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Treherne JM, Miller AF. Novel hydrogels: are they poised to transform 3D cell-based assay systems in early drug discovery? Expert Opin Drug Discov 2023; 18:335-346. [PMID: 36722285 DOI: 10.1080/17460441.2023.2175813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Success in drug discovery remains unpredictable. However, more predictive and relevant disease models are becoming pivotal to demonstrating the clinical benefits of new drugs earlier in the lengthy drug discovery process. Novel hydrogel scaffolds are being developed to transform the relevance of such 3D cell-based in vitro assay systems. AREAS COVERED Most traditional hydrogels are still of unknown composition and suffer significant batch-to-batch variations, which lead to technical constraints. This article looks at how a new generation of novel synthetic hydrogels that are based on self-assembling peptides are poised to transform 3D cell-based assay systems by improving their relevance, reproducibility and scalability. EXPERT OPINION The emerging advantages of using these novel hydrogels for human 3D screening assays should enable the discovery of more cost-effective drugs, leading to improved patient benefits. Such a disruptive change could also reduce the considerable time lag from obtaining in vitro assay data to initiating clinical trials. There is now a sufficient body of data available in the literature to enable this ambition to become a reality by significantly improving the predictive validity of 3D cell-based assays in early drug discovery. Novel hydrogels are key to unlocking the full potential of these assay systems.
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Affiliation(s)
- J Mark Treherne
- Talisman Therapeutics Ltd, Jonas Webb Building and Cell Guidance Sysyems Ltd, Babraham Research Campus, Cambridge, UK
| | - Aline F Miller
- Manchester Institute of Biotechnology, School of Engineering, The University of Manchester, Oxford Road, Manchester, UK
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2
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Amphipathic peptide-phospholipid nanofibers: Kinetics of fiber formation and molecular transfer between assemblies. Biophys Chem 2023; 296:106985. [PMID: 36863073 DOI: 10.1016/j.bpc.2023.106985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/13/2023] [Accepted: 02/23/2023] [Indexed: 02/27/2023]
Abstract
Understanding the kinetics of nano-assembly formation is important to elucidate the biological processes involved and develop novel nanomaterials with biological functions. In the present study, we report the kinetic mechanisms of nanofiber formation from a mixture of phospholipids and the amphipathic peptide 18A[A11C], carrying cysteine substitution of the apolipoprotein A-I-derived peptide 18A at residue 11. 18A[A11C] with acetylated N-terminus and amidated C-terminus can associate with phosphatidylcholine to form fibrous aggregates at neutral pH and lipid-to-peptide molar ratio of ∼1, although the reaction pathways of self-assembly remain unclear. Here, the peptide was added to giant 1-palmitoyl-2-oleoyl phosphatidylcholine vesicles to monitor nanofiber formation under fluorescence microscopy. The peptide initially solubilized the lipid vesicles into particles smaller than the resolution of optical microscope, and fibrous aggregates appeared subsequently. Transmission electron microscopy and dynamic light scattering analyses revealed that the vesicle-solubilized particles were spherical or circular, measuring ∼10-20 nm in diameter. The rate of nanofiber formation of 18A with 1,2-dipalmitoyl phosphatidylcholine from the particles was proportional to the square of lipid-peptide concentration in the system, suggesting that the association of particles, accompanied by conformational changes, was the rate-limiting step. Moreover, molecules in the nanofibers could be transferred between aggregates faster than those in the lipid vesicles. These findings provide useful information for the development and control of nano-assembling structures using peptides and phospholipids.
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Fernandes R, Chowdhary S, Mikula N, Saleh N, Kanevche K, Berlepsch HV, Hosogi N, Heberle J, Weber M, Böttcher C, Koksch B. Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures. Angew Chem Int Ed Engl 2022; 61:e202208647. [PMID: 36161448 PMCID: PMC9828782 DOI: 10.1002/anie.202208647] [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: 06/13/2022] [Indexed: 01/12/2023]
Abstract
Synthetic multichromophore systems are of great importance in artificial light harvesting devices, organic optoelectronics, tumor imaging and therapy. Here, we introduce a promising strategy for the construction of self-assembled peptide templated dye stacks based on coupling of a de novo designed pH sensitive peptide with a cyanine dye Cy5 at its N-terminus. Microscopic techniques, in particular cryogenic TEM (cryo-TEM) and cryo-electron tomography technique (cryo-ET), reveal two types of highly ordered three-dimensional assembly structures on the micrometer scale. Unbranched compact layered rods are observed at pH 7.4 and two-dimensional membrane-like assemblies at pH 3.4, both species displaying spectral features of H-aggregates. Molecular dynamics simulations reveal that the coupling of Cy5 moieties promotes the formation of both ultrastructures, whereas the protonation states of acidic and basic amino acid side chains dictates their ultimate three-dimensional organization.
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Affiliation(s)
- Rita Fernandes
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Suvrat Chowdhary
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
| | - Natalia Mikula
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Noureldin Saleh
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Katerina Kanevche
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Hans v. Berlepsch
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | | | - Joachim Heberle
- Department of PhysicsExperimental Molecular BiophysicsFreie Universität BerlinArnimallee 1414195BerlinGermany
| | - Marcus Weber
- Mathematics for Life and Materials SciencesZuse Institute BerlinTakustraße 714195BerlinGermany
| | - Christoph Böttcher
- Research Center for Electron Microscopy and Core Facility BioSupraMolFreie Universität BerlinFabeckstraße 36a14195BerlinGermany
| | - Beate Koksch
- Department of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2014195BerlinGermany
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4
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Miller JG, Hughes SA, Modlin C, Conticello VP. Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers. Q Rev Biophys 2022; 55:1-103. [PMID: 35307042 DOI: 10.1017/s0033583522000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractSynthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.
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Affiliation(s)
- Jessalyn G Miller
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Spencer A Hughes
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
| | - Charles Modlin
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA30322
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5
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Zhu X, Duan R, Chan SY, Han L, Liu H, Sun B. Structural and photoactive properties of self-assembled peptide-based nanostructures and their optical bioapplication in food analysis. J Adv Res 2022; 43:27-44. [PMID: 36585113 PMCID: PMC9811376 DOI: 10.1016/j.jare.2022.02.001] [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: 11/09/2021] [Revised: 01/23/2022] [Accepted: 02/02/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Food processing plays an important role in the modern industry because food quality and security directly affect human health, life safety, and social and economic development. Accurate, efficient, and sensitive detection technology is the basis for ensuring food quality and security. Optosensor-based technology with the advantage of fast and visual real-time detection can be used to detect pesticides, metal ions, antibiotics, and nutrients in food. As excellent optical centres, self-assembled peptide-based nanostructures possess attractive advantages, such as simple preparation methods, controllable morphology, tunable functionality, and inherent biocompatibility. AIM OF REVIEW Self-assembled peptide nanostructures with good fabrication yield, stability, dispersity in a complex sample matrix, biocompatibility, and environmental friendliness are ideal development goals in the future. Owing to its flexible and unique optical properties, some short peptide self-assemblies can possibly be used to achieve the purpose of rapid and sensitive detection of composition in food, agriculture, and the environment, expanding the understanding and application of peptide-based optics in analytical chemistry. KEY SCIENTIFIC CONCEPT OF REVIEW The self-assembly process of peptides is driven by noncovalent interactions, including hydrogen bonding, electrostatic interactions, hydrophobic interactions, and π-π stacking, which are the key factors for obtaining stable self-assembled peptide nanostructures with peptides serving as assembly units. Controllable morphology of self-assembled peptide nanostructures can be achieved through adjustment in the type, concentration, and pH of organic solvents and peptides. The highly ordered nanostructures formed by the self-assembly of peptides have been proven to be novel biological structures and can be used for the construction of optosensing platforms in biological or other systems. Optosensing platforms make use of signal changes, including optical signals and electrical signals caused by specific reactions between analytes and active substances, to determine the content or concentration of an analyte.
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Affiliation(s)
- Xuecheng Zhu
- Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China
| | - Ruixue Duan
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Siew Yin Chan
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research, 2 Fusionopolis Way, #08-03 Innovis, Singapore 138634, Singapore
| | - Luxuan Han
- Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China
| | - Huilin Liu
- Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China,Corresponding author.
| | - Baoguo Sun
- Beijing Technology and Business University, 11 Fucheng Road, Beijing 100048, China
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6
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Dai K, Tena-Solsona M, Rodon Fores J, Bergmann AM, Boekhoven J. Morphological transitions in chemically fueled self-assembly. NANOSCALE 2021; 13:19864-19869. [PMID: 34825692 DOI: 10.1039/d1nr04954b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In chemically fueled self-assembly, a reaction cycle activates and deactivates molecules for self-assembly. The resulting assembly is dynamic and should be endowed with unique behavior in this kinetically controlled regime. Recent works have mainly focused on design rules for the activation of molecules for self-assembly, thereby assuming that disassembly upon deactivation inherently follows. However, that is not always the case. This work shows a family of peptides that assemble into colloids regulated through a chemical reaction cycle. Despite their similarity in assembly, we find that they follow a different disassembly pathway upon deactivation. The colloids from several peptides completely disassemble as fuel depletes while others transition into fibers. Our findings demonstrate that assembly and disassembly should be taken into account in chemically fueled self-assembly.
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Affiliation(s)
- Kun Dai
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Marta Tena-Solsona
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Jennifer Rodon Fores
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Alexander M Bergmann
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
| | - Job Boekhoven
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2a, 85748 Garching, Germany
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7
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Das S, Das D. Rational Design of Peptide-based Smart Hydrogels for Therapeutic Applications. Front Chem 2021; 9:770102. [PMID: 34869218 PMCID: PMC8635208 DOI: 10.3389/fchem.2021.770102] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Peptide-based hydrogels have captivated remarkable attention in recent times and serve as an excellent platform for biomedical applications owing to the impressive amalgamation of unique properties such as biocompatibility, biodegradability, easily tunable hydrophilicity/hydrophobicity, modular incorporation of stimuli sensitivity and other functionalities, adjustable mechanical stiffness/rigidity and close mimicry to biological molecules. Putting all these on the same plate offers smart soft materials that can be used for tissue engineering, drug delivery, 3D bioprinting, wound healing to name a few. A plethora of work has been accomplished and a significant progress has been realized using these peptide-based platforms. However, designing hydrogelators with the desired functionalities and their self-assembled nanostructures is still highly serendipitous in nature and thus a roadmap providing guidelines toward designing and preparing these soft-materials and applying them for a desired goal is a pressing need of the hour. This review aims to provide a concise outline for that purpose and the design principles of peptide-based hydrogels along with their potential for biomedical applications are discussed with the help of selected recent reports.
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Affiliation(s)
- Saurav Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
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8
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Ikeda K, Horiuchi A, Yoshino M, Shimizu C, Nakao H, Nakano M. Amphipathic Peptide-Phospholipid Nanofibers: Phospholipid Specificity and Dependence on Concentration and Temperature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:713-721. [PMID: 33400880 DOI: 10.1021/acs.langmuir.0c02819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The design of nanoassemblies is an important part of the development of new materials for applications in nanomedicine and biosensors. In our previous study, cysteine substitution of the apolipoprotein A-I-derived peptide 18A at residue 11, 18A[A11C], bound to 1-palmitoyl-2-oleoylphosphatidylcholine to form fibrous aggregates at a lipid-to-peptide molar ratio of ≤2 and a fiber diameter of 10-20 nm. However, the mechanisms underlying the lipid-peptide interactions that enable nanofiber formation remain unclear. Here, we evaluated the phospholipid specificity, concentration dependence, and temperature dependence of the formation of 18A[A11C]-lipid nanofibers. Nanofibers were found to form in the presence of specific phospholipids and have a constant lipid/peptide stoichiometry of 1.2 ± 0.2. Moreover, an increase in the length of the acyl chain in phosphatidylcholines was found to increase the structural stability of the nanofibers. These results indicate that specific molecular interactions between peptides and both the headgroups and acyl chains of phospholipids are involved in nanofiber formation. Furthermore, the formation and disassembly of the nanofibers were reversibly controlled by changes in temperature and concentration. The results of the present study provide an insight into the creation of nanoassembling structures.
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Affiliation(s)
- Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Ayame Horiuchi
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Misa Yoshino
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Chinatsu Shimizu
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0194, Japan
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9
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Castillo-Díaz LA, Ruiz-Pacheco JA, Elsawy MA, Reyes-Martínez JE, Enríquez-Rodríguez AI. Self-Assembling Peptides as an Emerging Platform for the Treatment of Metabolic Syndrome. Int J Nanomedicine 2020; 15:10349-10370. [PMID: 33376325 PMCID: PMC7762440 DOI: 10.2147/ijn.s278189] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Metabolic syndrome comprises a cluster of comorbidities that represent a major risk of developing chronic diseases, such as type II diabetes, cardiovascular diseases, and stroke. Alarmingly, metabolic syndrome reaches epidemic proportions worldwide. Today, lifestyle changes and multiple drug-based therapies represent the gold standard to address metabolic syndrome. However, such approaches face two major limitations: complicated drug therapeutic regimes, which in most cases could lead to patient incompliance, and limited drug efficacy. This has encouraged scientists to search for novel routes to deal with metabolic syndrome and related diseases. Within such approaches, self-assembled peptide formulations have emerged as a promising alternative for treating metabolic syndrome. In particular, self-assembled peptide hydrogels, either as acellular or cell-load three-dimensional scaffoldings have reached significant relevance in the biomedical field to prevent and restore euglycemia, as well as for controlling cardiovascular diseases and obesity. This has been possible thanks to the physicochemical tunability of peptides, which are developed from a chemical toolbox of versatile amino acids enabling flexibility of designing a wide range of self-assembled/co-assembled nanostructures forming biocompatible viscoelastic hydrogels. Peptide hydrogels can be combined with several biological entities, such as extracellular matrix proteins, drugs or cells, forming functional biologics with therapeutic ability for treatment of metabolic syndrome-comorbidities. Additionally, self-assembly peptides combine safety, tolerability, and effectivity attributes; by this presenting a promising platform for the development of novel pharmaceuticals capable of addressing unmet therapeutic needs for diabetes, cardiovascular disorders and obesity. In this review, recent advances in developing self-assembly peptide nanostructures tailored for improving treatment of metabolic syndrome and related diseases will be discussed from basic research to preclinical research studies. Challenges facing the development of approved medicinal products based on self-assembling peptide nanomaterials will be discussed in light of regulatory requirement for clinical authorization.
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Affiliation(s)
| | - Juan Alberto Ruiz-Pacheco
- West Biomedical Research Center, National Council of Science and Technology, Guadalajara, Jalisco, Mexico
| | - Mohamed Ahmed Elsawy
- Leicester Institute for Pharmaceutical Innovation, Leicester School of Pharmacy, De Montfort University, Leicester, Leicestershire, UK
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10
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Li J, Zhao Y, Zhou P, Hu X, Wang D, King SM, Rogers SE, Wang J, Lu JR, Xu H. Ordered Nanofibers Fabricated from Hierarchical Self-Assembling Processes of Designed α-Helical Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003945. [PMID: 33015967 DOI: 10.1002/smll.202003945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/15/2020] [Indexed: 06/11/2023]
Abstract
Peptide self-assembly is fast evolving into a powerful method for the development of bio-inspired nanomaterials with great potential for many applications, but it remains challenging to control the self-assembling processes and nanostrucutres because of the intricate interplay of various non-covalent interactions. A group of 28-residue α-helical peptides is designed including NN, NK, and HH that display distinct hierarchical events. The key of the design lies in the incorporation of two asparagine (Asn) or histidine (His) residues at the a positions of the second and fourth heptads, which allow one sequence to pack into homodimers with sticky ends through specific interhelical Asn-Asn or metal complexation interactions, followed by their longitudinal association into ordered nanofibers. This is in contrast to classical self-assembling helical peptide systems consisting of two complementary peptides. The collaborative roles played by the four main non-covalent interactions, including hydrogen-bonding, hydrophobic interactions, electrostatic interactions, and metal ion coordination, are well demonstrated during the hierarchical self-assembling processes of these peptides. Different nanostructures, for example, long and short nanofibers, thin and thick fibers, uniform metal ion-entrapped nanofibers, and polydisperse globular stacks, can be prepared by harnessing these interactions at different levels of hierarchy.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Yurong Zhao
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Peng Zhou
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xuzhi Hu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Dong Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Stephen M King
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Sarah E Rogers
- ISIS Pulsed Neutron & Muon Source, STFC Rutherford Appleton Laboratory, Didcot, Oxon, OX11 0QX, UK
| | - Jiqian Wang
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
| | - Jian R Lu
- Biological Physics Group, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Hai Xu
- State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, 266580, China
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Abstract
Treatment strategies in clinics have been shifting from small molecules to protein drugs due to the promising results of a highly specific mechanism of action and reduced toxicity. Despite their prominent roles in disease treatment, delivery of the protein therapeutics is challenging due to chemical instability, immunogenicity and biological barriers. Peptide hydrogels with spatiotemporally tunable properties have shown an outstanding potential to deliver complex protein therapeutics, maintain drug efficacy and stability over time, mimicking the extracellular matrix, and responding to external stimuli. In this review, we present recent advances in peptide hydrogel design strategies, protein release kinetics and mechanisms for protein drug delivery in cellular engineering, tissue engineering, immunotherapy and disease treatments.
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12
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Liu R, Hudalla GA. Using Self-Assembling Peptides to Integrate Biomolecules into Functional Supramolecular Biomaterials. Molecules 2019; 24:E1450. [PMID: 31013712 PMCID: PMC6514692 DOI: 10.3390/molecules24081450] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
Throughout nature, self-assembly gives rise to functional supramolecular biomaterials that can perform complex tasks with extraordinary efficiency and specificity. Inspired by these examples, self-assembly is increasingly used to fabricate synthetic supramolecular biomaterials for diverse applications in biomedicine and biotechnology. Peptides are particularly attractive as building blocks for these materials because they are based on naturally derived amino acids that are biocompatible and biodegradable; they can be synthesized using scalable and cost-effective methods, and their sequence can be tailored to encode formation of diverse architectures. To endow synthetic supramolecular biomaterials with functional capabilities, it is now commonplace to conjugate self-assembling building blocks to molecules having a desired functional property, such as selective recognition of a cell surface receptor or soluble protein, antigenicity, or enzymatic activity. This review surveys recent advances in using self-assembling peptides as handles to incorporate biologically active molecules into supramolecular biomaterials. Particular emphasis is placed on examples of functional nanofibers, nanovesicles, and other nano-scale structures that are fabricated by linking self-assembling peptides to proteins and carbohydrates. Collectively, this review highlights the enormous potential of these approaches to create supramolecular biomaterials with sophisticated functional capabilities that can be finely tuned to meet the needs of downstream applications.
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Affiliation(s)
- Renjie Liu
- J. Crayton Pruitt Family Department of Biomedical Engineering, Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA.
| | - Gregory A Hudalla
- J. Crayton Pruitt Family Department of Biomedical Engineering, Wertheim College of Engineering, University of Florida, Gainesville, FL 32611, USA.
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13
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Wilson CJ, Bommarius AS, Champion JA, Chernoff YO, Lynn DG, Paravastu AK, Liang C, Hsieh MC, Heemstra JM. Biomolecular Assemblies: Moving from Observation to Predictive Design. Chem Rev 2018; 118:11519-11574. [PMID: 30281290 PMCID: PMC6650774 DOI: 10.1021/acs.chemrev.8b00038] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.
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Affiliation(s)
- Corey J. Wilson
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Andreas S. Bommarius
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Julie A. Champion
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Yury O. Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Laboratory of Amyloid Biology & Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia
| | - David G. Lynn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Anant K. Paravastu
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Chen Liang
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ming-Chien Hsieh
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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14
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Nambiar M, Wang LS, Rotello V, Chmielewski J. Reversible Hierarchical Assembly of Trimeric Coiled-Coil Peptides into Banded Nano- and Microstructures. J Am Chem Soc 2018; 140:13028-13033. [DOI: 10.1021/jacs.8b08163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Monessha Nambiar
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Li-Sheng Wang
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Vincent Rotello
- Department of Chemistry, University of Massachusetts−Amherst, 710 N. Pleasant Street, Amherst, Massachusetts 01002, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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15
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Polyserine repeats promote coiled coil-mediated fibril formation and length-dependent protein aggregation. J Struct Biol 2018; 204:572-584. [PMID: 30194983 DOI: 10.1016/j.jsb.2018.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/06/2018] [Accepted: 09/01/2018] [Indexed: 12/13/2022]
Abstract
Short polyserine (polyS) repeats are frequently found in proteins and longer ones are produced in neurological disorders such as Huntington disease (HD) owing to translational frameshifting or non-ATG-dependent translation, together with polyglutamine (polyQ) and polyalanine (polyA) repeats, forming intracellular aggregates. However, the physiological and pathological structures of polyS repeats are not clearly understood. Early studies highlighted their structural versatility, similar to other homopolymers whose conformation is influenced by the surrounding protein context. As polyS stretches are frequently near polyQ and polyA repeats, which can be part of coiled coil (CC) structures, and the frameshift-derived polyS repeats in HD directly flank CC heptads important for aggregation, we investigate here the structural and aggregation properties of polyS in the context of CC structures. We have taken advantage of peptide models, previously used to study polyQ and polyA in CCs, in which we inserted polyS repeats of variable length and studied them in comparison with polyQ and polyA peptides. We found that polyS repeats promote CC-mediated polymerization and fibrillization as revealed by circular dichroism, chemical crosslinking, and atomic force microscopy. Furthermore, they promote CC-based, length-dependent intracellular aggregation, which is negligible with 7 and widespread with 49 serines. These findings show that polyS repeats can participate in the formation of CCs, as previously found for polyQ and polyA, conferring to peptides distinctive structural properties with aggregation kinetics that are intermediate between those of polyA and polyQ CCs, and contribute to an overall structural definition of the pathophysiogical roles of homopolymeric repeats in CC structures.
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16
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Nagarkar RP, Miller SE, Zhong S, Pochan DJ, Schneider JP. Dynamic protein folding at the surface of stimuli-responsive peptide fibrils. Protein Sci 2018; 27:1243-1251. [PMID: 29493033 PMCID: PMC6032354 DOI: 10.1002/pro.3394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 01/01/2023]
Abstract
The repetitive self-assembled structure of amyloid can serve as inspiration to design functional materials. Herein, we describe the design of α/β6, a peptide that contains distinct α-helical and β-structure forming domains. The folding and association state of each domain can be controlled by temperature. At low temperatures, the α-domain favors a coiled-coil state while the β-domain is unstructured. Irreversible fibril formation via self-assembly of the β-domain is triggered at high temperatures where the α-domain is unfolded. Resultant fibrils serve as templates upon which reversible coiled coil formation of the α-domain can be thermally controlled. At concentrations of α/β6 ≥ 2.5 wt%, the peptide forms a mechanically defined hydrogel highlighting the possibility of designing materials whose function can be actively modulated by controlling the folded state of proteins displayed from the surface of fibrils that constitute the gel.
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Affiliation(s)
- Radhika P. Nagarkar
- Department of Chemistry and BiochemistryUniversity of DelawareNewarkDelaware19716
| | - Stephen E. Miller
- Chemical Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickMaryland21702
| | - Sheng Zhong
- Department of Materials Science and EngineeringUniversity of DelawareNewarkDelaware19716
| | - Darrin J. Pochan
- Department of Materials Science and EngineeringUniversity of DelawareNewarkDelaware19716
| | - Joel P. Schneider
- Chemical Biology LaboratoryNational Cancer Institute, National Institutes of HealthFrederickMaryland21702
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17
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Lawrie J, Song X, Niu W, Guo J. A high throughput approach for the generation of orthogonally interacting protein pairs. Sci Rep 2018; 8:867. [PMID: 29343761 PMCID: PMC5772552 DOI: 10.1038/s41598-018-19281-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/27/2017] [Indexed: 11/17/2022] Open
Abstract
In contrast to the nearly error-free self-assembly of protein architectures in nature, artificial assembly of protein complexes with pre-defined structure and function in vitro is still challenging. To mimic nature's strategy to construct pre-defined three-dimensional protein architectures, highly specific protein-protein interacting pairs are needed. Here we report an effort to create an orthogonally interacting protein pair from its parental pair using a bacteria-based in vivo directed evolution strategy. This high throughput approach features a combination of a negative and a positive selection. The newly developed negative selection from this work was used to remove any protein mutants that retain effective interaction with their parents. The positive selection was used to identify mutant pairs that can engage in effective mutual interaction. By using the cohesin-dockerin protein pair that is responsible for the self-assembly of cellulosome as a model system, we demonstrated that a protein pair that is orthogonal to its parent pair could be readily generated using our strategy. This approach could open new avenues to a wide range of protein-based assembly, such as biocatalysis or nanomaterials, with pre-determined architecture and potentially novel functions and properties.
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Affiliation(s)
- Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xi Song
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
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18
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Huang D, Hudson BC, Gao Y, Roberts EK, Paravastu AK. Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels. Methods Mol Biol 2018; 1777:23-68. [PMID: 29744827 PMCID: PMC7490753 DOI: 10.1007/978-1-4939-7811-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.
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Affiliation(s)
- Danting Huang
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Benjamin C Hudson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Yuan Gao
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Evan K Roberts
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anant K Paravastu
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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19
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Phambu N, Almarwani B, Garcia AM, Hamza NS, Muhsen A, Baidoo JE, Sunda-Meya A. Chain length effect on the structure and stability of antimicrobial peptides of the (RW)n series. Biophys Chem 2017; 227:8-13. [DOI: 10.1016/j.bpc.2017.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/21/2017] [Accepted: 05/21/2017] [Indexed: 01/10/2023]
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20
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Ikeda K, Horiuchi A, Egawa A, Tamaki H, Fujiwara T, Nakano M. Nanodisc-to-Nanofiber Transition of Noncovalent Peptide-Phospholipid Assemblies. ACS OMEGA 2017; 2:2935-2944. [PMID: 31457628 PMCID: PMC6641012 DOI: 10.1021/acsomega.7b00424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/09/2017] [Indexed: 06/10/2023]
Abstract
We report a novel molecular architecture of peptide-phospholipid coassemblies. The amphiphilic peptide Ac-18A-NH2 (18A), which was designed to mimic apolipoprotein α-helices, has been shown to form nanodisc structures with phospholipid bilayers. We show that an 18A peptide cysteine substitution at residue 11, 18A[A11C], forms fibrous assemblies with 1-palmitoyl-2-oleoyl-phosphatidylcholine at a lipid-to-peptide (L/P) molar ratio of 1, a fiber diameter of 10-20 nm, and a length of more than 1 μm. Furthermore, 18A[A11C] can form nanodiscs with these lipid bilayers at L/P ratios of 4-6. The peptide adopts α-helical structures in both the nanodisc and nanofiber assemblies, although the α-helical bundle structures were evident only in the nanofibers, and the phospholipids of the nanofibers were not lamellar. Fluorescence spectroscopic analysis revealed that the peptide and lipid molecules in the nanofibers exhibited different solvent accessibility and hydrophobicity from those of the nanodiscs. Furthermore, the cysteine substitution at residue 11 did not result in disulfide bond formation, although it was responsible for the nanofiber formation, suggesting that this free sulfhydryl group has an important functional role. Alternatively, the disulfide dimer of 18A[A11C] preferentially formed nanodiscs, even at an L/P ratio of 1. Interconversions of these discoidal and fibrous assemblies were induced by the stepwise addition of free 18A[A11C] or liposomes into the solution. Furthermore, these structural transitions could also be induced by the introduction of oxidative and reductive stresses to the assemblies. Our results demonstrate that heteromolecular lipid-peptide complexes represent a novel approach to the construction of controllable and functional nanoscale assemblies.
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Affiliation(s)
- Keisuke Ikeda
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ayame Horiuchi
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Ayako Egawa
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Hajime Tamaki
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Toshimichi Fujiwara
- Institute
for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Minoru Nakano
- Graduate
School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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21
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Aronsson C, Selegård R, Aili D. Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix–Loop–Helix Peptide Superstructures for Controlled Encapsulation and Release. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b01724] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christopher Aronsson
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Robert Selegård
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
| | - Daniel Aili
- Division
of Molecular Physics,
Department of Physics, Chemistry and Biology, Linköping University, 581 83 Linköping, Sweden
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22
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Lacou L, Léonil J, Gagnaire V. Functional properties of peptides: From single peptide solutions to a mixture of peptides in food products. Food Hydrocoll 2016. [DOI: 10.1016/j.foodhyd.2016.01.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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23
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Takei T, Tsumoto K, Yoshino M, Kojima S, Yazaki K, Ueda T, Takei T, Arisaka F, Miura KI. Role of positions e and g in the fibrous assembly formation of an amphipathic α-helix-forming polypeptide. Biopolymers 2016; 102:260-72. [PMID: 24615557 DOI: 10.1002/bip.22479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 02/02/2014] [Accepted: 02/13/2014] [Indexed: 12/30/2022]
Abstract
We previously characterized α3, a polypeptide that has a three times repeated sequence of seven amino acids (abcdefg: LETLAKA) and forms fibrous assemblies composed of amphipathic α-helices. Upon comparison of the amino acid sequences of α3 with other α-helix forming polypeptides, we proposed that the fibrous assemblies were formed due to the alanine (Ala) residues at positions e and g. Here, we characterized seven α3 analog polypeptides with serine (Ser), glycine (Gly), or charged residues substituted for Ala at positions e and g. The α-helix forming abilities of the substituted polypeptides were less than that of α3. The polypeptides with amino acid substitutions at position g and the polypeptide KEα3, in which Ala was substituted with charged amino acids, formed few fibrous assemblies. In contrast, polypeptides with Ala replaced by Ser at position e formed β-sheets under several conditions. These results show that Ala residues at position e and particularly at position g are involved in the formation of fibrous assemblies.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Tokyo, Japan
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24
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Kumar VA, Wang BK, Kanahara SM. Rational design of fiber forming supramolecular structures. Exp Biol Med (Maywood) 2016; 241:899-908. [PMID: 27022140 PMCID: PMC4950345 DOI: 10.1177/1535370216640941] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/24/2016] [Indexed: 12/28/2022] Open
Abstract
Recent strides in the development of multifunctional synthetic biomimetic materials through the self-assembly of multi-domain peptides and proteins over the past decade have been realized. Such engineered systems have wide-ranging application in bioengineering and medicine. This review focuses on fundamental fiber forming α-helical coiled-coil peptides, peptide amphiphiles, and amyloid-based self-assembling peptides; followed by higher order collagen- and elastin-mimetic peptides with an emphasis on chemical / biological characterization and biomimicry.
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Affiliation(s)
| | | | - Satoko M Kanahara
- Department of Internal Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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25
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Carr-Smith J, Pacheco-Gómez R, Little HA, Hicks MR, Sandhu S, Steinke N, Smith DJ, Rodger A, Goodchild SA, Lukaszewski RA, Tucker JHR, Dafforn TR. Polymerase Chain Reaction on a Viral Nanoparticle. ACS Synth Biol 2015; 4:1316-25. [PMID: 26046486 DOI: 10.1021/acssynbio.5b00034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The field of synthetic biology includes studies that aim to develop new materials and devices from biomolecules. In recent years, much work has been carried out using a range of biomolecular chassis including α-helical coiled coils, β-sheet amyloids and even viral particles. In this work, we show how hybrid bionanoparticles can be produced from a viral M13 bacteriophage scaffold through conjugation with DNA primers that can template a polymerase chain reaction (PCR). This unprecedented example of a PCR on a virus particle has been studied by flow aligned linear dichroism spectroscopy, which gives information on the structure of the product as well as a new protototype methodology for DNA detection. We propose that this demonstration of PCR on the surface of a bionanoparticle is a useful addition to ways in which hybrid assemblies may be constructed using synthetic biology.
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Affiliation(s)
| | | | | | | | | | | | | | - Alison Rodger
- Department
of Chemistry, University of Warwick, Coventry, Warwickshire CV4 7AL, United Kingdom
| | - Sarah A. Goodchild
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
| | - Roman A. Lukaszewski
- Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, United Kingdom
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26
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Takei T, Tsumoto K, Okonogi A, Kimura A, Kojima S, Yazaki K, Takei T, Ueda T, Miura KI. pH responsiveness of fibrous assemblies of repeat-sequence amphipathic α-helix polypeptides. Protein Sci 2015; 24:883-94. [PMID: 25694229 DOI: 10.1002/pro.2665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/24/2022]
Abstract
We reported previously that our designed polypeptide α3 (21 residues), which has three repeats of a seven-amino-acid sequence (LETLAKA)3, forms not only an amphipathic α-helix structure but also long fibrous assemblies in aqueous solution. To address the relationship between the electrical states of the polypeptide and its α-helix and fibrous assembly formation, we characterized mutated polypeptides in which charged amino acid residues of α3 were replaced with Ser. We prepared the following polypeptides: 2Sα3 (LSTLAKA)3, in which all Glu residues were replaced with Ser residues; 6Sα3 (LETLASA)3, in which all Lys residues were replaced with Ser; and 2S6Sα3 (LSTLASA)3; in which all Glu and Lys residues were replaced with Ser. In 0.1M KCl, 2Sα3 formed an α-helix under basic conditions and 6Sα3 formed an α-helix under acid conditions. In 1M KCl, they both formed α-helices under a wide pH range. In addition, 2Sα3 and 6Sα3 formed fibrous assemblies under the same buffer conditions in which they formed α-helices. α-Helix and fibrous assembly formation by these polypeptides was reversible in a pH-dependent manner. In contrast, 2S6Sα3 formed an α-helix under basic conditions in 1M KCl. Taken together, these findings reveal that the charge states of the charged amino acid residues and the charge state of the Leu residue located at the terminus play an important role in α-helix formation.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier, The university of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan; Institute for Biomolecular Science, Gakushuin University, Toshima-ku, Tokyo, Japan
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27
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Jalan AA, Jochim KA, Hartgerink JD. Rational Design of a Non-canonical “Sticky-Ended” Collagen Triple Helix. J Am Chem Soc 2014; 136:7535-8. [DOI: 10.1021/ja5001246] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Abhishek A. Jalan
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Katherine A. Jochim
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D. Hartgerink
- Departments of Chemistry
and Bioengineering, Rice University, 6100 Main Street, Houston, Texas 77005, United States
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28
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Meng Q, Kou Y, Ma X, Guo L, Liu K. Nanostructures from the self-assembly of α
-helical peptide amphiphiles. J Pept Sci 2014; 20:223-8. [DOI: 10.1002/psc.2606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Revised: 11/19/2013] [Accepted: 11/26/2013] [Indexed: 01/02/2023]
Affiliation(s)
- Qingbin Meng
- Beijing Institute of Pharmacology and Toxicology; Beijing 100850 China
| | - Yingying Kou
- Beijing Institute of Pharmacology and Toxicology; Beijing 100850 China
| | - Xin Ma
- Beijing Institute of Pharmacology and Toxicology; Beijing 100850 China
| | - Lei Guo
- Beijing Institute of Pharmacology and Toxicology; Beijing 100850 China
| | - Keliang Liu
- Beijing Institute of Pharmacology and Toxicology; Beijing 100850 China
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29
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Panda JJ, Chauhan VS. Short peptide based self-assembled nanostructures: implications in drug delivery and tissue engineering. Polym Chem 2014. [DOI: 10.1039/c4py00173g] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Self-assembling peptides with many potential biomedical applications.
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Affiliation(s)
- Jiban Jyoti Panda
- International Centre for Genetic Engineering and Biotechnology
- New Delhi 110067, India
- Institute of Nano Science and Technology
- Mohali, India
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30
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Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments. Nat Chem Biol 2013; 9:362-6. [PMID: 23624438 PMCID: PMC3661711 DOI: 10.1038/nchembio.1248] [Citation(s) in RCA: 234] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/28/2013] [Indexed: 01/30/2023]
Abstract
Protein structures evolved through a complex interplay of cooperative interactions and it is still very challenging to design new protein folds de novo. Here, we present a strategy to design self-assembling polypeptide nanostructured polyhedra, based on modularization using orthogonal dimerizing segments. We designed end experimentally demonstrated formation of the tetrahedron that self-assembles from a single polypeptide chain comprising 12 concatenated coiled-coil-forming segments separated by flexible peptide hinges. Path of the polypeptide chain is guided by the defined order of segments that traverse each of the 6 edges of the tetrahedron exactly twice, forming coiled-coil dimers with their corresponding partners. Coincidence of the polypeptide termini in the same vertex is demonstrated by reconstitution of the split fluorescent protein by the polypeptide with the correct tetrahedral topology, while polypeptides with a deleted or scrambled segment order fail to self-assemble correctly. This design platform provides the basis for construction of new topological polypeptide folds based on the set of orthogonal interacting polypeptide segments.
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31
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Takei T, Hasegawa K, Imada K, Namba K, Tsumoto K, Kuriki Y, Yoshino M, Yazaki K, Kojima S, Takei T, Ueda T, Miura KI. Effects of chain length of an amphipathic polypeptide carrying the repeated amino acid sequence (LETLAKA)(n) on α-helix and fibrous assembly formation. Biochemistry 2013; 52:2810-20. [PMID: 23530905 DOI: 10.1021/bi400001c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Polypeptide α3 (21 residues), with three repeats of a seven-amino-acid sequence (LETLAKA)(3), forms an amphipathic α-helix and a long fibrous assembly. Here, we investigated the ability of α3-series polypeptides (with 14-42 residues) of various chain lengths to form α-helices and fibrous assemblies. Polypeptide α2 (14 residues), with two same-sequence repeats, did not form an α-helix, but polypeptide α2L (15 residues; α2 with one additional leucine residue on its carboxyl terminal) did form an α-helix and fibrous assembly. Fibrous assembly formation was associated with polypeptides at least as long as polypeptide α2L and with five leucine residues, indicating that the C-terminal leucine has a critical element for stabilization of α-helix and fibril formation. In contrast, polypeptides α5 (35 residues) and α6 (42 residues) aggregated easily, although they formed α-helices. A 15-35-residue chain was required for fibrous assembly formation. Electron microscopy and X-ray fiber diffraction showed that the thinnest fibrous assemblies of polypeptides were about 20 Å and had periodicities coincident with the length of the α-helix in a longitudinal direction. These results indicated that the α-helix structures were orientated along the fibrous axis and assembled into a bundle. Furthermore, the width and length of fibrous assemblies changed with changes in the pH value, resulting in variations in the charged states of the residues. Our results suggest that the formation of fibrous assemblies of amphipathic α-helices is due to the assembly of bundles via the hydrophobic faces of the helices and extension with hydrophobic noncovalent bonds containing a leucine.
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Affiliation(s)
- Toshiaki Takei
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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32
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33
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Walker AA, Weisman S, Kameda T, Sutherland TD. Natural Templates for Coiled-Coil Biomaterials from Praying Mantis Egg Cases. Biomacromolecules 2012; 13:4264-72. [DOI: 10.1021/bm301570v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andrew A. Walker
- Research School of Biology, Australian National University, Canberra, Australia,
0200
- Ecosystem Sciences,
Commonwealth
Scientific and Industrial Research Organisation, Black Mountain Laboratories, Acton, Canberra, Australia, 2601
| | - Sarah Weisman
- Ecosystem Sciences,
Commonwealth
Scientific and Industrial Research Organisation, Black Mountain Laboratories, Acton, Canberra, Australia, 2601
| | - Tsunenori Kameda
- National Institute of Agrobiological Sciences, Tsukaba, Ibaraki, Japan,
305-8602
| | - Tara D. Sutherland
- Ecosystem Sciences,
Commonwealth
Scientific and Industrial Research Organisation, Black Mountain Laboratories, Acton, Canberra, Australia, 2601
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34
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Engineering protein filaments with enhanced thermostability for nanomaterials. Biotechnol J 2012; 8:228-36. [DOI: 10.1002/biot.201200009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/07/2012] [Accepted: 08/30/2012] [Indexed: 11/07/2022]
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35
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Boyle AL, Bromley EHC, Bartlett GJ, Sessions RB, Sharp TH, Williams CL, Curmi PMG, Forde NR, Linke H, Woolfson DN. Squaring the circle in peptide assembly: from fibers to discrete nanostructures by de novo design. J Am Chem Soc 2012; 134:15457-67. [PMID: 22917063 DOI: 10.1021/ja3053943] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The design of bioinspired nanostructures and materials of defined size and shape is challenging as it pushes our understanding of biomolecular assembly to its limits. In such endeavors, DNA is the current building block of choice because of its predictable and programmable self-assembly. The use of peptide- and protein-based systems, however, has potential advantages due to their more-varied chemistries, structures and functions, and the prospects for recombinant production through gene synthesis and expression. Here, we present the design and characterization of two complementary peptides programmed to form a parallel heterodimeric coiled coil, which we use as the building blocks for larger, supramolecular assemblies. To achieve the latter, the two peptides are joined via peptidic linkers of variable lengths to produce a range of assemblies, from flexible fibers of indefinite length, through large colloidal-scale assemblies, down to closed and discrete nanoscale objects of defined stoichiometry. We posit that the different modes of assembly reflect the interplay between steric constraints imposed by short linkers and the bulk of the helices, and entropic factors that favor the formation of many smaller objects as the linker length is increased. This approach, and the resulting linear and proteinogenic polypeptides, represents a new route for constructing complex peptide-based assemblies and biomaterials.
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Affiliation(s)
- Aimee L Boyle
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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36
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Lalatsa A, Schätzlein AG, Mazza M, Le TBH, Uchegbu IF. Amphiphilic poly(l-amino acids) — New materials for drug delivery. J Control Release 2012; 161:523-36. [DOI: 10.1016/j.jconrel.2012.04.046] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/17/2012] [Accepted: 04/18/2012] [Indexed: 01/16/2023]
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37
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King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 2012; 336:1171-4. [PMID: 22654060 PMCID: PMC4138882 DOI: 10.1126/science.1219364] [Citation(s) in RCA: 488] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We describe a general computational method for designing proteins that self-assemble to a desired symmetric architecture. Protein building blocks are docked together symmetrically to identify complementary packing arrangements, and low-energy protein-protein interfaces are then designed between the building blocks in order to drive self-assembly. We used trimeric protein building blocks to design a 24-subunit, 13-nm diameter complex with octahedral symmetry and a 12-subunit, 11-nm diameter complex with tetrahedral symmetry. The designed proteins assembled to the desired oligomeric states in solution, and the crystal structures of the complexes revealed that the resulting materials closely match the design models. The method can be used to design a wide variety of self-assembling protein nanomaterials.
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Affiliation(s)
- Neil P. King
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - William Sheffler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Breanna S. Vollmar
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - John P. Sumida
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98177, USA
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tamir Gonen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Todd O. Yeates
- UCLA Department of Chemistry and Biochemistry, Los Angeles, CA 90095, USA,UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA,To whom correspondence should be addressed.
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Thompson KE, Bashor CJ, Lim WA, Keating AE. SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth Biol 2012; 1:118-29. [PMID: 22558529 PMCID: PMC3339576 DOI: 10.1021/sb200015u] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Indexed: 12/20/2022]
Abstract
![]()
The synthetic biology toolkit contains a growing number
of parts
for regulating transcription and translation, but very few that can
be used to control protein association. Here we report characterization
of 22 previously published heterospecific synthetic coiled-coil peptides
called SYNZIPs. We present biophysical analysis of the oligomerization
states, helix orientations, and affinities of 27 SYNZIP pairs. SYNZIP
pairs were also tested for interaction in two cell-based assays. In
a yeast two-hybrid screen, >85% of 253 comparable interactions
were
consistent with prior in vitro measurements made
using coiled-coil microarrays. In a yeast-signaling assay controlled
by coiled-coil mediated scaffolding, 12 SYNZIP pairs were successfully
used to down-regulate the expression of a reporter gene following
treatment with α-factor. Characterization of these interaction
modules dramatically increases the number of available protein interaction
parts for synthetic biology and should facilitate a wide range of
molecular engineering applications. Summary characteristics of 27
SYNZIP peptide pairs are reported in specification sheets available
in the Supporting Information and at the SYNZIP Web site [http://keatingweb.mit.edu/SYNZIP/].
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Affiliation(s)
- Kenneth Evan Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | | | | | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
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39
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Cavalli S, Robson Marsden H, Albericio F, Kros A. Peptide Self-Assembly. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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40
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Ryan DM, Nilsson BL. Self-assembled amino acids and dipeptides as noncovalent hydrogels for tissue engineering. Polym Chem 2012. [DOI: 10.1039/c1py00335f] [Citation(s) in RCA: 202] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This review critically assesses progress in the use of self-assembling dipeptides and amino acids as hydrogel materials for tissue engineering.
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Affiliation(s)
- Derek M. Ryan
- University of Rochester
- Department of Chemistry
- Rochester
- USA
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41
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Govindaraju T. Spontaneous self-assembly of aromatic cyclic dipeptide into fibre bundles with high thermal stability and propensity for gelation. Supramol Chem 2011. [DOI: 10.1080/10610278.2011.628393] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- T. Govindaraju
- a Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore, 560064, India
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42
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Rodríguez-Rodríguez M, Treviño MA, Laurents DV, Arranz R, Valpuesta JM, Rico M, Bruix M, Jiménez MA. Characterization of the structure and self-recognition of the human centrosomal protein NA14: implications for stability and function. Protein Eng Des Sel 2011; 24:883-92. [PMID: 22008182 DOI: 10.1093/protein/gzr050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The protein NA14 is a key adaptor protein mediating the intermolecular interactions of microtubules and Spastin. To gain insight into its structure and function, we have expressed, purified and characterized human NA14 and some variants. NA14 is rather insoluble and tends to oligomerize and form fibrils. Successive mutation of the three Cys and two potentially exposed Leu residues (83 and 93) yielded a water-soluble quintuple variant, named 3CS-2LR. NA14 and its variants have a high helical content as determined by circular dichroism (CD). Based on nuclear magnetic resonance data of the quintuple mutant and the wild-type (wt) protein in the presence of dodecylphosphocholine micelles, the N-(M1-N13) and C-termini (K105-S119) were found to lack preferred structure. The remaining residues (14-104) participate in NA14 self-association, probably by forming a parallel coiled-coil structure. We hypothesize that Leu 83 and Leu 93 mediate interactions among NA14, Spastin and microtubules. We have also examined urea and thermal denaturation of the quintuple and other NA14 variants at different pH values by CD. The pH dependence of the conformational stability and the elevated native-state pK(a) determined for the two conserved Tyr allow us to propose that the NA14 structure may be stabilized by two Glu-COO(-) ||| HO-Tyr H-bonds, highly conserved in NA14-like proteins in other species.
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Affiliation(s)
- Mar Rodríguez-Rodríguez
- Departamento de Química Física Biológica, Instituto de Química Física Rocasolano, CSIC, Serrano-119, 28006 Madrid, Spain
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Tsang BP, Bretscher HS, Kokona B, Manning RS, Fairman R. Thermodynamic Analysis of Self-Assembly in Coiled-Coil Biomaterials. Biochemistry 2011; 50:8548-58. [DOI: 10.1021/bi201038j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Betty P. Tsang
- Department of Biology and ‡Department of
Mathematics, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Heidi S. Bretscher
- Department of Biology and ‡Department of
Mathematics, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Bashkim Kokona
- Department of Biology and ‡Department of
Mathematics, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Robert S. Manning
- Department of Biology and ‡Department of
Mathematics, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
| | - Robert Fairman
- Department of Biology and ‡Department of
Mathematics, Haverford College, 370 Lancaster Ave., Haverford, Pennsylvania 19041, United States
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44
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Ardejani MS, Li NX, Orner BP. Stabilization of a protein nanocage through the plugging of a protein-protein interfacial water pocket. Biochemistry 2011; 50:4029-37. [PMID: 21488690 DOI: 10.1021/bi200207w] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The unique structural properties of the ferritin protein cages have provided impetus to focus on the methodical study of these self-assembling nanosystems. Among these proteins, Escherichia coli bacterioferritin (EcBfr), although architecturally very similar to other members of the family, shows structural instability and an incomplete self-assembly behavior by populating two oligomerization states. Through computational analysis and comparison to its homologues, we have found that this protein has a smaller than average dimeric interface on its 2-fold symmetry axis mainly because of the existence of an interfacial water pocket centered around two water-bridged asparagine residues. To investigate the possibility of engineering EcBfr for modified structural stability, we have used a semiempirical computational method to virtually explore the energy differences of the 480 possible mutants at the dimeric interface relative to that of wild-type EcBfr. This computational study also converged on the water-bridged asparagines. Replacing these two asparagines with hydrophobic amino acids resulted in proteins that folded into α-helical monomers and assembled into cages as evidenced by circular dichroism and transmission electron microscopy. Both thermal and chemical denaturation confirmed that, in all cases, these proteins, in agreement with the calculations, possessed increased stability. One of the three mutations shifts the population in favor of the higher-order oligomerization state in solution as evidenced by both size exclusion chromatography and native gel electrophoresis. These results taken together suggest that our low-level design was successful and that it may be possible to apply the strategy of targeting water pockets at protein--protein interfaces to other protein cage and self-assembling systems. More generally, this study further demonstrates the power of jointly employing in silico and in vitro techniques to understand and enhance biostructural energetics.
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Affiliation(s)
- Maziar S Ardejani
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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45
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Fiumara F, Fioriti L, Kandel ER, Hendrickson WA. Essential role of coiled coils for aggregation and activity of Q/N-rich prions and PolyQ proteins. Cell 2011; 143:1121-35. [PMID: 21183075 DOI: 10.1016/j.cell.2010.11.042] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 08/23/2010] [Accepted: 11/16/2010] [Indexed: 11/19/2022]
Abstract
The functional switch of glutamine/asparagine (Q/N)-rich prions and the neurotoxicity of polyQ-expanded proteins involve complex aggregation-prone structural transitions, commonly presumed to be forming β sheets. By analyzing sequences of interaction partners of these proteins, we discovered a recurrent presence of coiled-coil domains both in the partners and in segments that flank or overlap Q/N-rich and polyQ domains. Since coiled coils can mediate protein interactions and multimerization, we studied their possible involvement in Q/N-rich and polyQ aggregations. Using circular dichroism and chemical crosslinking, we found that Q/N-rich and polyQ peptides form α-helical coiled coils in vitro and assemble into multimers. Using structure-guided mutagenesis, we found that coiled-coil domains modulate in vivo properties of two Q/N-rich prions and polyQ-expanded huntingtin. Mutations that disrupt coiled coils impair aggregation and activity, whereas mutations that enhance coiled-coil propensity promote aggregation. These findings support a coiled-coil model for the functional switch of Q/N-rich prions and for the pathogenesis of polyQ-expansion diseases.
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Affiliation(s)
- Ferdinando Fiumara
- Department of Neuroscience, Columbia University, New York, NY 10032, USA
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46
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Bromley EHC, Channon KJ. Alpha-helical peptide assemblies giving new function to designed structures. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:231-75. [PMID: 21999998 PMCID: PMC7150058 DOI: 10.1016/b978-0-12-415906-8.00001-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
The design of alpha-helical tectons for self-assembly is maturing as a science. We have now reached the point where many different coiled-coil topologies can be reliably produced and validated in synthetic systems and the field is now moving on towards more complex, discrete structures and applications. Similarly the design of infinite or fiber assemblies has also matured, with the creation fibers that have been modified or functionalized in a variety of ways. This chapter discusses the progress made in both of these areas as well as outlining the challenges still to come.
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47
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Singh Y, Sharpe PC, Hoang HN, Lucke AJ, McDowall AW, Bottomley SP, Fairlie DP. Amyloid Formation from an α-Helix Peptide Bundle Is Seeded by 310-Helix Aggregates. Chemistry 2010; 17:151-60. [DOI: 10.1002/chem.201002500] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Indexed: 11/08/2022]
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48
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Mahmoud ZN, Grundy DJ, Channon KJ, Woolfson DN. The non-covalent decoration of self-assembling protein fibers. Biomaterials 2010; 31:7468-74. [PMID: 20638122 DOI: 10.1016/j.biomaterials.2010.06.041] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/23/2010] [Indexed: 01/07/2023]
Abstract
The design of self-assembling fibers presents challenges in basic science, and has potential for developing materials for applications in areas such as tissue engineering. A contemporary issue in the field is the construction of multi-component, functionalized systems. Previously, we have developed peptide-based fibers, the SAF system, that comprises two complementary peptides, which affords considerable control over assembly and morphology. Here we present a straightforward route to functionalizing the SAFs with small molecules and, subsequently, other moieties. This is achieved via non-covalent recruitment of charged peptide tags, which offers advantages such as further control, reversibility, and future prospects for developing recombinant tags. We demonstrate the concept by appending fluorescent labels and biotin (and thence gold nanoparticles) to the peptides, and visualising the resulting decorated SAFs by light and electron microscopy. The peptide tags bind in the nm-mum range, and show specificity compared with control peptides, and for the SAFs over similar alpha-helix-based peptide fibers.
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49
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Cnudde SE, Prorok M, Castellino FJ, Geiger JH. Metal ion determinants of conantokin dimerization as revealed in the X-ray crystallographic structure of the Cd(2+)/Mg (2+)-con-T[K7gamma] complex. J Biol Inorg Chem 2010; 15:667-75. [PMID: 20195692 PMCID: PMC3693470 DOI: 10.1007/s00775-010-0633-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
Predatory sea snails from the Conus family produce a variety of venomous small helical peptides called conantokins that are rich in gamma-carboxyglutamic acid (Gla) residues. As potent and selective antagonists of the N-methyl-D: -aspartate receptor, these peptides are potential therapeutic agents for a variety of neurological conditions. The two most studied members of this family of peptides are con-G and con-T. Con-G has Gla residues at sequence positions 3, 4, 7, 10, and 14, and requires divalent cation binding to adopt a helical conformation. Although both Ca(2+) and Mg(2+) can fulfill this role, Ca(2+) induces dimerization of con-G, whereas the Mg(2+)-complexed peptide remains monomeric. A variant of con-T, con-T[K7gamma] (gamma is Gla), contains Gla residues at the same five positions as in con-G and behaves very similarly with respect to metal ion binding and dimerization; each peptide binds two Ca(2+) ions and two Mg(2+) ions per helix. To understand the difference in metal ion selectivity, affinity, and the dependence on Ca(2+) for dimer formation, we report here the structure of the monomeric Cd(2+)/Mg(2+)-con-T[K7gamma] complex, and, by comparison with the previously published con-T[K7gamma]/Ca(2+) dimer structure, we suggest explanations for both metal ion binding site specificity and metal-ion-dependent dimerization.
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Affiliation(s)
- Sara E. Cnudde
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Mary Prorok
- Department of Chemistry and Biochemistry, W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Francis J. Castellino
- Department of Chemistry and Biochemistry, W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46556, USA
| | - James H. Geiger
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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50
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Woolfson DN. Building fibrous biomaterials from alpha-helical and collagen-like coiled-coil peptides. Biopolymers 2010; 94:118-27. [PMID: 20091877 DOI: 10.1002/bip.21345] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Over the decade and a half, interest has soared in the development of peptide-based biomaterials and their potential applications in biotechnology. This review outlines the advances during this time in the construction of biomaterials based on the alpha-helical coiled-coil and collagen-like peptides. These structures and the resulting designs are distinct from the more commonly used beta-structured peptides, which often lead to hydrogels comprising amyloid-like fibrils. The review covers basic design rules for these helical assemblies, and the various fibrous biomaterials that can be accomplished with them, which include rigid structures with straight, branched, or networked structures, decorated and functionalized systems, and most recently flexible fibers and entangled hydrogel networks. This plethora of alpha-helix-based biomaterials, together with more recent collagen-like assemblies, that are emerging from various laboratories complement those developed using beta-structured peptides, and open exciting new avenues for biomaterials research and potential new application areas.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom.
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