1
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Fobe TL, Walker CC, Meek GA, Shirts MR. Folding Coarse-Grained Oligomer Models with PyRosetta. J Chem Theory Comput 2022; 18:6354-6369. [PMID: 36179376 DOI: 10.1021/acs.jctc.2c00519] [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
Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.
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Affiliation(s)
- Theodore L Fobe
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Christopher C Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Garrett A Meek
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
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2
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Herlan CN, Feser D, Schepers U, Bräse S. Bio-instructive materials on-demand - combinatorial chemistry of peptoids, foldamers, and beyond. Chem Commun (Camb) 2021; 57:11131-11152. [PMID: 34611672 DOI: 10.1039/d1cc04237h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Combinatorial chemistry allows for the rapid synthesis of large compound libraries for high throughput screenings in biology, medicinal chemistry, or materials science. Especially compounds from a highly modular design are interesting for the proper investigation of structure-to-activity relationships. Permutations of building blocks result in many similar but unique compounds. The influence of certain structural features on the entire structure can then be monitored and serve as a starting point for the rational design of potent molecules for various applications. Peptoids, a highly diverse class of bioinspired oligomers, suit perfectly for combinatorial chemistry. Their straightforward synthesis on a solid support using repetitive reaction steps ensures easy handling and high throughput. Applying this modular approach, peptoids are readily accessible, and their interchangeable side-chains allow for various structures. Thus, peptoids can easily be tuned in their solubility, their spatial structure, and, consequently, their applicability in various fields of research. Since their discovery, peptoids have been applied as antimicrobial agents, artificial membranes, molecular transporters, and much more. Studying their three-dimensional structure, various foldamers with fascinating, unique properties were discovered. This non-comprehensive review will state the most interesting discoveries made over the past years and arouse curiosity about what may come.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Dominik Feser
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Functional Interfaces (IFG), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
| | - Stefan Bräse
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann von Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany. .,Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz Haber Weg 6, 76131 Karlsruhe, Germany
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3
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DeStefano A, Segalman RA, Davidson EC. Where Biology and Traditional Polymers Meet: The Potential of Associating Sequence-Defined Polymers for Materials Science. JACS AU 2021; 1:1556-1571. [PMID: 34723259 PMCID: PMC8549048 DOI: 10.1021/jacsau.1c00297] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 05/08/2023]
Abstract
Polymers with precisely defined monomeric sequences present an exquisite tool for controlling material properties by harnessing both the robustness of synthetic polymers and the ability to tailor the inter- and intramolecular interactions so crucial to many biological materials. While polymer scientists traditionally synthesized and studied the physics of long molecules best described by their statistical nature, many biological polymers derive their highly tailored functions from precisely controlled sequences. Therefore, significant effort has been applied toward developing new methods of synthesizing, characterizing, and understanding the physics of non-natural sequence-defined polymers. This perspective considers the synergistic advantages that can be achieved via tailoring both precise sequence control and attributes of traditional polymers in a single system. Here, we focus on the potential of sequence-defined polymers in highly associating systems, with a focus on the unique properties, such as enhanced proton conductivity, that can be attained by incorporating sequence. In particular, we examine these materials as key model systems for studying previously unresolvable questions in polymer physics including the role of chain shape near interfaces and how to tailor compatibilization between dissimilar polymer blocks. Finally, we discuss the critical challenges-in particular, truly scalable synthetic approaches, characterization and modeling tools, and robust control and understanding of assembly pathways-that must be overcome for sequence-defined polymers to attain their potential and achieve ubiquity.
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Affiliation(s)
- Audra
J. DeStefano
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Rachel A. Segalman
- Department
of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department
of Materials, University of California, Santa Barbara, California 93106, United States
| | - Emily C. Davidson
- Department
of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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4
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Rajale T, Miner JC, Michalczyk R, Phipps ML, Schmidt JG, Gilbertson RD, Williams RF, Strauss CEM, Martinez JS. Conformational control via sequence for a heteropeptoid in water: coupled NMR and Rosetta modelling. Chem Commun (Camb) 2021; 57:9922-9925. [PMID: 34498621 DOI: 10.1039/d1cc01992a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We report a critical advance in the generation and characterization of peptoid hetero-oligomers. A library of sub-monomers with amine and carboxylate side-chains are combined in different sequences using microwave-assisted synthesis. Their sequence-structure propensity is confirmed by circular dichroism, and conformer subtypes are enumerated by NMR. Biasing the ψ-angle backbone to trans (180°) in Monte Carlo modelling favors i to i + 3 naphthyl-naphthyl stacking, and matches experimental ensemble distributions. Taken together, high-yield synthesis of heterooligomers and NMR with structure prediction enables rapid determination of sequences that induce secondary structural propensities for predictive design of hydrophilic peptidomimetic foldamers and their future libraries.
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Affiliation(s)
- Trideep Rajale
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jacob C Miner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.,Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Ryszard Michalczyk
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - M Lisa Phipps
- Center for Integrated Nanotechnologies, (CINT), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jurgen G Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert D Gilbertson
- Materials Science and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Robert F Williams
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Charlie E M Strauss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jennifer S Martinez
- Center for Materials Interfaces in Research and Applications, Northern Arizona University, Flagstaff, Arizona 86011, USA. .,Department of Applied Physics and Materials Science, Northern Arizona University, Flagstaff, Arizona 86011, USA
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5
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Li Z, Cai B, Yang W, Chen CL. Hierarchical Nanomaterials Assembled from Peptoids and Other Sequence-Defined Synthetic Polymers. Chem Rev 2021; 121:14031-14087. [PMID: 34342989 DOI: 10.1021/acs.chemrev.1c00024] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In nature, the self-assembly of sequence-specific biopolymers into hierarchical structures plays an essential role in the construction of functional biomaterials. To develop synthetic materials that can mimic and surpass the function of these natural counterparts, various sequence-defined bio- and biomimetic polymers have been developed and exploited as building blocks for hierarchical self-assembly. This review summarizes the recent advances in the molecular self-assembly of hierarchical nanomaterials based on peptoids (or poly-N-substituted glycines) and other sequence-defined synthetic polymers. Modern techniques to monitor the assembly mechanisms and characterize the physicochemical properties of these self-assembly systems are highlighted. In addition, discussions about their potential applications in biomedical sciences and renewable energy are also included. This review aims to highlight essential features of sequence-defined synthetic polymers (e.g., high stability and protein-like high-information content) and how these unique features enable the construction of robust biomimetic functional materials with high programmability and predictability, with an emphasis on peptoids and their self-assembled nanomaterials.
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Affiliation(s)
- Zhiliang Li
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Bin Cai
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemistry and Chemical Engineering, Shandong University, Shandong 250100, China
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.,Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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6
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Xuan S, Zuckermann RN. Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122691] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Ren J, Tian Y, Hossain E, Ho JS, Mann YS, Zhang Y, Browne MD, Connolly MD, Zuckermann RN. Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids. Biopolymers 2020; 111:e23358. [DOI: 10.1002/bip.23358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Jianhua Ren
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuan Tian
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Ekram Hossain
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Joshua S. Ho
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yadwinder S. Mann
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuntao Zhang
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Browne
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Connolly
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
| | - Ronald N. Zuckermann
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
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8
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Fuller AA, Jimenez CJ, Martinetto EK, Moreno JL, Calkins AL, Dowell KM, Huber J, McComas KN, Ortega A. Sequence Changes Modulate Peptoid Self-Association in Water. Front Chem 2020; 8:260. [PMID: 32391314 PMCID: PMC7191062 DOI: 10.3389/fchem.2020.00260] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/17/2020] [Indexed: 01/15/2023] Open
Abstract
Peptoids, N-substituted glycine oligomers, are a class of diverse and sequence-specific peptidomimetics with wide-ranging applications. Advancing the functional repertoire of peptoids to emulate native peptide and protein functions requires engineering peptoids that adopt regular secondary and tertiary structures. An understanding of how changes to peptoid sequence change structural features, particularly in water-soluble systems, is underdeveloped. To address this knowledge gap, five 15-residue water-soluble peptoids that include naphthalene-functionalized side chains were designed, prepared, and subjected to a structural study using a palette of techniques. Peptoid sequence designs were based on a putative amphiphilic helix peptoid bearing structure-promoting (S)-N-(1-naphthylethyl)glycine residues whose self-association in water has been studied previously. New peptoid variants reported here include sequence changes that influenced peptoid conformational flexibility, functional group patterning (amphiphilicity), and hydrophobicity. Peptoid structures were evaluated and compared using circular dichroism spectroscopy, fluorescence spectroscopy, and size exclusion chromatography. Spectral data confirmed that sequence changes alter peptoids' degree of assembly and the organization of self-assembled structures in aqueous solutions. Insights gained in these studies will inform the design of new water-soluble peptoids with regular structural features, including desirable higher-order (tertiary and quaternary) structural features.
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Affiliation(s)
- Amelia A Fuller
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Christian J Jimenez
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Ella K Martinetto
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Jose L Moreno
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Anna L Calkins
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Kalli M Dowell
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Jonathan Huber
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Kyra N McComas
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Alberto Ortega
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, United States
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9
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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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10
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Perez Bakovic GR, Roberts JL, Colford B, Joyce M, Servoss SL. Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength. Biopolymers 2019; 110:e23283. [DOI: 10.1002/bip.23283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/08/2019] [Accepted: 04/04/2019] [Indexed: 12/17/2022]
Affiliation(s)
- German R. Perez Bakovic
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas Fayetteville Fayetteville Arkansas
| | - Jesse L. Roberts
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas Fayetteville Fayetteville Arkansas
| | - Bryce Colford
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas Fayetteville Fayetteville Arkansas
| | - Myles Joyce
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas Fayetteville Fayetteville Arkansas
| | - Shannon L. Servoss
- Ralph E. Martin Department of Chemical EngineeringUniversity of Arkansas Fayetteville Fayetteville Arkansas
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11
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Fuller AA, Huber J, Jimenez CJ, Dowell KM, Hough S, Ortega A, McComas KN, Kunkel J, Asuri P. Solution effects on the self‐association of a water‐soluble peptoid. Biopolymers 2018; 110:e23248. [DOI: 10.1002/bip.23248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 01/15/2023]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Jonathan Huber
- Department of Bioengineering Santa Clara University Santa Clara California USA
| | - Christian J. Jimenez
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Kalli M. Dowell
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Samuel Hough
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Alberto Ortega
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Kyra N. McComas
- Department of Chemistry and Biochemistry Santa Clara University Santa Clara California USA
| | - Jeffrey Kunkel
- Department of Bioengineering Santa Clara University Santa Clara California USA
| | - Prashanth Asuri
- Department of Bioengineering Santa Clara University Santa Clara California USA
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12
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Grubbs RB, Grubbs RH. 50th Anniversary Perspective: Living Polymerization—Emphasizing the Molecule in Macromolecules. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01440] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert B. Grubbs
- Chemistry
Department, Stony Brook University, Stony Brook, New York 11794, United States
| | - Robert H. Grubbs
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
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13
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Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, USA
| | - Kristiana Tenorio
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, USA
| | - Jonathan Huber
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, USA
| | - Samuel Hough
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, USA
| | - Kalli M. Dowell
- Department of Chemistry & Biochemistry, Santa Clara University, Santa Clara, CA, USA
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14
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Ganesh SD, Saha N, Zandraa O, Zuckermann RN, Sáha P. Peptoids and polypeptoids: biomimetic and bioinspired materials for biomedical applications. Polym Bull (Berl) 2017. [DOI: 10.1007/s00289-016-1902-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Ren J, Tian Y, Hossain E, Connolly MD. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:646-661. [PMID: 26832347 DOI: 10.1007/s13361-016-1341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/07/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
| | - Yuan Tian
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ekram Hossain
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael D Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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16
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Robertson EJ, Battigelli A, Proulx C, Mannige RV, Haxton TK, Yun L, Whitelam S, Zuckermann RN. Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets. Acc Chem Res 2016; 49:379-89. [PMID: 26741294 DOI: 10.1021/acs.accounts.5b00439] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Two-dimensional (2D) atomically defined organic nanomaterials are an important material class with broad applications. However, few general synthetic methods exist to produce such materials in high yields and to precisely functionalize them. One strategy to form ordered 2D organic nanomaterials is through the supramolecular assembly of sequence-defined synthetic polymers. Peptoids, one such class of polymer, are designable bioinspired heteropolymers whose main-chain length and monomer sequence can be precisely controlled. We have recently discovered that individual peptoid polymers with a simple sequence of alternating hydrophobic and ionic monomers can self-assemble into highly ordered, free-floating nanosheets. A detailed understanding of their molecular structure and supramolecular assembly dynamics provides a robust platform for the discovery of new classes of nanosheets with tunable properties and novel applications. In this Account, we discuss the discovery, characterization, assembly, molecular modeling, and functionalization of peptoid nanosheets. The fundamental properties of peptoid nanosheets, their mechanism of formation, and their application as robust scaffolds for molecular recognition and as templates for the growth of inorganic minerals have been probed by an arsenal of experimental characterization techniques (e.g., scanning probe, electron, and optical microscopy, X-ray diffraction, surface-selective vibrational spectroscopy, and surface tensiometry) and computational techniques (coarse-grained and atomistic modeling). Peptoid nanosheets are supramolecular assemblies of 16-42-mer chains that form molecular bilayers. They span tens of microns in lateral dimensions and freely float in water. Their component chains are highly ordered, with chains nearly fully extended and packed parallel to one another as a result of hydrophobic and electrostatic interactions. Nanosheets form via a novel interface-catalyzed monolayer collapse mechanism. Peptoid chains first assemble into a monolayer at either an air-water or oil-water interface, on which peptoid chains extend, order, and pack into a brick-like pattern. Upon mechanical compression of the interface, the monolayer buckles into stable bilayer structures. Recent work has focused on the design of nanosheets with tunable properties and functionality. They are readily engineerable, as functional monomers can be readily incorporated onto the nanosheet surface or into the interior. For example, functional hydrophilic "loops" have been displayed on the surfaces of nanosheets. These loops can interact with specific protein targets, serving as a potentially general platform for molecular recognition. Nanosheets can also bind metal ions and serve as 2D templates for mineral growth. Through our understanding of the formation mechanism, along with predicted features ascertained from molecular modeling, we aim to further design and synthesize nanosheets as robust protein mimetics with the potential for unprecedented functionality and stability.
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Affiliation(s)
- Ellen J. Robertson
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alessia Battigelli
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline Proulx
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ranjan V. Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Thomas K. Haxton
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Lisa Yun
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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17
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Gangloff N, Ulbricht J, Lorson T, Schlaad H, Luxenhofer R. Peptoids and Polypeptoids at the Frontier of Supra- and Macromolecular Engineering. Chem Rev 2015; 116:1753-802. [DOI: 10.1021/acs.chemrev.5b00201] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Niklas Gangloff
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Juliane Ulbricht
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Thomas Lorson
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
| | - Helmut Schlaad
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Robert Luxenhofer
- Functional Polymer
Materials, Chair for Chemical Technology of Materials Synthesis, University of Würzburg, Röntgenring 11, 97070 Würzburg, Germany
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18
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Mukherjee S, Zhou G, Michel C, Voelz VA. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential. J Phys Chem B 2015; 119:15407-17. [PMID: 26584227 DOI: 10.1021/acs.jpcb.5b09625] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consistent with experiment. We validate our results against both QM calculations and NMR experiments. For this latter task, we make quantitative comparisons to sparse NOE data using the Bayesian Inference of Conformational Populations (BICePs) algorithm, a method we have recently developed for this purpose. We then performed extensive REMD simulations of Nspe oligomers as a function of chain length and temperature to probe the molecular forces driving cooperative helix formation. Analysis of simulation data by Lifson-Roig helix-coil theory show that the modified potential predicts much more cooperative folding for Nspe helices. Unlike peptides, per-residue entropy changes for helix nucleation and extension are mostly positive, suggesting that steric bulk provides the main driving force for folding. We expect these results to inform future work aimed at predicting and designing peptoid peptidomimetics and tertiary assemblies of peptoid helices.
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Affiliation(s)
- Sudipto Mukherjee
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Guangfeng Zhou
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Chris Michel
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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19
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Jobin S, Vézina-Dawod S, Herby C, Derson A, Biron E. Preparation of N-Substituted N-Arylsulfonylglycines and Their Use in Peptoid Synthesis. Org Lett 2015; 17:5626-9. [DOI: 10.1021/acs.orglett.5b02862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Steve Jobin
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Simon Vézina-Dawod
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Claire Herby
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Antoine Derson
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
| | - Eric Biron
- Faculty of Pharmacy, Université Laval, Québec, Québec G1V 0A6, Canada
- Laboratory
of Medicinal Chemistry, Centre de Recherche du Centre Hospitalier Universitaire de Québec, 2705 Boulevard Laurier, Québec, Québec G1V 4G2, Canada
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20
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Knight AS, Zhou EY, Francis MB, Zuckermann RN. Sequence Programmable Peptoid Polymers for Diverse Materials Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5665-5691. [PMID: 25855478 DOI: 10.1002/adma.201500275] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/13/2015] [Indexed: 06/04/2023]
Abstract
Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.
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Affiliation(s)
- Abigail S Knight
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Effie Y Zhou
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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21
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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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22
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McGuinness K, Khan IJ, Nanda V. Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains. ACS NANO 2014; 8:12514-12523. [PMID: 25390880 PMCID: PMC4278691 DOI: 10.1021/nn505369d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/12/2014] [Indexed: 06/01/2023]
Abstract
Synthetic collagen mimetic peptides are used to probe the role of hydrophobic forces in mediating protein self-assembly. Higher order association is an integral property of natural collagens, which assemble into fibers and meshes that comprise the extracellular matrix of connective tissues. The unique triple-helix fold fully exposes two-thirds of positions in the protein to solvent, providing ample opportunities for engineering interaction sites. Inclusion of just a few hydrophobic groups in a minimal peptide promotes a rich variety of self-assembly behaviors, resulting in hundred-nanometer to micron size nanodiscs and nanofibers. Morphology depends primarily on the length of hydrophobic domains. Peptide discs contain lipophilic domains capable of sequestering small hydrophobic dyes. Combining multiple peptide types result in composite structures of discs and fibers ranging from stars to plates-on-a-string. These systems provide valuable tools to shed insight into the fundamental principles underlying hydrophobicity-driven higher order protein association that will facilitate the design of self-assembling systems in biomaterials and nanomedical applications.
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Affiliation(s)
| | | | - Vikas Nanda
- Address correspondence to . Phone: 732-235-5328
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23
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Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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24
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Nandel FS, Jaswal RR, Saini A, Nandel V, Shafique M. Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures. J Mol Model 2014; 20:2429. [DOI: 10.1007/s00894-014-2429-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/07/2014] [Indexed: 12/29/2022]
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25
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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26
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Gao Y, Kodadek T. Split-and-pool synthesis and characterization of peptide tertiary amide library. J Vis Exp 2014:e51299. [PMID: 24998250 DOI: 10.3791/51299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both α-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.
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Affiliation(s)
- Yu Gao
- Scripps Florida, The Scripps Research Institute
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27
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Kölmel DK, Hörner A, Rönicke F, Nieger M, Schepers U, Bräse S. Cell-penetrating peptoids: introduction of novel cationic side chains. Eur J Med Chem 2014; 79:231-43. [PMID: 24739871 DOI: 10.1016/j.ejmech.2014.03.078] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 03/25/2014] [Accepted: 03/27/2014] [Indexed: 12/17/2022]
Abstract
During the last decade peptoid-based molecular transporters have been broadly applied. They are highly valued for their easy synthesis and their superior stability against enzymatic degradation. The special structure of peptoids generally allows introducing a variety of different side chains. Yet, the cationic side chains of cell-penetrating peptoids displayed solely lysine- or arginine-like structures. Thus this report is intended to extend the spectrum of cationic peptoid side chains. Herein, we present novel functional groups, like polyamines, aza-crown ethers, or triphenylphosphonium ions that are introduced into peptoids for the first time. In addition, the obtained peptoids were tested for their cell-penetrating properties.
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Affiliation(s)
- Dominik K Kölmel
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Anna Hörner
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Light Technology Institute, Engesserstraße 13, D-76131 Karlsruhe, Germany
| | - Franziska Rönicke
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Martin Nieger
- University of Helsinki, Laboratory of Inorganic Chemistry, PO Box 55, FIN-00014, Finland
| | - Ute Schepers
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany; Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany.
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28
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Wu CF, Li ZM, Xu XN, Zhao ZX, Zhao X, Wang RX, Li ZT. Folding-Induced Folding: The Assembly of Aromatic Amide and 1,2,3-Triazole Hybrid Helices. Chemistry 2014; 20:1418-26. [DOI: 10.1002/chem.201304161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 12/15/2022]
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29
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Kim S, Biswas G, Park S, Kim A, Park H, Park E, Kim J, Kwon YU. Unusual truncation of N-acylated peptoids under acidic conditions. Org Biomol Chem 2014; 12:5222-6. [DOI: 10.1039/c3ob42572j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Systematic studies on the unusual truncation of N-acylated peptoids were carried out to examine the electronic effects of acyl groups, and thus to control the formation of deletion sequences based on a plausible mechanism.
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Affiliation(s)
- Soomin Kim
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Goutam Biswas
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Shinae Park
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Arim Kim
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Hyunjung Park
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Eunsook Park
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Jeongmi Kim
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
| | - Yong-Uk Kwon
- Department of Chemistry and Nano Science
- Ewha Global Top 5 Program
- Ewha Womans University
- Seoul 120-750, Korea
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30
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Fuller AA, Yurash BA, Schaumann EN, Seidl FJ. Self-Association of Water-Soluble Peptoids Comprising (S)-N-1-(Naphthylethyl)glycine Residues. Org Lett 2013; 15:5118-21. [DOI: 10.1021/ol4025502] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Brett A. Yurash
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Erik N. Schaumann
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
| | - Frederick J. Seidl
- Department of Chemistry & Biochemistry, Santa Clara University, 500 El Camino Real, Santa Clara, California 95053, United States
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31
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Fuller AA, Holmes CA, Seidl FJ. A fluorescent peptoid pH-sensor. Biopolymers 2013; 100:380-6. [DOI: 10.1002/bip.22242] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 03/17/2013] [Indexed: 01/30/2023]
Affiliation(s)
- Amelia A. Fuller
- Department of Chemistry & Biochemistry; Santa Clara University; 500 El Camino Real; Santa Clara; CA; 95053
| | - Courtney A. Holmes
- Department of Chemistry & Biochemistry; Santa Clara University; 500 El Camino Real; Santa Clara; CA; 95053
| | - Frederick J. Seidl
- Department of Chemistry & Biochemistry; Santa Clara University; 500 El Camino Real; Santa Clara; CA; 95053
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32
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Taylor L, Chen X, Ayres N. Synthesis of a glycosaminoglycan polymer mimetic using an N
-alkyl-N
,N
-linked urea oligomer containing glucose pendant groups. POLYM INT 2013. [DOI: 10.1002/pi.4567] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Leeanne Taylor
- University of Cincinnati; Department of Chemistry; 301 Clifton Court, PO Box 210172 Cincinnati OH 45221 USA
| | - Xiaoping Chen
- University of Cincinnati; Department of Chemistry; 301 Clifton Court, PO Box 210172 Cincinnati OH 45221 USA
| | - Neil Ayres
- University of Cincinnati; Department of Chemistry; 301 Clifton Court, PO Box 210172 Cincinnati OH 45221 USA
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33
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Sun J, Zuckermann RN. Peptoid polymers: a highly designable bioinspired material. ACS NANO 2013; 7:4715-32. [PMID: 23721608 DOI: 10.1021/nn4015714] [Citation(s) in RCA: 307] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Bioinspired polymeric materials are attracting increasing attention due to significant advantages over their natural counterparts: the ability to precisely tune their structures over a broad range of chemical and physical properties, increased stability, and improved processability. Polypeptoids, a promising class of bioinspired polymer based on a N-substituted glycine backbone, have a number of unique properties that bridge the material gap between proteins and bulk polymers. Peptoids combine the sequence specificity of biopolymers with the simpler intra/intermolecular interactions and robustness of traditional synthetic polymers. They are highly designable because hundreds of chemically diverse side chains can be introduced from simple building blocks. Peptoid polymers can be prepared by two distinct synthetic techniques offering access to two material subclasses: (1) automated solid-phase synthesis which enables precision sequence control and near absolute monodispersity up to chain lengths of ~50 monomers, and (2) a classical polymerization approach which allows access to higher molecular weights and larger-scale yields, but with less control over length and sequence. This combination of facile synthetic approaches makes polypeptoids a highly tunable, rapid polymer prototyping platform to investigate new materials that are intermediate between proteins and bulk polymers, in both their structure and their properties. In this paper, we review the methods to synthesize peptoid polymers and their applications in biomedicine and nanoscience, as both sequence-specific materials and as bulk polymers.
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Affiliation(s)
- Jing Sun
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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34
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Gangloff N, Luxenhofer R. Peptoids for Biomimetic Hierarchical Structures. HIERARCHICAL MACROMOLECULAR STRUCTURES: 60 YEARS AFTER THE STAUDINGER NOBEL PRIZE II 2013. [DOI: 10.1007/12_2013_237] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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35
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Cardenal C, Vollrath SBL, Schepers U, Bräse S. Synthesis of Functionalized Glutamine- and Asparagine-Type Peptoids - Scope and Limitations. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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36
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Zhang D, Lahasky SH, Guo L, Lee CU, Lavan M. Polypeptoid Materials: Current Status and Future Perspectives. Macromolecules 2012. [DOI: 10.1021/ma202319g] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Donghui Zhang
- Department of Chemistry and Macromolecular
Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Samuel H. Lahasky
- Department of Chemistry and Macromolecular
Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Li Guo
- Department of Chemistry and Macromolecular
Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Chang-Uk Lee
- Department of Chemistry and Macromolecular
Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Monika Lavan
- Department of Chemistry and Macromolecular
Studies Group, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Jordan PA, Paul B, Butterfoss GL, Renfrew PD, Bonneau R, Kirshenbaum K. Oligo(N-alkoxy glycines): trans substantiating peptoid conformations. Biopolymers 2012; 96:617-26. [PMID: 22180909 DOI: 10.1002/bip.21675] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Peptoid oligomers possess many desirable attributes bioactive peptidomimetic agents, including their ease of synthesis, chemical diversity, and capability for molecular recognition. Ongoing efforts to develop functional peptoids will necessitate improved capability for control of peptoid structure, particularly of the backbone amide conformation. We introduce alkoxyamines as a new reagent for solid phase peptoid synthesis. Herein, we describe the synthesis of N-alkoxy peptoids, and present NMR data indicating that the oligomers adopt a single stable conformation featuring trans amide bonds. These findings, combined with results from computational modeling, suggest that N-alkoxy peptoid oligomers have a strong propensity to adopt a polyproline II type secondary structure.
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Affiliation(s)
- Peter A Jordan
- Department of Chemistry, New York University, NY 10003, USA
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Abstract
Peptoid oligomers were initially developed as part of a larger basic research effort to accelerate the drug-discovery process in the biotech/biopharma industry. Their ease of synthesis, stability, and structural similarity to polypeptides made them ideal candidates for the combinatorial discovery of novel peptidomimetic drug candidates. Diverse libraries of short peptoid oligomers provided one of the first demonstrations in the mid-1990s that high-affinity ligands to pharmaceutically relevant receptors could be discovered from combinatorial libraries of synthetic compounds. The solid-phase submonomer method of peptoid synthesis was so efficient and general that it soon became possible to explore the properties of longer polypeptoid chains in a variety of areas beyond drug discovery (e.g., diagnostics, drug delivery, and materials science). Exploration into protein-mimetic materials soon followed, with the fundamental goal of folding a non-natural sequence-specific heteropolymer into defined secondary or tertiary structures. This effort first yielded the peptoid helix and much later the peptoid sheet, both of which are secondary-structure mimetics that are close relatives to their natural counterparts. These crucial discoveries have brought us closer to building proteinlike structure and function from a non-natural polymer and have provided great insight into the rules governing polymer and protein folding. The accessibility of peptoid synthesis to chemists and nonchemists alike, along with a lack of information-rich non-natural polymers available to study, has led to a rapid growth in the field of peptoid science by many new investigators. This work provides an overview of the initial discovery and early developments in the peptoid field.
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Affiliation(s)
- Ronald N Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
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Tran H, Gael SL, Connolly MD, Zuckermann RN. Solid-phase submonomer synthesis of peptoid polymers and their self-assembly into highly-ordered nanosheets. J Vis Exp 2011:e3373. [PMID: 22083233 PMCID: PMC3308608 DOI: 10.3791/3373] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Peptoids are a novel class of biomimetic, non-natural, sequence-specific heteropolymers that resist proteolysis, exhibit potent biological activity, and fold into higher order nanostructures. Structurally similar to peptides, peptoids are poly N-substituted glycines, where the side chains are attached to the nitrogen rather than the alpha-carbon. Their ease of synthesis and structural diversity allows testing of basic design principles to drive de novo design and engineering of new biologically-active and nanostructured materials. Here, a simple manual peptoid synthesis protocol is presented that allows the synthesis of long chain polypeptoids ( up to 50mers) in excellent yields. Only basic equipment, simple techniques (e.g. liquid transfer, filtration), and commercially available reagents are required, making peptoids an accessible addition to many researchers' toolkits. The peptoid backbone is grown one monomer at a time via the submonomer method which consists of a two-step monomer addition cycle: acylation and displacement. First, bromoacetic acid activated in situ with N,N'-diisopropylcarbodiimide acylates a resin-bound secondary amine. Second, nucleophilic displacement of the bromide by a primary amine follows to introduce the side chain. The two-step cycle is iterated until the desired chain length is reached. The coupling efficiency of this two-step cycle routinely exceeds 98% and enables the synthesis of peptoids as long as 50 residues. Highly tunable, precise and chemically diverse sequences are achievable with the submonomer method as hundreds of readily available primary amines can be directly incorporated. Peptoids are emerging as a versatile biomimetic material for nanobioscience research because of their synthetic flexibility, robustness, and ordering at the atomic level. The folding of a single-chain, amphiphilic, information-rich polypeptoid into a highly-ordered nanosheet was recently demonstrated. This peptoid is a 36-mer that consists of only three different commercially available monomers: hydrophobic, cationic and anionic. The hydrophobic phenylethyl side chains are buried in the nanosheet core whereas the ionic amine and carboxyl side chains align on the hydrophilic faces. The peptoid nanosheets serve as a potential platform for membrane mimetics, protein mimetics, device fabrication, and sensors. Methods for peptoid synthesis, sheet formation, and microscopy imaging are described and provide a simple method to enable future peptoid nanosheet designs.
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Affiliation(s)
- Helen Tran
- Molecular Foundry, Lawrence Berkeley National Laboratory
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Affiliation(s)
- W Seth Horne
- University of Pittsburgh, Department of Chemistry,
219 Parkman Ave., Pittsburgh, PA 15260, USA
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Sanii B, Kudirka R, Cho A, Venkateswaran N, Olivier GK, Olson AM, Tran H, Harada RM, Tan L, Zuckermann RN. Shaken, not stirred: collapsing a peptoid monolayer to produce free-floating, stable nanosheets. J Am Chem Soc 2011; 133:20808-15. [PMID: 21939206 DOI: 10.1021/ja206199d] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two-dimensional nanomaterials play a critical role in biology (e.g., lipid bilayers) and electronics (e.g., graphene) but are difficult to directly synthesize with a high level of precision. Peptoid nanosheet bilayers are a versatile synthetic platform for constructing multifunctional, precisely ordered two-dimensional nanostructures. Here we show that nanosheet formation occurs through an unusual monolayer intermediate at the air-water interface. Lateral compression of a self-assembled peptoid monolayer beyond a critical collapse pressure results in the irreversible production of nanosheets. An unusual thermodynamic cycle is employed on a preparative scale, where mechanical energy is used to buckle an intermediate monolayer into a more stable nanosheet. Detailed physical studies of the monolayer-compression mechanism revealed a simple preparative technique to produce nanosheets in 95% overall yield by cyclical monolayer compressions in a rotating closed vial. Compression of monolayers into stable, free-floating products may be a general and preparative approach to access 2D nanomaterials.
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Affiliation(s)
- Babak Sanii
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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Paul B, Butterfoss GL, Boswell MG, Renfrew PD, Yeung FG, Shah NH, Wolf C, Bonneau R, Kirshenbaum K. Peptoid Atropisomers. J Am Chem Soc 2011; 133:10910-9. [DOI: 10.1021/ja2028684] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - Mikki G. Boswell
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | | | - Fanny G. Yeung
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
| | | | - Christian Wolf
- Department of Chemistry, Georgetown University, Washington, D.C. 20057, United States
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Pilsl LKA, Reiser O. α/β-Peptide foldamers: state of the art. Amino Acids 2011; 41:709-18. [DOI: 10.1007/s00726-011-0894-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 03/18/2011] [Indexed: 11/24/2022]
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Wetzler M, Barron AE. Commentary progress in the de novo design of structured peptoid protein mimics. Biopolymers 2011; 96:556-60. [DOI: 10.1002/bip.21621] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Fuller AA, Seidl FJ, Bruno PA, Plescia MA, Palla KS. Use of the environmentally sensitive fluorophore 4-N,N-dimethylamino-1,8-naphthalimide to study peptoid helix structures. Biopolymers 2011; 96:627-38. [DOI: 10.1002/bip.21605] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Kudirka R, Tran H, Sanii B, Nam KT, Choi PH, Venkateswaran N, Chen R, Whitelam S, Zuckermann RN. Folding of a single-chain, information-rich polypeptoid sequence into a highly ordered nanosheet. Biopolymers 2011; 96:586-95. [DOI: 10.1002/bip.21590] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Godballe T, Nilsson LL, Petersen PD, Jenssen H. Antimicrobial β-Peptides and α-Peptoids. Chem Biol Drug Des 2011; 77:107-16. [DOI: 10.1111/j.1747-0285.2010.01067.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Price JL, Horne WS, Gellman SH. Structural consequences of beta-amino acid preorganization in a self-assembling alpha/beta-peptide: fundamental studies of foldameric helix bundles. J Am Chem Soc 2010; 132:12378-87. [PMID: 20718422 DOI: 10.1021/ja103543s] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report high-resolution crystal structures of six new alpha/beta-peptide foldamers that have a regular alpha-residue/alpha-residue/beta-residue (alphaalphabeta) backbone repeat pattern. All of these foldamers were crystallized from aqueous solution, and all display four-helix bundle quaternary structure in the crystalline state. These oligomers are based on the well-studied 33-residue alpha-peptide GCN4-pLI, which is an engineered derivative of the dimerization domain of GCN4, a yeast transcription factor. GCN4-pLI forms a stable tetramer in solution and crystallizes as a four-helix bundle (Harbury et al. Science 1993, 262, 1401-1407). Previously we described a foldamer (designated 1 here) that was generated from GCN4-pLI by replacing every third alpha-amino acid residue with the homologous beta(3)-amino acid residue; this alphaalphabeta oligomer retains the side chain sequence of the original alpha-peptide, but the backbone contains 11 additional CH(2) units, which are evenly distributed (Horne et al. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 9151-9156). Despite the expanded backbone, 1 was found to retain the ability to form a tetrameric quaternary structure in which the individual molecules adopt an alpha-helix-like conformation. Here we compare nine analogues of 1 that have the same alphaalphabeta backbone but in which one or more of the flexible beta(3)-amino acid residues is/are replaced with an analogous cyclic beta-residue. The motivation for beta(3)-->cyclic replacements is to enhance conformational stability; however, a crystal structure of the one previously reported example (designated 2 here) revealed a "stammer" distortion of the helix-bundle architecture relative to 1. The results reported here suggest that the stammer is a peculiarity of 2, because all six of the new alpha/beta-peptides display undistorted four-helix bundle quaternary structures. More broadly, our results indicate that beta(3)-->cyclic replacements are generally well-accommodated in helix-bundle quaternary structure, but that such replacements can be destabilizing in certain instances.
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Affiliation(s)
- Joshua L Price
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Korendovych IV, Kim YH, Ryan AH, Lear JD, Degrado WF, Shandler SJ. Computational design of a self-assembling β-peptide oligomer. Org Lett 2010; 12:5142-5. [PMID: 20945888 DOI: 10.1021/ol102092r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The first computationally designed self-assembling oligomer consisting of exclusively β-amino acids (βAAs) is presented. The packing of a β-3(14) helix into coiled-coils of varying stoichiometries as a function of amino acid sequence is examined. β-Peptides with hVal repeating every third residue in the sequence appeared to have a strong propensity to pack into hexameric bundles. The designed sequence was synthesized and characterized with CD spectroscopy, NMR, and analytical ultracentrifugation, suggesting that the peptide adopts a well-folded hexameric structure.
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Affiliation(s)
- Ivan V Korendovych
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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50
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Culf AS, Ouellette RJ. Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives. Molecules 2010; 15:5282-335. [PMID: 20714299 PMCID: PMC6257730 DOI: 10.3390/molecules15085282] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/14/2010] [Accepted: 08/02/2010] [Indexed: 12/02/2022] Open
Abstract
Peptoids (N-substituted polyglycines and extended peptoids with variant backbone amino-acid monomer units) are oligomeric synthetic polymers that are becoming a valuable molecular tool in the biosciences. Of particular interest are their applications to the exploration of peptoid secondary structures and drug design. Major advantages of peptoids as research and pharmaceutical tools include the ease and economy of synthesis, highly variable backbone and side-chain chemistry possibilities. At the same time, peptoids have been demonstrated as highly active in biological systems while resistant to proteolytic decay. This review with 227 references considers the solid-phase synthetic aspects of peptoid preparation and utilization up to 2010 from the instigation, by R. N. Zuckermann et al., of peptoid chemistry in 1992.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute, Moncton, NB, Canada.
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