1
|
Collie GW, Lombardo CM, Yoo SH, Pułka-Ziach K, Gabelica V, Mackereth CD, Rosu F, Guichard G. Crystal structures capture multiple stoichiometric states of an aqueous self-assembling oligourea foldamer. Chem Commun (Camb) 2021; 57:9514-9517. [PMID: 34546254 DOI: 10.1039/d1cc03604a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here an oligourea foldamer able to self-assemble in aqueous conditions into helix bundles of multiple stoichiometries. Importantly, we report crystal structures of several of these stoichiometries, providing a series of high-resolution snap-shots of the structural polymorphism of this foldamer and uncovering a novel self-assembly.
Collapse
Affiliation(s)
| | - Caterina M Lombardo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
| | | | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Cameron D Mackereth
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Bordeaux, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607, Pessac, France.
| |
Collapse
|
2
|
Abstract
Enzymes are predominantly proteins able to effectively and selectively catalyze highly complex biochemical reactions in mild reaction conditions. Nevertheless, they are limited to the arsenal of reactions that have emerged during natural evolution in compliance with their intrinsic nature, three-dimensional structures and dynamics. They optimally work in physiological conditions for a limited range of reactions, and thus exhibit a low tolerance for solvent and temperature conditions. The de novo design of synthetic highly stable enzymes able to catalyze a broad range of chemical reactions in variable conditions is a great challenge, which requires the development of programmable and finely tunable artificial tools. Interestingly, over the last two decades, chemists developed protein secondary structure mimics to achieve some desirable features of proteins, which are able to interfere with the biological processes. Such non-natural oligomers, so called foldamers, can adopt highly stable and predictable architectures and have extensively demonstrated their attractiveness for widespread applications in fields from biomedical to material science. Foldamer science was more recently considered to provide original solutions to the de novo design of artificial enzymes. This review covers recent developments related to peptidomimetic foldamers with catalytic properties and the principles that have guided their design.
Collapse
|
3
|
Buchanan C, Garvey CJ, Puskar L, Perlmutter P, Mechler A. Coordination crosslinking of helical substituted oligoamide nanorods with Cu(II). Supramol Chem 2020. [DOI: 10.1080/10610278.2020.1730839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Claire Buchanan
- Department of Chemistry and Physics, La Trobe University, Bundoora, Australia
| | - Christopher J Garvey
- Australian Nuclear Science and Technology Organization (ANSTO), Lucas Heights, Australia
- Lund Institute for Advanced Neutron and X-ray Science (LINXS), Lund, Sweden
- Biofilms Research Center for Biointerfaces, Department of Biomedical Science, Health and Society, Malmö University, Malmö, Sweden
| | - Ljiljana Puskar
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Patrick Perlmutter
- Department of Chemistry and Physics, La Trobe University, Bundoora, Australia
| | - Adam Mechler
- Department of Chemistry and Physics, La Trobe University, Bundoora, Australia
| |
Collapse
|
4
|
Kulkarni K, Habila N, Del Borgo MP, Aguilar MI. Novel Materials From the Supramolecular Self-Assembly of Short Helical β 3-Peptide Foldamers. Front Chem 2019; 7:70. [PMID: 30828574 PMCID: PMC6384263 DOI: 10.3389/fchem.2019.00070] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/25/2019] [Indexed: 11/13/2022] Open
Abstract
Self-assembly is the spontaneous organization of small components into higher-order structures facilitated by the collective balance of non-covalent interactions. Peptide-based self-assembly systems exploit the ability of peptides to adopt distinct secondary structures and have been used to produce a range of well-defined nanostructures, such as nanotubes, nanofibres, nanoribbons, nanospheres, nanotapes, and nanorods. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been reported to undergo supramolecular self-assembly, and have been used to produce materials-such as hydrogels-that are tailored for applications in tissue engineering, cell culture and drug delivery. This review provides an overview of self-assembled peptide nanostructures obtained via the supramolecular self-assembly of short β-peptide foldamers with a specific focus on N-acetyl-β3-peptides and their applications as bio- and nanomaterials.
Collapse
Affiliation(s)
| | | | - Mark P. Del Borgo
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute, Monash Univdersity, Melbourne, VIC, Australia
| | - Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology and Biomedicine Discovery Institute, Monash Univdersity, Melbourne, VIC, Australia
| |
Collapse
|
5
|
Collie GW, Bailly R, Pulka-Ziach K, Lombardo CM, Mauran L, Taib-Maamar N, Dessolin J, Mackereth CD, Guichard G. Molecular Recognition within the Cavity of a Foldamer Helix Bundle: Encapsulation of Primary Alcohols in Aqueous Conditions. J Am Chem Soc 2017; 139:6128-6137. [DOI: 10.1021/jacs.7b00181] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gavin W. Collie
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Remy Bailly
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Karolina Pulka-Ziach
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Caterina M. Lombardo
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| | - Laura Mauran
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Nada Taib-Maamar
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Jean Dessolin
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, All. Geoffroy Saint-Hilaire, 33600 Pessac, France
| | - Cameron D. Mackereth
- Univ. Bordeaux, Inserm, CNRS, ARNA Laboratory, U1212, UMR 5320, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33076 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert
Escarpit, 33607 Pessac, France
| |
Collapse
|
6
|
Satav T, Korevaar P, de Greef TFA, Huskens J, Jonkheijm P. Modulating the Nucleated Self-Assembly of Tri-β(3) -Peptides Using Cucurbit[n]urils. Chemistry 2016; 22:12675-9. [PMID: 27434777 PMCID: PMC6680354 DOI: 10.1002/chem.201602896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 01/18/2023]
Abstract
The modulation of the hierarchical nucleated self-assembly of tri-β(3) -peptides has been studied. β(3) -Tyrosine provided a handle to control the assembly process through host-guest interactions with CB[7] and CB[8]. By varying the cavity size from CB[7] to CB[8] distinct phases of assembling tri-β(3) -peptides were arrested. Given the limited size of the CB[7] cavity, only one aromatic β(3) -tyrosine can be simultaneously hosted and, hence, CB[7] was primarily acting as an inhibitor of self-assembly. In strong contrast, the larger CB[8] can form a ternary complex with two aromatic amino acids and hence CB[8] was acting primarily as cross-linker of multiple fibers and promoting the formation of larger aggregates. General insights on modulating supramolecular assembly can lead to new ways to introduce functionality in supramolecular polymers.
Collapse
Affiliation(s)
- Tushar Satav
- Molecular Nanofabrication Group of the MESA+, Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, Netherlands
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500AE, Enschede, Netherlands
| | - Peter Korevaar
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, Netherlands
| | - Tom F A de Greef
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication Group of the MESA+, Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, Netherlands.
| | - Pascal Jonkheijm
- Molecular Nanofabrication Group of the MESA+, Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500AE, Enschede, Netherlands.
- Bioinspired Molecular Engineering Laboratory of the MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, P.O. Box 217, 7500AE, Enschede, Netherlands.
| |
Collapse
|
7
|
Wang PSP, Schepartz A. β-Peptide bundles: Design. Build. Analyze. Biosynthesize. Chem Commun (Camb) 2016; 52:7420-32. [PMID: 27146019 DOI: 10.1039/c6cc01546h] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Peptides containing β-amino acids are unique non-natural polymers known to assemble into protein-like tertiary and quaternary structures. When composed solely of β-amino acids, the structures formed, defined assemblies of 14-helices called β-peptide bundles, fold cooperatively in water solvent into unique and discrete quaternary assemblies that are highly thermostable, bind complex substrates and metal ion cofactors, and, in certain cases, catalyze chemical reactions. In this Perspective, we recount the design and elaboration of β-peptide bundles and provide an outlook on recent, unexpected discoveries that could influence research on β-peptides and β-peptide bundles (and β-amino acid-containing proteins) for decades to come.
Collapse
Affiliation(s)
- Pam S P Wang
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, CT 06511, USA.
| | | |
Collapse
|
8
|
M. B. Reddy M, Basuroy K, Chandrappa S, Dinesh B, Vasantha B, A. Venkatesha M, Balaram P. Structural characterization of folded and extended conformations in peptides containing γ amino acids with proteinogenic side chains: crystal structures of γn, (αγ)n and γγδγ sequences. NEW J CHEM 2015. [DOI: 10.1039/c5nj00132c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
γn amino acid residues can be incorporated into structures in γn and hybrid sequences containing folded and extended α and δ residues.
Collapse
Affiliation(s)
| | - K. Basuroy
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560 012
- India
| | - S. Chandrappa
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560 012
- India
| | - B. Dinesh
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560 012
- India
| | - B. Vasantha
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560 012
- India
| | | | - P. Balaram
- Molecular Biophysics Unit
- Indian Institute of Science
- Bangalore 560 012
- India
| |
Collapse
|
9
|
Miller J, Melicher MS, Schepartz A. Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle. J Am Chem Soc 2014; 136:14726-9. [PMID: 25290247 PMCID: PMC4210112 DOI: 10.1021/ja508872q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Indexed: 01/19/2023]
Abstract
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.
Collapse
Affiliation(s)
- Jonathan
P. Miller
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Michael S. Melicher
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
10
|
Wang PSP, Nguyen JB, Schepartz A. Design and high-resolution structure of a β³-peptide bundle catalyst. J Am Chem Soc 2014; 136:6810-3. [PMID: 24802883 DOI: 10.1021/ja5013849] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Despite the widespread exploration of α-peptides as catalysts, there are few examples of β-peptides that alter the course of a chemical transformation. Our previous work demonstrated that a special class of β(3)-peptides spontaneously self-assembles in water into discrete protein-like bundles possessing unique quaternary structures and exceptional thermodynamic stability. Here we describe a series of β(3)-peptide bundles capable of both substrate binding and chemical catalysis--ester hydrolysis. A combination of kinetic and high-resolution structural analysis suggests an active site triad composed of residues from at least two strands of the octameric bundle structure.
Collapse
Affiliation(s)
- Pam S P Wang
- Department of Chemistry and ‡Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, Connecticut 06520-8107, United States
| | | | | |
Collapse
|
11
|
Mándity IM, Monsignori A, Fülöp L, Forró E, Fülöp F. Exploiting aromatic interactions for β-peptide foldamer helix stabilization: a significant design element. Chemistry 2014; 20:4591-7. [PMID: 24664416 DOI: 10.1002/chem.201304448] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Indexed: 11/09/2022]
Abstract
Tetrameric H10/12 helix stabilization was achieved by the application of aromatic side-chains in β-peptide oligomers by intramolecular backbone-side chain CH-π interactions. Because of the enlarged hydrophobic surface of the oligomers, a further aim was the investigation of the self-assembly in a polar medium for the β-peptide H10/12 helices. NMR, ECD, and molecular modeling results indicated that the oligomers formed by cis-[1S,2S]- or cis-[1R,2R]-1-amino-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (ATENAC) and cis-[1R,2S]- or cis-[1S,2R]-2-aminocyclohex-3-enecarboxylic acid (ACHEC) residues promote stable H10/12 helix formation with an alternating backbone configuration even at the tetrameric chain length. These results support the view that aromatic side-chains can be applied for helical structure stabilization. Importantly, this is the first observation of a stable H10/12 helix with tetrameric chain-length. The hydrophobically driven self-assembly was achieved for the helix-forming oligomers, seen as vesicles in transmission electron microscopy images. The self-association phenomenon, which supports the helical secondary structure of these oligomers, depends on the hydrophobic surface area, because a higher number of aromatic side-chains yielded larger vesicles. These results serve as an essential element for the design of helices relating to the H10/12 helix. Moreover, they open up a novel area for bioactive foldamer construction, while the hydrophobic area gained through the aromatic side-chains may yield important receptor-ligand interaction surfaces, which can provide amplified binding strength.
Collapse
Affiliation(s)
- István M Mándity
- Institute of Pharmaceutical Chemistry, University of Szeged, Eötvös u. 6, 6720 Szeged (Hungary), Fax: (+36) 62-545705
| | | | | | | | | |
Collapse
|
12
|
Melicher MS, Chu J, Walker AS, Miller SJ, Baxter RHG, Schepartz A. A β-Boronopeptide Bundle of Known Structure As a Vehicle for Polyol Recognition. Org Lett 2013; 15:5048-51. [DOI: 10.1021/ol402381n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Michael S. Melicher
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - John Chu
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Allison S. Walker
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Richard H. G. Baxter
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department of Chemistry, Department of Molecular Biophysics and Biochemistry, and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
13
|
Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). PLoS One 2013; 8:e63906. [PMID: 23717507 PMCID: PMC3661552 DOI: 10.1371/journal.pone.0063906] [Citation(s) in RCA: 275] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/04/2013] [Indexed: 11/21/2022] Open
Abstract
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers. Despite its free availability to academic users and improving documentation, use of Rosetta has largely remained confined to developers and their immediate collaborators due to the code's difficulty of use, the requirement for large computational resources, and the unavailability of servers for most of the Rosetta applications. Here, we present a unified web framework for Rosetta applications called ROSIE (Rosetta Online Server that Includes Everyone). ROSIE provides (a) a common user interface for Rosetta protocols, (b) a stable application programming interface for developers to add additional protocols, (c) a flexible back-end to allow leveraging of computer cluster resources shared by RosettaCommons member institutions, and (d) centralized administration by the RosettaCommons to ensure continuous maintenance. This paper describes the ROSIE server infrastructure, a step-by-step 'serverification' protocol for use by Rosetta developers, and the deployment of the first nine ROSIE applications by six separate developer teams: Docking, RNA de novo, ERRASER, Antibody, Sequence Tolerance, Supercharge, Beta peptide design, NCBB design, and VIP redesign. As illustrated by the number and diversity of these applications, ROSIE offers a general and speedy paradigm for serverification of Rosetta applications that incurs negligible cost to developers and lowers barriers to Rosetta use for the broader biological community. ROSIE is available at http://rosie.rosettacommons.org.
Collapse
Affiliation(s)
- Sergey Lyskov
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fang-Chieh Chou
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shane Ó. Conchúir
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kevin Drew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Daisuke Kuroda
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Brian D. Weitzner
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - P. Douglas Renfrew
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
| | - Parin Sripakdeevong
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Benjamin Borgo
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - James J. Havranek
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Tanja Kortemme
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Graduate Group in Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Richard Bonneau
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York, United States of America
- Computer Science Department, Courant Institute of Mathematical Sciences, New York University, New York, New York, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Physics, Stanford University, Stanford, California, United States of America
| |
Collapse
|
14
|
Thorat VH, Ingole TS, Vijayadas KN, Nair RV, Kale SS, Ramesh VVE, Davis HC, Prabhakaran P, Gonnade RG, Gawade RL, Puranik VG, Rajamohanan PR, Sanjayan GJ. The Ant-Pro Reverse-Turn Motif. Structural Features and Conformational Characteristics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201739] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
15
|
Sonti R, Gopi HN, Muddegowda U, Ragothama S, Balaram P. A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide. Chemistry 2013; 19:5955-65. [DOI: 10.1002/chem.201204327] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Indexed: 01/25/2023]
|
16
|
Molski MA, Goodman JL, Chou FC, Baker D, Das R, Schepartz A. Remodeling a β-peptide bundle. Chem Sci 2013. [DOI: 10.1039/c2sc21117c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
17
|
Wang PSP, Craig CJ, Schepartz A. Relationship between side-chain branching and stoichiometry in β(3)-peptide bundles. Tetrahedron 2012; 68:4342-4345. [PMID: 22822272 DOI: 10.1016/j.tet.2012.03.079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The stability and stoichiometry of β(3)-peptide bundles is influenced by side-chain identity. β(3)-peptides containing β(3)-homoleucine on one helical face assemble into octamers, whereas those containing β(3)-homovaline form tetramers. From a structural perspective, the side chains of β(3)-homoleucine and β(3)-homovaline differ in terms of both side-chain length and γ-carbon branching. To evaluate the extent to which these two parameters control β(3)-peptide bundle stoichiometry, we synthesized the β(3)-peptide Acid-3Y, which contains β(3)-homoisoleucine in place of β(3)-homoleucine or β(3)-homovaline. Acid-3Y assembles into a stable tetramer whose stability resembles that of the previously characterized Acid-VY tetramer. These results suggest that β(3)-peptide bundle stoichiometry is dominated by the presence or absence of γ-carbon branching on core side chains.
Collapse
Affiliation(s)
- Pam Shou-Ping Wang
- Department of Chemistry, Yale University, 275 Prospect St., New Haven, CT 06520-8107
| | | | | |
Collapse
|