1
|
Luo X, Yu T, Li NK, Zuckermann RN, Jiang X, Balsara NP, Prendergast D. Thermodynamic Driving Forces for the Self-Assembly of Diblock Polypeptoids. ACS NANO 2024; 18:14917-14924. [PMID: 38811008 PMCID: PMC11171762 DOI: 10.1021/acsnano.3c12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Peptoid polymers with sequence-defined side chains are observed to self-assemble into a variety of structures spanning nanometer and micron scales. We explored a diblock copolypeptoid, poly(N-decylglycine)10-block-poly(N-2-(2-(2-methoxyethoxy)ethoxy)-ethylglycine)10 (abbreviated as Ndc10-Nte10), which forms crystalline nanofibers and nanosheets as evidenced by recent cryo-transmission electron microscopy, atomic force microscopy, X-ray diffraction, and calorimetry. Using all-atom molecular dynamics simulations, we examined the thermodynamic forces driving such self-assembly and how nanoscale morphology is tailored through modification of the N-terminus or via the addition of small molecules (urea). We have found that the hydrophobic Ndc domain alignment is key to the formation of molecular stacks whose growth is limited by electrostatic repulsion between protonated N-termini. These stacks are the building blocks that assemble via cooperative van der Waals attraction between the tips of extended decyl side chains to form nanofibers or nanosheets with a well-converged intermolecular interaction energy. Assemblies are significantly more stable in urea solution due to its strong attraction to the peptoid-solvent interface. Isolated peptoids exhibit curved all-cis backbones, which straighten within molecular stacks to maximize contact and registry between neighboring molecules. We hypothesize that competition between this attractive interaction and a strain cost for straightening the backbone is what leads to finite stack widths that define crystalline nanofibers of protonated Ndc10-Nte10. Growth is proposed to proceed through backbone unfurling via trans defects, which is more prevalent in aqueous solution than in THF, indicating a possible pathway to self-assembly under experimentally defined synthesis conditions (viz., THF evaporation).
Collapse
Affiliation(s)
- Xubo Luo
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Nan K. Li
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- The
Molecular Foundry, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
2
|
Swanson HWA, van Teijlingen A, Lau KHA, Tuttle T. Martinoid: the peptoid martini force field. Phys Chem Chem Phys 2024; 26:4939-4953. [PMID: 38275003 DOI: 10.1039/d3cp05907c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Many exciting innovations have been made in the development of assembling peptoid materials. Typically, these have utilised large oligomeric sequences, though elsewhere the study of peptide self-assembly has yielded numerous examples of assemblers below 6-8 residues in length, evidencing that minimal peptoid assemblers are not only feasible but expected. A productive means of discovering such materials is through the application of in silico screening methods, which often benefit from the use of coarse-grained molecular dynamics (CG-MD) simulations. At the current level of development, CG models for peptoids are insufficient and we have been motivated to develop a Martini forcefield compatible peptoid model. A dual bottom-up and top-down parameterisation approach has been adopted, in keeping with the Martini parameterisation methodology, targeting the reproduction of atomistic MD dynamics and trends in experimentally obtained log D7.4 partition coefficients, respectively. This work has yielded valuable insights into the practicalities of parameterising peptoid monomers. Additionally, we demonstrate that our model can reproduce the experimental observations of two very different peptoid assembly systems, namely peptoid nanosheets and minimal tripeptoid assembly. Further we can simulate the peptoid helix secondary structure relevant for antimicrobial sequences. To be of maximum usefulness to the peptoid research community, we have developed freely available code to generate all requisite simulation files for the application of this model with Gromacs MD software.
Collapse
Affiliation(s)
- Hamish W A Swanson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - Alexander van Teijlingen
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - King Hang Aaron Lau
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK.
| |
Collapse
|
3
|
Swanson HA, Lau KHA, Tuttle T. Minimal Peptoid Dynamics Inform Self-Assembly Propensity. J Phys Chem B 2023; 127:10601-10614. [PMID: 38038956 PMCID: PMC10726364 DOI: 10.1021/acs.jpcb.3c03725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023]
Abstract
Peptoids are structural isomers of natural peptides, with side chain attachment at the amide nitrogen, conferring this class of compounds with the ability to access both cis and trans ω torsions as well as an increased diversity of ψ/φ states with respect to peptides. Sampling within these dimensions is controlled through side chain selection, and an expansive set of viable peptoid residues exists. It has been shown recently that "minimal" di- and tripeptoids with aromatic side chains can self-assemble into highly ordered structures, with size and morphological definition varying as a function of sequence pattern (e.g., XFF and FXF, where X = a nonaromatic peptoid monomer). Aromatic groups, such as phenylalanine, are regularly used in the design of minimal peptide assemblers. In recognition of this, and to draw parallels between these compounds classes, we have developed a series of descriptors for intramolecular dynamics of aromatic side chains to discern whether these dynamics, in a preassembly condition, can be related to experimentally observed nanoscale assemblies. To do this, we have built on the atomistic peptoid force field reported by Weiser and Santiso (CGenFF-WS) through the rigorous fitting of partial charges and the collation of Charmm General Force Field (CGenFF) parameters relevant to these systems. Our study finds that the intramolecular dynamics of side chains, for a given sequence, is dependent on the specific combination of backbone ω torsions and that homogeneity of sampling across these states correlates well with the experimentally observed ability to assemble into nanomorphologies with long-range order. Sequence patterning is also shown to affect sampling, in a manner consistent for both tripeptoids and tripeptides. Additionally, sampling similarities between the nanofiber forming tripeptoid, Nf-Nke-Nf in the cc state, and the nanotube forming dipeptide FF, highlight a structural motif which may be relevant to the emergence of extended linear assemblies. To assess these properties, a variety of computational approaches have been employed.
Collapse
Affiliation(s)
- Hamish
W. A. Swanson
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - King Hang Aaron Lau
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Tell Tuttle
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| |
Collapse
|
4
|
Schunk HC, Austin MJ, Taha BZ, McClellan MS, Suggs LJ, Rosales AM. Oxidative Degradation of Sequence-Defined Peptoid Oligomers. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2023; 8:92-104. [PMID: 37123435 PMCID: PMC10147340 DOI: 10.1039/d2me00179a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Due to their N-substitution, peptoids are generally regarded as resistant to biological degradation, such as enzymatic and hydrolytic mechanisms. This stability is an especially attractive feature for therapeutic development and is a selling point of many previous biological studies. However, another key mode of degradation remains to be fully explored, namely oxidative degradation mediated by reactive oxygen and nitrogen species (ROS/RNS). ROS and RNS are biologically relevant in numerous contexts where biomaterials may be present, thus, improving understanding of peptoid oxidative susceptibility is crucial to exploit their full potential in the biomaterials field, where an oxidatively-labile but enzymatically stable molecule can offer attractive properties. Toward this end, we demonstrate a fundamental characterization of sequence-defined peptoid chains in the presence of chemically generated ROS, as compared to ROS-susceptible peptides such as proline and lysine oligomers. Lysine oligomers showed the fastest degradation rates to ROS and the enzyme trypsin. Peptoids degraded in metal catalyzed oxidation conditions at rates on par with poly(prolines), while maintaining resistance to enzymatic degradation. Furthermore, lysine-containing peptide-peptoid hybrid molecules showed tunability in both ROS-mediated and enzyme-mediated degradation, with rates intermediate to lysine and peptoid oligomers. When lysine-mimetic side-chains were incorporated into a peptoid backbone, the rate of degradation matched that of the lysine peptide oligomers, but remained resistant to enzymatic degradation. These results expand understanding of peptoid degradation to oxidative and enzymatic mechanisms, and demonstrate the potential for peptoid incorporation into materials where selectivity towards oxidative degradation is necessary, or directed enzymatic susceptibility is desired.
Collapse
Affiliation(s)
- Hattie C. Schunk
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Mariah J. Austin
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Bradley Z. Taha
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Matthew S. McClellan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Laura J. Suggs
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| | - Adrianne M. Rosales
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, United States
| |
Collapse
|
5
|
Angelici G, Bhattacharjee N, Pypec M, Jouffret L, Didierjean C, Jolibois F, Perrin L, Roy O, Taillefumier C. Unveiling the conformational landscape of achiral all- cis tert-butyl β-peptoids. Org Biomol Chem 2022; 20:7907-7915. [PMID: 36173021 DOI: 10.1039/d2ob01351g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and conformational study of N-substituted β-alanines with tert-butyl side chains is described. The oligomers prepared by submonomer synthesis and block coupling methods are up to 15 residues long and are characterised by amide bonds in the cis-conformation. A conformational study comprising experimental solution NMR spectroscopy, X-ray crystallography and molecular modeling shows that despite their intrinsic higher conformational flexibility compared to their α-peptoid counterparts, this family of achiral oligomers adopt preferred secondary structures including a helical conformation close to that described with (1-naphthyl)ethyl side chains but also a novel ribbon-like conformation.
Collapse
Affiliation(s)
- Gaetano Angelici
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Nicholus Bhattacharjee
- Université de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - Maxime Pypec
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Laurent Jouffret
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | | | - Franck Jolibois
- Université de Toulouse-INSA-UPS, LPCNO, CNRS UMR 5215, 135 av. Rangueil, F-31077, Toulouse, France
| | - Lionel Perrin
- Université de Lyon, Université Claude Bernard Lyon I, CNRS, INSA, CPE, UMR 5246, ICBMS, 1 rue Victor Grignard, F-69622 Villeurbanne, France
| | - Olivier Roy
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| | - Claude Taillefumier
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, 63000 Clermont-Ferrand, France.
| |
Collapse
|
6
|
Boruah A, Roy A. Advances in hybrid peptide-based self-assembly systems and their applications. Biomater Sci 2022; 10:4694-4723. [PMID: 35899853 DOI: 10.1039/d2bm00775d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.
Collapse
Affiliation(s)
- Alpana Boruah
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Arup Roy
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Chen J, Zhou Y, Fu Y, Pan J, Mohammed OF, Bakr OM. Oriented Halide Perovskite Nanostructures and Thin Films for Optoelectronics. Chem Rev 2021; 121:12112-12180. [PMID: 34251192 DOI: 10.1021/acs.chemrev.1c00181] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Oriented semiconductor nanostructures and thin films exhibit many advantageous properties, such as directional exciton transport, efficient charge transfer and separation, and optical anisotropy, and hence these nanostructures are highly promising for use in optoelectronics and photonics. The controlled growth of these structures can facilitate device integration to improve optoelectronic performance and benefit in-depth fundamental studies of the physical properties of these materials. Halide perovskites have emerged as a new family of promising and cost-effective semiconductor materials for next-generation high-power conversion efficiency photovoltaics and for versatile high-performance optoelectronics, such as light-emitting diodes, lasers, photodetectors, and high-energy radiation imaging and detectors. In this Review, we summarize the advances in the fabrication of halide perovskite nanostructures and thin films with controlled dimensionality and crystallographic orientation, along with their applications and performance characteristics in optoelectronics. We examine the growth methods, mechanisms, and fabrication strategies for several technologically relevant structures, including nanowires, nanoplates, nanostructure arrays, single-crystal thin films, and highly oriented thin films. We highlight and discuss the advantageous photophysical properties and remarkable performance characteristics of oriented nanostructures and thin films for optoelectronics. Finally, we survey the remaining challenges and provide a perspective regarding the opportunities for further progress in this field.
Collapse
Affiliation(s)
- Jie Chen
- Division of Physical Science and Engineering (PSE) and KAUST Catalysis Center (KCC), Advanced Membranes and Porous Materials Center (AMPMC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yang Zhou
- Division of Physical Science and Engineering (PSE) and KAUST Catalysis Center (KCC), Advanced Membranes and Porous Materials Center (AMPMC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yongping Fu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jun Pan
- College of Materials Science and Engineering, Zhejiang University of Technology, Hangzhou 310014, People's Republic of China
| | - Omar F Mohammed
- Division of Physical Science and Engineering (PSE) and KAUST Catalysis Center (KCC), Advanced Membranes and Porous Materials Center (AMPMC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Osman M Bakr
- Division of Physical Science and Engineering (PSE) and KAUST Catalysis Center (KCC), Advanced Membranes and Porous Materials Center (AMPMC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
9
|
Babi J, Zhu L, Lin A, Uva A, El‐Haddad H, Peloewetse A, Tran H. Self‐assembled free‐floating
nanomaterials from
sequence‐defined
polymers. JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1002/pol.20210366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jon Babi
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Linglan Zhu
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Angela Lin
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Azalea Uva
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Hana El‐Haddad
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Atang Peloewetse
- Department of Chemistry University of Toronto Toronto Ontario Canada
| | - Helen Tran
- Department of Chemistry University of Toronto Toronto Ontario Canada
- Department of Chemical Engineering University of Toronto Toronto Ontario Canada
| |
Collapse
|
10
|
Pushpavanam K, Ma J, Cai Y, Naser NY, Baneyx F. Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication. Annu Rev Chem Biomol Eng 2021; 12:333-357. [PMID: 33852353 DOI: 10.1146/annurev-chembioeng-102020-015923] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is considerable interest in the development of hybrid organic-inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.
Collapse
Affiliation(s)
- Karthik Pushpavanam
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Jinrong Ma
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| | - Yifeng Cai
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - Nada Y Naser
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA;
| | - François Baneyx
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98115, USA; .,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98115, USA
| |
Collapse
|
11
|
Xuan S, Jiang X, Balsara NP, Zuckermann RN. Crystallization and self-assembly of shape-complementary sequence-defined peptoids. Polym Chem 2021. [DOI: 10.1039/d1py00426c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Shape complementarity between polymers is a hallmark of biological systems (e.g. DNA base pairing and protein binding interactions). Here we explore the role of shape complementarity between sequence-defined N-alkyl peptoids in crystal lattices.
Collapse
Affiliation(s)
- Sunting Xuan
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xi Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nitash P. Balsara
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- College of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ronald N. Zuckermann
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| |
Collapse
|
12
|
|
13
|
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]
|
14
|
Rinaldi S. The Diverse World of Foldamers: Endless Possibilities of Self-Assembly. Molecules 2020; 25:E3276. [PMID: 32708440 PMCID: PMC7397133 DOI: 10.3390/molecules25143276] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 02/07/2023] Open
Abstract
Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.
Collapse
Affiliation(s)
- Samuele Rinaldi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
15
|
Xuan S, Zuckermann RN. Diblock copolypeptoids: a review of phase separation, crystallization, self-assembly and biological applications. J Mater Chem B 2020; 8:5380-5394. [DOI: 10.1039/d0tb00477d] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Diblock copolypeptoids have the capacity to phase separate, crystallize, and self-assemble into a variety of nanostructures, which have shown great potential in a variety of biological applications.
Collapse
Affiliation(s)
- Sunting Xuan
- Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- Materials Sciences Division
| | - Ronald N. Zuckermann
- Molecular Foundry
- Lawrence Berkeley National Laboratory
- Berkeley
- USA
- Materials Sciences Division
| |
Collapse
|
16
|
Solid-Phase Insertion of N-mercaptoalkylglycine Residues into Peptides. Molecules 2019; 24:molecules24234261. [PMID: 31766740 PMCID: PMC6930625 DOI: 10.3390/molecules24234261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
N-mercaptoalkylglycine residues were inserted into peptides by reacting N-free amino groups of peptides, which were initially synthesized on 2-chlorotrityl resin (Cltr) using the Fmoc/tBu method, with bromoacetic acid and subsequent nucleophilic replacement of the bromide by reacting with S-4-methoxytrityl- (Mmt)/S-trityl- (Trt) protected aminothiols. The synthesized thiols containing peptide–peptoid hybrids were cleaved from the resin, either protected by treatment with dichloromethane (DCM)/trifluoroethanol (TFE)/acetic acid (AcOH) (7:2:1), or deprotected (fully or partially) by treatment with trifluoroacetic acid (TFA) solution using triethylsilane (TES) as a scavenger.
Collapse
|