Service de Chimie Inorganique et Biologique (UMR E3 CEA UJF), Commissariat à l'Energie Atomique, 17 rue des martyrs 38054 Grenoble cedex (France), Fax: (+33) 438785090
| | - Christelle Gateau
- INAC, Service de Chimie Inorganique et Biologique (UMR E3 CEA UJF), Commissariat à l'Energie Atomique, 17 rue des martyrs 38054 Grenoble cedex (France), Fax: (+33) 438785090
| | - Colette Lebrun
- INAC, Service de Chimie Inorganique et Biologique (UMR E3 CEA UJF), Commissariat à l'Energie Atomique, 17 rue des martyrs 38054 Grenoble cedex (France), Fax: (+33) 438785090
| | - Pascale Delangle
- INAC, Service de Chimie Inorganique et Biologique (UMR E3 CEA UJF), Commissariat à l'Energie Atomique, 17 rue des martyrs 38054 Grenoble cedex (France), Fax: (+33) 438785090
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17
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Kim YW, Kutchukian PS, Verdine GL. Introduction of all-hydrocarbon i,i+3 staples into alpha-helices via ring-closing olefin metathesis. Org Lett 2010; 12:3046-9. [PMID: 20527740 DOI: 10.1021/ol1010449] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The introduction of all-hydrocarbon i,i+3 staples into alpha-helical peptide scaffolds via ring-closing olefin metathesis (RCM) between two alpha-methyl,alpha-pentenylglycine residues incorporated at i and i+3 positions, which lie on the same face of the helix, has been investigated. The reactions were found to be highly dependent upon the side-chain stereochemistry of the amino acids undergoing RCM. The i,i+3 stapling system established here provides a potentially useful alternative to the well-established i,i+4 stapling system now in widespread use.
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Affiliation(s)
- Young-Woo Kim
- Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138, USA
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18
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Sheet T, Banerjee R. Sulfate ion interaction with 'anion recognition' short peptide motif at the N-terminus of an isolated helix: A conformational landscape. J Struct Biol 2010; 171:345-52. [PMID: 20570734 DOI: 10.1016/j.jsb.2010.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
Anion-binding motifs in proteins are typically conserved in sequence and conformation. Crystal structural studies have shown that such motifs often occur in loop regions preceding a helix and interaction with the anions can induce their well defined conformational changes. In order to understand the properties of such motifs in isolation, we have synthesized an 18-residue chimeric polypeptide whose C-terminal part is a designed helix and its N-terminal consists of a C(alpha)NN anion binding structural motif containing residues Leu-Gly-Lys-Gln (residues 107-110 of protein DNA-glycosylase). We present evidence for the interaction of a sulfate (SO(4)(2-)) ion with the L-G-K-Q segment using complementary spectroscopic techniques. Moreover, upon interaction with SO(4)(2-) ion the N-terminal L-G-K-Q segment undergoes a non-helical to helical transition similar to what is observed in protein crystal structure. This work clearly demonstrates the "local" nature of anion binding and the accompanying conformational change that helps in understanding the influence of sequence/structural context of anion binding in proteins.
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Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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19
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Helix Induction by Dirhodium: Access to Biocompatible Metallopeptides with Defined Secondary Structure. Chemistry 2010; 16:6651-9. [DOI: 10.1002/chem.200903092] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Madden MM, Vera CIR, Song W, Lin Q. Facile synthesis of stapled, structurally reinforced peptide helices via a photoinduced intramolecular 1,3-dipolar cycloaddition reaction. Chem Commun (Camb) 2009:5588-90. [PMID: 19753366 PMCID: PMC2765658 DOI: 10.1039/b912094g] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report the first use of a photoinduced 1,3-dipolar cycloaddition reaction in "stapling" peptide sidechains to reinforce a model peptide helical structure with moderate to excellent yields; the resulting pyrazoline "staplers" exhibit unique fluorescence useful in a cell permeability study.
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Affiliation(s)
- Michael M. Madden
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Claudia I. Rivera Vera
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Wenjiao Song
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260 USA
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21
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Banerjee R, Chattopadhyay S, Basu G. Conformational preferences of a short Aib/Ala-based water-soluble peptide as a function of temperature. Proteins 2009; 76:184-200. [PMID: 19137603 DOI: 10.1002/prot.22337] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amino acid Aib predisposes a peptide to be helical with context-dependent preference for either 3(10)- or alpha- or a mixed helical conformation. Short peptides also show an inherent tendency to be unfolded. To characterize helical and unfolded states adopted by water-soluble Aib-containing peptides, the conformational preference of Ac-Ala-Aib-Ala-Lys-Ala-Aib-Lys-Ala-Lys-Ala-Aib-Tyr-NH(2) was determined by CD, NMR and MD simulations as a function of temperature. Temperature-dependent CD data indicated the contribution of two major components, each an admixture of helical and extended/polyproline II structures. Both right- and left-handed helical conformations were detected from deconvolution of CD data and (13)C NMR experiments. The presence of a helical backbone, more pronounced at the N-terminal, and a temperature-induced shift in alpha-helix/3(10)-helix equilibrium, more pronounced at the C-terminal, emerged from NMR data. Starting from polyproline II, the N-terminal of the peptide folded into a helical backbone in MD simulations within 5 ns at 60 degrees C. Longer simulations showed a mixed-helical backbone to be stable over the entire peptide at 5 degrees C while at 60 degrees C the mixed-helix was either stable at the N-terminus or occurred in short stretches through out the peptide, along with a significant population of polyproline II. Our results point towards conformational heterogeneity of water-soluble Aib-based peptide helices and the associated subtleties. The problem of analyzing CD and NMR data of both left- and right-handed helices are discussed, especially the validity of the ellipticity ratio [theta](222)/[theta](207), as a reporter of alpha-/3(10)- population ratio, in right- and left-handed helical mixtures.
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Affiliation(s)
- Raja Banerjee
- Department of Biotechnology, West Bengal University of Technology, Kolkata 700064, India.
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22
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A 310-helix single turn enforced by crosslinking of lysines with 1,1′-ferrocenedicarboxylic acid. J Organomet Chem 2009. [DOI: 10.1016/j.jorganchem.2008.11.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Ousaka N, Sato T, Kuroda R. Total Helical-Sense Bias of an Achiral Peptide Main Chain Induced by a Chiral Side-Chain Bridge. J Am Chem Soc 2009; 131:3820-1. [DOI: 10.1021/ja8091714] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoki Ousaka
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tomohiro Sato
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Reiko Kuroda
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo 153-0041, Japan, and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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24
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Ousaka N, Tani N, Sekiya R, Kuroda R. Decelerated chirality interconversion of an optically inactive 310-helical peptide by metal chelation. Chem Commun (Camb) 2008:2894-6. [DOI: 10.1039/b803080d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Ousaka N, Sato T, Kuroda R. Intramolecular Crosslinking of an Optically Inactive 310-Helical Peptide: Stabilization of Structure and Helix Sense. J Am Chem Soc 2007; 130:463-5. [DOI: 10.1021/ja077857h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Naoki Ousaka
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo, Japan 153-0041 and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan 153-8902
| | - Tomohiro Sato
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo, Japan 153-0041 and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan 153-8902
| | - Reiko Kuroda
- Japan Science and Technology Agency, ERATO-SORST Kuroda Chiromorphology Team, 4-7-6, Komaba, Meguro-ku, Tokyo, Japan 153-0041 and Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, Japan 153-8902
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26
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Schweitzer-Stenner R, Gonzales W, Bourne GT, Feng JA, Marshall GR. Conformational Manifold of α-Aminoisobutyric Acid (Aib) Containing Alanine-Based Tripeptides in Aqueous Solution Explored by Vibrational Spectroscopy, Electronic Circular Dichroism Spectroscopy, and Molecular Dynamics Simulations. J Am Chem Soc 2007; 129:13095-109. [PMID: 17918837 DOI: 10.1021/ja0738430] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Widalys Gonzales
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Gregory T. Bourne
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Jianwen A. Feng
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
| | - Garland R. Marshall
- Contribution from the Department of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104 and Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110
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27
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Ahmed Z, Asher SA. UV resonance Raman investigation of a 3(10)-helical peptide reveals a rough energy landscape. Biochemistry 2006; 45:9068-73. [PMID: 16866352 DOI: 10.1021/bi060858m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used UVRRS at 194 and 204 nm excitation to examine the backbone conformation of a 13-residue polypeptide (gp41(659-671)) that has been shown by NMR to predominantly fold into a 3(10)-helix. Examination of the conformation sensitive AmIII(3) region indicates the peptide has significant populations of beta-turn, PPII, 3(10)-helix, and pi-helix-like conformations but little alpha-helix. We estimate that at 1 degree C on average six of the 12 peptide bonds are in folded conformations (predominantly 3(10)- and pi-helix), while the other six are in unfolded (beta-turn/PPII) conformations. The folded and unfolded populations do not change significantly as the temperature is increased from 1 to 60 degrees C, suggesting a unique energy landscape where the folded and unfolded conformations are essentially degenerate in energy and exhibit identical temperature dependences.
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Affiliation(s)
- Zeeshan Ahmed
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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28
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Schievano E, Pagano K, Mammi S, Peggion E. Conformational studies of Aib-rich peptides containing lactam-bridged side chains: evidence of 3(10)-helix formation. Biopolymers 2005; 80:294-302. [PMID: 15633206 DOI: 10.1002/bip.20199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Aib-rich side-chain lactam-bridged oligomers Ac-(Glu-Aib-Aib-Lys)n-Ala-OH with n = 1,2,3 were designed and synthesized as putative models of the 3(10)-helix. The lactam bridge between the side chains of L-Glu and L-Lys in (i)--(i + 3) positions was introduced in order to enhance the structural preference toward the right-handed 3(10)-helix. The conformational properties of the three peptides were studied in trifluoroethanol (TFE) solution by CD, NMR, and computer simulations. The structural information was derived mainly from the analysis of nuclear Overhauser effect spectroscopy spectra. The presence of alpha H(i)-HN(i + 2) and of alpha H(i)-HN(i + 3) connectivities and the absence of alpha H(i)-HN(i + 4) connectivities indicate that these peptides fold into a 3(10)-helix rather than into an alpha-helix. Based on these conformational features, stereospecific assignment of the Aib methyl groups was possible. The results of such experiments and of the subsequent distance geometry and restrained molecular dynamics simulations reveal a marked preference of these peptides for 3(10)-helix. The CD spectra of these peptides indicate that the helix content increases upon chain elongation. The CD spectrum of the trimer is characterized by a negative band at 200 nm and by a weak positive band around 220 nm. The CD spectrum in TFE is different from that observed in aqueous solution in the presence of SDS micelles, reported in our previous work, and from those reported by a different research group for 3(10)-helical peptides. A possible reason for these differences could rest in the presence of different equilibria of the conformer populations of the various peptides in different solvent systems.
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Affiliation(s)
- E Schievano
- Department of Chemistry, University of Padova, Institute of Biomolecular Chemistry, CNR, Via Marzolo 1, 35131 Padova, Italy
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29
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Futaki S, Kiwada T, Sugiura Y. Control of Peptide Structure and Recognition by Fe(III)-Induced Helix Destabilization. J Am Chem Soc 2004; 126:15762-9. [PMID: 15571399 DOI: 10.1021/ja046870o] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helical peptide segments that change their conformation due to external stimuli have often been employed in peptide-based molecular devices and materials. Using helices containing a pair of the iminodiacetic acid derivatives of lysine (Ida), we show that metal-induced helix destabilization is a promising approach to functional switching, especially for helices that are intrinsically stable. By i and i + 2 positioning of the Ida residues in a 17-residue model peptide, a significant decrease in the helical content was observed by the addition of Fe(III), whereas Fe(II) had no influence on the stability of the helix. The possibility of redox control of the helical structure was exemplified by the reduction of Fe(III) to Fe(II) using Na(2)S(2)O(4) followed by the subsequent reoxidation. Mutual recognition of the transcription factor Jun-derived leucine-zipper peptide segment with the Fos leucine-zipper segment containing Ida residues was also modulated in the presence of Fe(III).
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Affiliation(s)
- Shiroh Futaki
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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30
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Schievano E, Calisti T, Menegazzo I, Battistutta R, Peggion E, Mammi S, Palù G, Loregian A. pH-Dependent Conformational Changes and Topology of a Herpesvirus Translocating Peptide in a Membrane-Mimetic Environment. Biochemistry 2004; 43:9343-51. [PMID: 15260477 DOI: 10.1021/bi0496438] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pol peptide, an oligopeptide corresponding to the 27 C-terminal amino acids of DNA polymerase from herpes simplex virus type 1, has recently been suggested to translocate from endosomal compartments into the cytosol after being intracellularly delivered via a protein carrier. While an acidic environment was thought to be important for Pol peptide membrane translocation, the mechanism of translocation remains unclear. To investigate the influence of an acidic environment on the conformational properties of the peptide and on its propensity to interact with lipid bilayers, we characterized the structure of Pol peptide at different pH values by both circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. The influence of detergent micelles, which mimic biological lipid membranes, on the peptide secondary structure was also studied. Our CD results indicate that the peptide is in a random conformation in aqueous solution at both acidic and basic pH, whereas in the presence of dodecylphosphocholine (DPC) micelles, it assumes a partial alpha-helical structure which is significantly pH-dependent. An NMR study confirmed that, in the presence of DPC micelles, a short C-terminal alpha-helix is present at pH 6.5, whereas almost two-thirds of the peptide (residues 10-26) fold into an extended amphipathic alpha-helix at pH 4.0. The orientation of Pol peptide relative to the DPC micelle was investigated using paramagnetic probes at both pH 4.0 and 6.5. These studies show that the peptide inserts deeply into the micelle at pH 4.0, whereas it is more exposed to the aqueous environment at pH 6.5. On the basis of these results, a model which might explain the mechanism of translocation of Pol peptide from acidic endosomes to the cytosol is discussed.
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31
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Abstract
Side-chain lactam bridges linking amino acid residues that are spaced several residues apart in the linear sequence offer a convenient and flexible method for introducing conformational constraints into a peptide structure. The availability of a variety of selectively cleavable protecting groups for amines and carboxylic acids allows for several approaches to the synthesis of monocyclic, dicyclic, and bicyclic lactam-bridged peptides by solid-phase methods. Multicyclic structures are also accessible, but segment-condensation syntheses with solution-phase cyclizations are most likely to provide the best synthetic approach to these more complex constrained peptides. Lactam bridges linking (i, i + 3)-, (i, i + 4), and (i, i + 7)-spaced residue pairs have all proven useful for stabilization of alpha helices, and (i, i + 3)-linked residues have also been demonstrated to stabilize beta-turns. These structures are finding an increasing number of applications in protein biology, including studies of protein folding, protein aggregation, peptide ligand-receptor recognition, and the development of more potent peptide therapeutics. Defining the functional roles of the amphiphilic alpha-helices in medium-sized peptide hormones, and studying helix propagation from rigid, alpha-helix initiating bicyclic peptides are among the most exciting developments currently underway in this field.
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Affiliation(s)
- John W Taylor
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
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