1
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Ikbal SA, Zhao P, Ehara M, Akine S. Acceleration and deceleration of chirality inversion speeds in a dynamic helical metallocryptand by alkali metal ion binding. SCIENCE ADVANCES 2023; 9:eadj5536. [PMID: 37922347 PMCID: PMC10624348 DOI: 10.1126/sciadv.adj5536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/02/2023] [Indexed: 11/05/2023]
Abstract
We report that the chirality inversion kinetics of a trinickel(II) cryptand can be controlled by guest recognition in the cryptand cavity. When the guest was absent, the nickel(II) cryptand underwent a dynamic interconversion between the P and M forms in solution, preferring the M form, with a half-life of t1/2 = 4.99 min. The P/M equilibrium is reversed to P-favored by binding with an alkali metal ion in the cryptand cavity. The timescale of this M→P inversion kinetics was both notably accelerated and decelerated by the guest binding (t1/2 = 0.182 min for K+ complex; 186 min for Cs+ complex); thus, the equilibration rate constants differed by up to 1000-fold depending on the guest metal ions. This acceleration/deceleration can be explained in terms of the virtual binding constants at the transition state of the P/M chirality inversion; K+ binding more stabilizes the transition state rather than the P and M forms to result in the acceleration.
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Affiliation(s)
- Sk Asif Ikbal
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Pei Zhao
- Research Center for Computational Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Masahiro Ehara
- Research Center for Computational Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Shigehisa Akine
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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2
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Ousaka N, MacLachlan MJ, Akine S. Stapling strategy for slowing helicity interconversion of α-helical peptides and isolating chiral auxiliary-free one-handed forms. Nat Commun 2023; 14:6834. [PMID: 37884515 PMCID: PMC10603036 DOI: 10.1038/s41467-023-42493-y] [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: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
In nature, α-helical peptides adopt right-handed conformations that are dictated by L-amino acids. Isolating one-handed α-helical peptides composed of only achiral components remains a significant challenge. Here, this goal is achieved by optical resolution of the corresponding racemic (quasi-)static α-helical peptide with double stapling, which effectively freezes the interconversion between the right-handed (P)- and left-handed (M)-α-helices. An as-obtained doubly stapled analogue having an unprotected L-valine residue at the C-terminus transforms from a kinetically trapped (M)-α-helix to a thermodynamically stable (P)-α-helix upon heating. In contrast, the corresponding singly stapled α-helical peptide undergoes an acid/base-triggered and solvent-induced reversible inversion of its preferred helicity within minutes. The interconversion rates of the singly and doubly stapled α-helical peptide foldamers are approximately 106 and 1012 times slower, respectively, than that of a non-stapled dynamic helical peptide. Therefore, the enantiopure doubly-stapled (quasi-)static α-helical peptide would retain its optical activity for several years at 25 °C.
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Affiliation(s)
- Naoki Ousaka
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
| | - Mark J MacLachlan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Quantum Matter Institute, University of British Columbia, 2355 East Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Shigehisa Akine
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, 920-1192, Japan.
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3
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Rohmer M, Freudenberg J, Binder WH. Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp). Macromol Biosci 2022; 23:e2200344. [PMID: 36377468 DOI: 10.1002/mabi.202200344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/02/2022] [Indexed: 11/16/2022]
Abstract
The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 "Polymers under multiple constraints: restricted and controlled molecular order and mobility" this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.
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Affiliation(s)
- Matthias Rohmer
- Macromolecular Chemistry, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Jan Freudenberg
- Macromolecular Chemistry, Von-Danckelmann-Platz 4, 06120, Halle, Germany
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4
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Bodero L, Guitot K, Lensen N, Lequin O, Brigaud T, Ongeri S, Chaume G. Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib foldamers to Control, Quantify and Assign the Helical Screw-Sense. Chemistry 2021; 28:e202103887. [PMID: 34890083 DOI: 10.1002/chem.202103887] [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: 10/28/2021] [Indexed: 11/11/2022]
Abstract
Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 3 10 helical structures with equal population of left- and right-handed conformers. Yet, the screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1 H and 19 F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N -terminus induces a reversal of the screw-sense preference of the 3 10 -helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19 F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest.
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Affiliation(s)
| | | | | | - Olivier Lequin
- Sorbonne Université Campus Pierre et Marie Curie: Sorbonne Universite Campus Pierre et Marie Curie, chemistry, FRANCE
| | | | | | - Grégory Chaume
- CY Cergy Paris Universite, Chemistry, 5 mail Gay Lussac, 95000, Cergy-Pontoise, FRANCE
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5
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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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6
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Zheng L, Guo S, Wang C, Wang Y, Fan Y, Chen X, Zhang K, Jiang H. Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains. Chempluschem 2021; 86:340-346. [PMID: 33624952 DOI: 10.1002/cplu.202000824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/13/2021] [Indexed: 11/09/2022]
Abstract
A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by 1 H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.
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Affiliation(s)
- Lu Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, P. R. China
| | - Shengzhu Guo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Chu Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanqing Fan
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Hua Jiang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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7
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Lister FGA, Eccles N, Pike SJ, Brown RA, Whitehead GFS, Raftery J, Webb SJ, Clayden J. Bis-pyrene probes of foldamer conformation in solution and in phospholipid bilayers. Chem Sci 2018; 9:6860-6870. [PMID: 30310619 PMCID: PMC6114994 DOI: 10.1039/c8sc02532k] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/16/2018] [Indexed: 11/21/2022] Open
Abstract
Exploring the detailed structural features of synthetic molecules in the membrane phase requires sensitive probes of conformation. Here we describe the design, synthesis and characterization of bis(pyrene) probes that report conformational changes in membrane-active dynamic foldamers. The probes were designed to distinguish between left-handed (M) and right-handed (P) screw-sense conformers of 310-helical α-aminoisobutyric acid (Aib) peptide foldamers, both in solution and in bilayer membranes. Several different bis(pyrene) probes were synthesized and ligated to the C-terminus of Aib tetramers that had different chiral residues at the N-terminus, residues that favored either an M or a P screw-sense in the 310-helix. The readily synthesized and conveniently incorporated N-acetyl-1,2-bis(pyren-1'-yl)ethylenediamine probe proved to have the best properties. In solution, changes in foldamer screw-sense induced substantial changes in the ratio of excimer/monomer fluorescence emission (E/M) for this reporter of conformation, with X-ray crystallography revealing that opposite screw-senses produce very different interpyrene distances in the reporter. In bilayers, this convenient and sensitive fluorescent reporter allowed, for the first time, an investigation of how the chirality of natural phospholipids affects foldamer conformation.
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Affiliation(s)
- Francis G A Lister
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - Natasha Eccles
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK . .,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Sarah J Pike
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK . .,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK.,Faculty of Life Sciences , University of Bradford , Bradford , West Yorkshire BD7 1DP , UK
| | - Robert A Brown
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - George F S Whitehead
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - James Raftery
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - Simon J Webb
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK . .,Manchester Institute of Biotechnology , University of Manchester , 131 Princess St , Manchester M1 7DN , UK
| | - Jonathan Clayden
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK .
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8
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Cho J, Ishida Y, Aida T. Helical Oligopeptides of a Quaternized Amino Acid with Tunable Chiral-Induction Ability and an Anomalous pH Response. Chemistry 2017; 23:4818-4826. [DOI: 10.1002/chem.201605460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Joonil Cho
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
- Emergent Bioinspired Soft Matter Research Team; Center for Emergent Matter Science; RIKEN; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Yasuhiro Ishida
- Emergent Bioinspired Soft Matter Research Team; Center for Emergent Matter Science; RIKEN; 2-1 Hirosawa, Wako Saitama 351-0198 Japan
| | - Takuzo Aida
- Department of Chemistry and Biotechnology; School of Engineering; The University of Tokyo; 7-3-1 Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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9
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Shin S, Lee M, Guzei IA, Kang YK, Choi SH. 12/10-Helical β-Peptide with Dynamic Folding Propensity: Coexistence of Right- and Left-Handed Helices in an Enantiomeric Foldamer. J Am Chem Soc 2016; 138:13390-13395. [DOI: 10.1021/jacs.6b08235] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Seonho Shin
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Mihye Lee
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Ilia A. Guzei
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, Chungbuk 28644, Korea
| | - Soo Hyuk Choi
- Department
of Chemistry, Yonsei University, Seoul 03722, Korea
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10
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Crisma M, Toniolo C. Helical screw-sense preferences of peptides based on chiral, Cα-tetrasubstituted α-amino acids. Biopolymers 2016; 104:46-64. [PMID: 25363510 DOI: 10.1002/bip.22581] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/14/2014] [Accepted: 10/24/2014] [Indexed: 01/09/2023]
Abstract
The preferred helical screw senses of chiral α-amino acids with a C(α)-tetrasubstituted α-carbon atom, as determined in the crystal state by X-ray diffraction analyses on derivatives and peptides, are reviewed. This survey covers C(α)-methylated and C(α)-ethylated α-amino acids, as well as α-amino acids cyclized on the α-carbon, including those characterized by the combination of lack of chirality at the α-carbon with either side-chain or axial chirality. Although, in general, chiral C(α)-tetrasubstituted α-amino acids show a less pronounced bias toward a single helical screw sense than their proteinogenic (C(α)-trisubstituted) counterparts, our analysis highlights significant differences in terms of magnitude and direction of such a bias among the various sub-families of residues, and between individual amino acids within each sub-family as well. The experimental findings can be rationalized, at least in part, on the basis of steric considerations.
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Affiliation(s)
- Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131, Padova, Italy
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11
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Brioche J, Pike S, Tshepelevitsh S, Leito I, Morris GA, Webb SJ, Clayden J. Conformational Switching of a Foldamer in a Multicomponent System by pH-Filtered Selection between Competing Noncovalent Interactions. J Am Chem Soc 2015; 137:6680-91. [PMID: 25915163 PMCID: PMC4520694 DOI: 10.1021/jacs.5b03284] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 12/26/2022]
Abstract
Biomolecular systems are able to respond to their chemical environment through reversible, selective, noncovalent intermolecular interactions. Typically, these interactions induce conformational changes that initiate a signaling cascade, allowing the regulation of biochemical pathways. In this work, we describe an artificial molecular system that mimics this ability to translate selective noncovalent interactions into reversible conformational changes. An achiral but helical foldamer carrying a basic binding site interacts selectively with the most acidic member of a suite of chiral ligands. As a consequence of this noncovalent interaction, a global absolute screw sense preference, detectable by (13)C NMR, is induced in the foldamer. Addition of base, or acid, to the mixture of ligands competitively modulates their interaction with the binding site, and reversibly switches the foldamer chain between its left and right-handed conformations. As a result, the foldamer-ligand mixture behaves as a biomimetic chemical system with emergent properties, functioning as a "proton-counting" molecular device capable of providing a tunable, pH-dependent conformational response to its environment.
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Affiliation(s)
- Julien Brioche
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
| | - Sarah
J. Pike
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
| | - Sofja Tshepelevitsh
- Institute
of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Ivo Leito
- Institute
of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Gareth A. Morris
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
| | - Simon J. Webb
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess
Street, Manchester M1 7DN, United Kingdom
| | - Jonathan Clayden
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United
Kingdom
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12
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Le Bailly BAF, Byrne L, Diemer V, Foroozandeh M, Morris GA, Clayden J. Flaws in foldamers: conformational uniformity and signal decay in achiral helical peptide oligomers. Chem Sci 2015; 6:2313-2322. [PMID: 29308146 PMCID: PMC5645781 DOI: 10.1039/c4sc03944k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/19/2015] [Indexed: 11/21/2022] Open
Abstract
Although foldamers, by definition, are extended molecular structures with a well-defined conformation, minor conformers must be populated at least to some extent in solution. We present a quantitative analysis of these minor conformers for a series of helical oligomers built from achiral but helicogenic α-amino acids. By measuring the chain length dependence or chain position dependence of NMR or CD quantities that measure screw-sense preference in a helical oligomer, we quantify values for the decay constant of a conformational signal as it passes through the molecular structure. This conformational signal is a perturbation of the racemic mixture of M and P helices that such oligomers typically adopt by the inclusion of an N or C terminal chiral inducer. We show that decay constants may be very low (<1% signal loss per residue) in non-polar solvents, and we evaluate the increase in decay constant that results in polar solvents, at higher temperatures, and with more conformationally flexible residues such as Gly. Decay constants are independent of whether the signal originates from the N or the C terminus. By interpreting the decay constant in terms of the probability with which conformations containing a screw-sense reversal are populated, we quantify the populations of these alternative minor conformers within the overall ensemble of secondary structures adopted by the foldamer. We deduce helical persistence lengths for Aib polymers that allow us to show that in a non-polar solvent a peptide helix, even in the absence of chiral residues, may continue with the same screw sense for approximately 200 residues.
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Affiliation(s)
- Bryden A F Le Bailly
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - Liam Byrne
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - Vincent Diemer
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | | | - Gareth A Morris
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
| | - Jonathan Clayden
- School of Chemistry , University of Manchester , Oxford Road , Manchester M13 9PL , UK .
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13
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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14
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Maffucci I, Pellegrino S, Clayden J, Contini A. Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids. J Phys Chem B 2015; 119:1350-61. [PMID: 25528885 DOI: 10.1021/jp510775e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21 20133 Milano, Italy
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15
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Byrne L, Solà J, Clayden J. Screw sense alone can govern enantioselective extension of a helical peptide by kinetic resolution of a racemic amino acid. Chem Commun (Camb) 2015; 51:10965-8. [DOI: 10.1039/c5cc01790d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Helical secondary structure alone, even in the absence of local chiral residues, can direct the enantioselectivity of peptide coupling.
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Affiliation(s)
- Liam Byrne
- School of Chemistry
- University of Manchester
- Manchester M13 9PL
- UK
| | - Jordi Solà
- School of Chemistry
- University of Manchester
- Manchester M13 9PL
- UK
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16
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Bocchinfuso G, Conflitti P, Raniolo S, Caruso M, Mazzuca C, Gatto E, Placidi E, Formaggio F, Toniolo C, Venanzi M, Palleschi A. Aggregation propensity of Aib homo-peptides of different length: an insight from molecular dynamics simulations. J Pept Sci 2014; 20:494-507. [DOI: 10.1002/psc.2648] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/16/2014] [Accepted: 04/16/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Gianfranco Bocchinfuso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Paolo Conflitti
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Stefano Raniolo
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Mario Caruso
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Claudia Mazzuca
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Emanuela Gatto
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Ernesto Placidi
- Department of Physics; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
- CNR-ISM; Via Fosso del Cavaliere 100 I-00133 Roma Italy
| | - Fernando Formaggio
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Claudio Toniolo
- Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry; University of Padova; I-35131 Padua Italy
| | - Mariano Venanzi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome ‘Tor Vergata’; I-00133 Rome Italy
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17
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De Poli M, Byrne L, Brown RA, Solà J, Castellanos A, Boddaert T, Wechsel R, Beadle JD, Clayden J. Engineering the Structure of an N-Terminal β-Turn To Maximize Screw-Sense Preference in Achiral Helical Peptide Chains. J Org Chem 2014; 79:4659-75. [DOI: 10.1021/jo500714b] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matteo De Poli
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Liam Byrne
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Robert A. Brown
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jordi Solà
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | | | - Thomas Boddaert
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Romina Wechsel
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan D. Beadle
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan Clayden
- School
of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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18
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Orcel U, De Poli M, De Zotti M, Clayden J. The N-Terminal Nonapeptide of Cephaibols A and C: A Naturally Occurring Example of Mismatched Helical Screw-Sense Control. Chemistry 2013; 19:16357-65. [DOI: 10.1002/chem.201302648] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Indexed: 12/14/2022]
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19
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De Poli M, De Zotti M, Raftery J, Aguilar JA, Morris GA, Clayden J. Left-handed helical preference in an achiral peptide chain is induced by an L-amino acid in an N-terminal type II β-turn. J Org Chem 2013; 78:2248-55. [PMID: 23316729 DOI: 10.1021/jo302705k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oligomers of the achiral amino acid Aib adopt helical conformations in which the screw-sense may be controlled by a single N-terminal residue. Using crystallographic and NMR techniques, we show that the left- or right-handed sense of helical induction arises from the nature of the β-turn at the N terminus: the tertiary amino acid L-Val induces a left-handed type II β-turn in both the solid state and in solution, while the corresponding quaternary amino acid L-α-methylvaline induces a right-handed type III β-turn.
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Affiliation(s)
- Matteo De Poli
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK
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20
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Ceccacci F, Mancini G, Rossi P, Scrimin P, Sorrenti A, Tecilla P. Deracemization and the first CD spectrum of a 310-helical peptide made of achiral α-amino-isobutyric acid residues in a chiral membrane mimetic environment. Chem Commun (Camb) 2013; 49:10133-5. [DOI: 10.1039/c3cc44713h] [Citation(s) in RCA: 8] [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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21
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Pike SJ, De Poli M, Zawodny W, Raftery J, Webb SJ, Clayden J. Diastereotopic fluorine substituents as 19F NMR probes of screw-sense preference in helical foldamers. Org Biomol Chem 2013; 11:3168-76. [DOI: 10.1039/c3ob40463c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Brown RA, Marcelli T, De Poli M, Solà J, Clayden J. Induction of Unexpected Left-Handed Helicity by an N-Terminal L-Amino Acid in an Otherwise Achiral Peptide Chain. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107583] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Brown RA, Marcelli T, De Poli M, Solà J, Clayden J. Induction of unexpected left-handed helicity by an N-terminal L-amino acid in an otherwise achiral peptide chain. Angew Chem Int Ed Engl 2012; 51:1395-9. [PMID: 22294355 DOI: 10.1002/anie.201107583] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Robert A Brown
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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24
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Solà J, Morris GA, Clayden J. Measuring Screw-Sense Preference in a Helical Oligomer by Comparison of 13C NMR Signal Separation at Slow and Fast Exchange. J Am Chem Soc 2011; 133:3712-5. [DOI: 10.1021/ja1097034] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jordi Solà
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Gareth A. Morris
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan Clayden
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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25
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Nanometer-Range Communication of Stereochemical Information by Reversible Switching of Molecular Helicity. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001130] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Nanometer-Range Communication of Stereochemical Information by Reversible Switching of Molecular Helicity. Angew Chem Int Ed Engl 2010; 49:6836-9. [DOI: 10.1002/anie.201001130] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Solà J, Helliwell M, Clayden J. N- versus C-Terminal Control over the Screw-Sense Preference of the Configurationally Achiral, Conformationally Helical Peptide Motif Aib8GlyAib8. J Am Chem Soc 2010; 132:4548-9. [DOI: 10.1021/ja100662d] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jordi Solà
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Madeleine Helliwell
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jonathan Clayden
- School of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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28
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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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29
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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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30
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Shenkarev ZO, Paramonov AS, Nadezhdin KD, Bocharov EV, Kudelina IA, Skladnev DA, Tagaev AA, Yakimenko ZA, Ovchinnikova TV, Arseniev AS. Antiamoebin I in Methanol Solution: Rapid Exchange between Right-Handed and Left-Handed310-Helical Conformations. Chem Biodivers 2007; 4:1219-42. [PMID: 17589862 DOI: 10.1002/cbdv.200790106] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antiamoebin I (Aam-I) is a membrane-active peptaibol antibiotic isolated from fungal species belonging to the genera Cephalosporium, Emericellopsis, Gliocladium, and Stilbella. Antiamoebin I has the amino acid sequence: Ac-Phe(1)-Aib-Aib-Aib-Iva-Gly-Leu-Aib(8)-Aib-Hyp-Gln-Iva-Hyp-Aib-Pro-Phl(16). By using the uniformly (13)C,(15)N-labeled sample of Aam-I, the set of conformationally dependent J couplings and (3h)J(NC) couplings through H-bonds were measured. Analysis of these data along with the data on magnetic nonequivalence of the (13)C(beta) nuclei (Deltadelta((13)C(beta))) in Aib and Iva residues allowed us to draw the univocal conclusion that the N-terminal part (Phe(1)-Gly(6)) of Aam-I in MeOH solution is in fast exchange between the right-handed and left-handed 3(10)-helical conformations, with an approximately equal population of both states. An additional conformational exchange process was found at the Aib(8) residue. The (15)N-NMR-relaxation and CD-spectroscopy measurements confirmed these findings. Molecular modeling and Monte Carlo simulations revealed that both exchange processes are correlated and coupled with significant hinge-bending motions around the Aib(8) residue. Our results explain relatively low activity of Aam-I with respect to other 15-amino acid residue peptaibols (for example, zervamicin) in functional and biological tests. The high dynamic 'propensity' possibly prevents both initial binding of the antiamoebin to the membrane and subsequent formation of stable ionic channels according to the barrel-stave mechanism.
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Affiliation(s)
- Zakhar O Shenkarev
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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31
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Kubasik M, Blom A. Acceleration of Short Helical Peptide Conformational Dynamics by Trifluoroethanol in an Organic Solvent. Chembiochem 2005; 6:1187-90. [PMID: 15937985 DOI: 10.1002/cbic.200400198] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew Kubasik
- Department of Chemistry, Fairfield University, Fairfield, CT 06824, USA.
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