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Dormán G, Nakamura H, Pulsipher A, Prestwich GD. The Life of Pi Star: Exploring the Exciting and Forbidden Worlds of the Benzophenone Photophore. Chem Rev 2016; 116:15284-15398. [PMID: 27983805 DOI: 10.1021/acs.chemrev.6b00342] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The widespread applications of benzophenone (BP) photochemistry in biological chemistry, bioorganic chemistry, and material science have been prominent in both academic and industrial research. BP photophores have unique photochemical properties: upon n-π* excitation at 365 nm, a biradicaloid triplet state is formed reversibly, which can abstract a hydrogen atom from accessible C-H bonds; the radicals subsequently recombine, creating a stable covalent C-C bond. This light-directed covalent attachment process is exploited in many different ways: (i) binding/contact site mapping of ligand (or protein)-protein interactions; (ii) identification of molecular targets and interactome mapping; (iii) proteome profiling; (iv) bioconjugation and site-directed modification of biopolymers; (v) surface grafting and immobilization. BP photochemistry also has many practical advantages, including low reactivity toward water, stability in ambient light, and the convenient excitation at 365 nm. In addition, several BP-containing building blocks and reagents are commercially available. In this review, we explore the "forbidden" (transitions) and excitation-activated world of photoinduced covalent attachment of BP photophores by touring a colorful palette of recent examples. In this exploration, we will see the pros and cons of using BP photophores, and we hope that both novice and expert photolabelers will enjoy and be inspired by the breadth and depth of possibilities.
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Affiliation(s)
- György Dormán
- Targetex llc , Dunakeszi H-2120, Hungary.,Faculty of Pharmacy, University of Szeged , Szeged H-6720, Hungary
| | - Hiroyuki Nakamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology , Yokohama 226-8503, Japan
| | - Abigail Pulsipher
- GlycoMira Therapeutics, Inc. , Salt Lake City, Utah 84108, United States.,Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
| | - Glenn D Prestwich
- Division of Head and Neck Surgery, Rhinology - Sinus and Skull Base Surgery, Department of Surgery, University of Utah School of Medicine , Salt Lake City, Utah 84108, United States
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Tavenor NA, Silva KI, Saxena S, Horne WS. Origins of structural flexibility in protein-based supramolecular polymers revealed by DEER spectroscopy. J Phys Chem B 2014; 118:9881-9. [PMID: 25060334 PMCID: PMC4141697 DOI: 10.1021/jp505643w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Modular assembly of bio-inspired supramolecular polymers is a powerful technique to develop new soft nanomaterials, and protein folding is a versatile basis for preparing such materials. Previous work demonstrated a significant difference in the physical properties of closely related supramolecular polymers composed of building blocks in which identical coiled-coil-forming peptides are cross-linked by one of two subtly different organic linkers (one flexible and the other rigid). Herein, we investigate the molecular basis for this observation by isolating a single subunit of the supramolecular polymer chain and probing its structure and conformational flexibility by double electron-electron resonance (DEER) spectroscopy. Experimental spin-spin distance distributions for two different labeling sites coupled with molecular dynamics simulations provide insights into how the linker structure impacts chain dynamics in the coiled-coil supramolecular polymer.
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Affiliation(s)
- Nathan A Tavenor
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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3
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Wright K, Alvarez AB, Crisma M, Toffoletti A, Formaggio F, Toniolo C. 2-Amino-1,2,3,6-tetrahydro-6-oxocyclopenta[c]fluorene-2-carboxylic Acid (FlAib), a Completely Rigidified, Fluoren-9-one-Basedα-Amino Acid. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200490] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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4
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Caliandro R, Carrozzini B, Cascarano GL, Comunale G, Giacovazzo C. On the use of theCmap in Patterson deconvolution procedures. Acta Crystallogr A 2012; 69:98-107. [DOI: 10.1107/s0108767312040469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/25/2012] [Indexed: 11/10/2022] Open
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Antimicrobial lipopeptaibol trichogin GA IV: role of the three Aib residues on conformation and bioactivity. Amino Acids 2012; 43:1761-77. [DOI: 10.1007/s00726-012-1261-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 02/28/2012] [Indexed: 11/26/2022]
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6
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Studying protein–peptide interactions using benzophenone units: A case study of protein kinase B/Akt and its inhibitor PTR6154. Anal Biochem 2012; 421:750-4. [DOI: 10.1016/j.ab.2011.11.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 11/17/2011] [Accepted: 11/23/2011] [Indexed: 11/20/2022]
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7
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The spin label amino acid TOAC and its uses in studies of peptides: chemical, physicochemical, spectroscopic, and conformational aspects. Biophys Rev 2012; 4:45-66. [PMID: 22347893 PMCID: PMC3271205 DOI: 10.1007/s12551-011-0064-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/20/2011] [Indexed: 01/21/2023] Open
Abstract
We review work on the paramagnetic amino acid 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid, TOAC, and its applications in studies of peptides and peptide synthesis. TOAC was the first spin label probe incorporated in peptides by means of a peptide bond. In view of the rigid character of this cyclic molecule and its attachment to the peptide backbone via a peptide bond, TOAC incorporation has been very useful to analyze backbone dynamics and peptide secondary structure. Many of these studies were performed making use of EPR spectroscopy, but other physical techniques, such as X-ray crystallography, CD, fluorescence, NMR, and FT-IR, have been employed. The use of double-labeled synthetic peptides has allowed the investigation of their secondary structure. A large number of studies have focused on the interaction of peptides, both synthetic and biologically active, with membranes. In the latter case, work has been reported on ligands and fragments of GPCR, host defense peptides, phospholamban, and β-amyloid. EPR studies of macroscopically aligned samples have provided information on the orientation of peptides in membranes. More recent studies have focused on peptide–protein and peptide–nucleic acid interactions. Moreover, TOAC has been shown to be a valuable probe for paramagnetic relaxation enhancement NMR studies of the interaction of labeled peptides with proteins. The growth of the number of TOAC-related publications suggests that this unnatural amino acid will find increasing applications in the future.
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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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9
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De Zotti M, Biondi B, Peggion C, Formaggio F, Park Y, Hahm KS, Toniolo C. Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics. Org Biomol Chem 2011; 10:1285-99. [PMID: 22179201 DOI: 10.1039/c1ob06178j] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131, Padova, Italy
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Moretto A, Crisma M, Formaggio F, Toniolo C. Building a bridge between peptide chemistry and organic chemistry: intramolecular macrocyclization reactions and supramolecular chemistry with helical peptide substrates. Biopolymers 2011; 94:721-32. [PMID: 20564031 DOI: 10.1002/bip.21445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In our ongoing efforts to build a bridge between peptide chemistry and organic chemistry, we are currently investigating: (1) two types of intramolecular macrocyclization reactions in 3(10)-helical peptides, and (2) a peptido[2]rotaxane molecular machine as a supramolecular tool using a 3(10)-helical peptide as the axle. More specifically, we studied the following two reactions: (a) the intramolecular ring-closing olefin metathesis between two amino acid residues with side chains bearing an allyl group, and (b) the intramolecular Paternò-Yang photoreaction, using a benzophenone-based amino acid as a photoaffinity reagent for a Met residue. Both reactions involve formation of a new C--C bond. As for the supramolecular system examined, we were able to identify the two stations of a new peptido[2]rotaxane characterized by an -(Aib)(6)- axle and to reversibly switch the aromatic tetramide macrocyclic wheel from one station to the next. This article summarizes the information available in the literature from other groups and the published/unpublished data originated from our laboratory on these research areas.
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Affiliation(s)
- Alessandro Moretto
- Department of Chemistry, Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
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11
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Arsenault J, Cabana J, Fillion D, Leduc R, Guillemette G, Lavigne P, Escher E. Temperature dependent photolabeling of the human angiotensin II type 1 receptor reveals insights into its conformational landscape and its activation mechanism. Biochem Pharmacol 2010; 80:990-9. [DOI: 10.1016/j.bcp.2010.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/07/2010] [Accepted: 06/07/2010] [Indexed: 11/15/2022]
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12
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Carrozzini B, Cascarano GL, Giacovazzo C. The cross-correlation function: main properties and first applications. J Appl Crystallogr 2010. [DOI: 10.1107/s0021889809049346] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
When a model structure, and more generally a model electron density ρM(r), is available, its cross-correlation functionC(u) with the unknown true structure ρ(r) cannot be exactly calculated. A useful approximation ofC(u) is obtained by replacing exp[i(φh − φMh)] by its expected value. In this caseC′(u), a potentially useful approximation of the functionC(u), is obtained. In this paper the main crystallographic properties of the functionsC(u) andC′(u) are established. It is also shown that such functions may be useful for the success of the phasing process.
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Wright K, Moretto A, Crisma M, Wakselman M, Mazaleyrat JP, Formaggio F, Toniolo C. A new tool for photoaffinity labeling studies: a partially constrained, benzophenone based, α-amino acid. Org Biomol Chem 2010; 8:3281-6. [DOI: 10.1039/c003943h] [Citation(s) in RCA: 10] [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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14
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Ghosh AK, Devenport M, Jethwaney D, Kalume DE, Pandey A, Anderson VE, Sultan AA, Kumar N, Jacobs-Lorena M. Malaria parasite invasion of the mosquito salivary gland requires interaction between the Plasmodium TRAP and the Anopheles saglin proteins. PLoS Pathog 2009; 5:e1000265. [PMID: 19148273 PMCID: PMC2613030 DOI: 10.1371/journal.ppat.1000265] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 12/14/2008] [Indexed: 11/24/2022] Open
Abstract
SM1 is a twelve-amino-acid peptide that binds tightly to the Anopheles salivary gland and inhibits its invasion by Plasmodium sporozoites. By use of UV-crosslinking experiments between the peptide and its salivary gland target protein, we have identified the Anopheles salivary protein, saglin, as the receptor for SM1. Furthermore, by use of an anti-SM1 antibody, we have determined that the peptide is a mimotope of the Plasmodium sporozoite Thrombospondin Related Anonymous Protein (TRAP). TRAP binds to saglin with high specificity. Point mutations in TRAP's binding domain A abrogate binding, and binding is competed for by the SM1 peptide. Importantly, in vivo down-regulation of saglin expression results in strong inhibition of salivary gland invasion. Together, the results suggest that saglin/TRAP interaction is crucial for salivary gland invasion by Plasmodium sporozoites. Transmission of Plasmodium, the causative agent of malaria, requires the completion of a complex life cycle in the mosquito, which includes invasion of the salivary glands. This invasion depends on the recognition of mosquito salivary gland surface components by the parasite. This work demonstrates that interaction between the salivary-gland-specific surface protein saglin and the parasite surface protein TRAP is essential for invasion to occur. A better understanding of the mechanisms used by the parasite to develop in the mosquito may lead to novel approaches to intervene with the spread of the disease.
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Affiliation(s)
- Anil K. Ghosh
- Department of Molecular Microbiology and Immunology and Malaria Research Institute, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Martin Devenport
- Department of Molecular Microbiology and Immunology and Malaria Research Institute, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
| | - Deepa Jethwaney
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Dario E. Kalume
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology, and Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology, and Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Vernon E. Anderson
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Ali A. Sultan
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Nirbhay Kumar
- Department of Molecular Microbiology and Immunology and Malaria Research Institute, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (NK); (MJ-L)
| | - Marcelo Jacobs-Lorena
- Department of Molecular Microbiology and Immunology and Malaria Research Institute, Johns Hopkins School of Public Health, Baltimore, Maryland, United States of America
- * E-mail: (NK); (MJ-L)
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Moretto A, Crisma M, Formaggio F, Huck L, Mangion D, Leigh W, Toniolo C. Photoinduced Intramolecular Macrocyclization Reaction between a Bpa and a Met Residue in a Helical Peptide: 3D Structures of the Diastereomeric Products. Chemistry 2009; 15:67-70. [DOI: 10.1002/chem.200802066] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Aravinda S, Shamala N, Balaram P. Aib Residues in Peptaibiotics and Synthetic Sequences: Analysis of Nonhelical Conformations. Chem Biodivers 2008; 5:1238-62. [PMID: 18649312 DOI: 10.1002/cbdv.200890112] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Arsenault J, Renaud MPLH, Clément M, Fillion D, Guillemette G, Leduc R, Lavigne P, Escher E. Temperature-dependent variations of ligand-receptor contact points in hAT1. J Pept Sci 2007; 13:575-80. [PMID: 17600857 DOI: 10.1002/psc.875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Photoaffinity labelling is regularly used to investigate proteins, including peptidergic G protein-coupled receptors (GPCR). To this purpose benzophenone photolabels have been widely used to identify many contact residues in ligand-binding pockets. The three-dimensional binding environment of the human angiotensin II type 1 receptor hAT(1) has been determined using an iterative methionine mutagenesis strategy based on the photochemical properties and preferential incorporation of benzophenone onto methionine. This has led to the construction of a ligand-bound receptor structure. The present study investigated the effect of temperature on the accessibility of some of these contact points. The hAT(1) receptor and two representative Met mutants (H256M-hAT(1) and F293M-hAT(1)) from the iterative mutagenesis study were photolabelled with the benzophenone-ligand (125)I-[Sar(1), Bpa(8)]AngII at temperatures ranging from - 15 degrees C to 37 degrees C. Labelled receptors were partially purified and digested with cyanogen bromide to identify the contact points or segments. There were no changes in receptor contacts or labelling in the 7th transmembrane domains (TMD) of hAT(1) and F293M-hAT(1) across the temperature range. However, a temperature-dependent change in the ligand-receptor contact of H256M-hAT(1) was observed. At - 15 degrees C, H256M labelling was identical to that of hAT(1), indicating that the interaction was specific to the 7th TMD. Significant labelling changes were observed at higher temperatures and at 37 degrees C labelling occurred almost exclusively at mutated residue H256M-hAT(1) in the 6th TMD. Simultaneous competitive labelling of different areas of this target protein indicated that the ligand-receptor structure became increasingly fluctual at physiological temperatures, while a more compact, low mobility, and low energy conformation prevailed at low temperatures.
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Affiliation(s)
- J Arsenault
- Département de pharmacologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001, 12ième Avenue Nord, Sherbrooke, Quebec, J1H 5N4, Canada
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Abstract
Relevant parameters and stereochemical consequences of helices [alpha-helix, 3(10)-helix, beta-bend ribbon spiral, gamma-helix, 2.0(5)-helix, poly(Pro)(n) type-I and -II helices, and collagen triple helix] of peptides based on alpha-amino acids for use as templates in various branches of chemistry are briefly discussed.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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