1
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Krins N, Wien F, Schmeltz M, Pérez J, Dems D, Debons N, Laberty-Robert C, Schanne-Klein MC, Aimé C. Angle-Resolved Linear Dichroism to Probe the Organization of Highly Ordered Collagen Biomaterials. Biomacromolecules 2024; 25:6181-6187. [PMID: 39096318 DOI: 10.1021/acs.biomac.4c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2024]
Abstract
Controlling the assembly of high-order structures is central to soft-matter and biomaterial engineering. Angle-resolved linear dichroism can probe the ordering of chiral collagen molecules in the dense state. Collagen triple helices were aligned by solvent evaporation. Their ordering gives a strong linear dichroism (LD) that changes sign and intensity with varying sample orientations with respect to the beam linear polarization. Being complementary to circular dichroism, which probes the structure of chiral (bio)molecules, LD can shift from the molecular to the supramolecular scale and from the investigation of the conformation to interactions. Supported by multiphoton microscopy and X-ray scattering, we show that LD provides a straightforward route to probe collagen alignment, determine the packing density, and monitor denaturation. This approach could be adapted to any assembly of chiral (bio)macromolecules, with key advantages in detecting large-scale assemblies with high specificity to aligned and chiral molecules and improved sensitivity compared to conventional techniques.
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Affiliation(s)
- Natacha Krins
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Sorbonne Université, CNRS, Paris F-75005, France
| | - Frank Wien
- SOLEIL Synchrotron, Saint Aubin 91190, France
| | - Margaux Schmeltz
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau F-91128, France
| | | | - Dounia Dems
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Sorbonne Université, CNRS, Paris F-75005, France
| | - Nicolas Debons
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Sorbonne Université, CNRS, Paris F-75005, France
| | - Christel Laberty-Robert
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Sorbonne Université, CNRS, Paris F-75005, France
| | - Marie-Claire Schanne-Klein
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, Palaiseau F-91128, France
| | - Carole Aimé
- Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Sorbonne Université, CNRS, Paris F-75005, France
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, Paris 75005, France
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2
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Vaglietti S, Villeri V, Dell’Oca M, Marchetti C, Cesano F, Rizzo F, Miller D, LaPierre L, Pelassa I, Monje FJ, Colnaghi L, Ghirardi M, Fiumara F. PolyQ length-based molecular encoding of vocalization frequency in FOXP2. iScience 2023; 26:108036. [PMID: 37860754 PMCID: PMC10582585 DOI: 10.1016/j.isci.2023.108036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
The transcription factor FOXP2, a regulator of vocalization- and speech/language-related phenotypes, contains two long polyQ repeats (Q1 and Q2) displaying marked, still enigmatic length variation across mammals. We found that the Q1/Q2 length ratio quantitatively encodes vocalization frequency ranges, from the infrasonic to the ultrasonic, displaying striking convergent evolution patterns. Thus, species emitting ultrasonic vocalizations converge with bats in having a low ratio, whereas species vocalizing in the low-frequency/infrasonic range converge with elephants and whales, which have higher ratios. Similar, taxon-specific patterns were observed for the FOXP2-related protein FOXP1. At the molecular level, we observed that the FOXP2 polyQ tracts form coiled coils, assembling into condensates and fibrils, and drive liquid-liquid phase separation (LLPS). By integrating evolutionary and molecular analyses, we found that polyQ length variation related to vocalization frequency impacts FOXP2 structure, LLPS, and transcriptional activity, thus defining a novel form of polyQ length-based molecular encoding of vocalization frequency.
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Affiliation(s)
- Serena Vaglietti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Veronica Villeri
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Marco Dell’Oca
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Chiara Marchetti
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Federico Cesano
- Department of Chemistry, University of Turin, 10125 Turin, Italy
| | - Francesca Rizzo
- Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 518057, China
| | - Dave Miller
- Cascades Pika Watch, Oregon Zoo, Portland, OR 97221, USA
| | - Louis LaPierre
- Deptartment of Natural Science, Lower Columbia College, Longview, WA 98632, USA
| | - Ilaria Pelassa
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Francisco J. Monje
- Department of Neurophysiology and Neuropharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Luca Colnaghi
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Mirella Ghirardi
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Turin, 10125 Turin, Italy
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3
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Britton D, Monkovic J, Jia S, Liu C, Mahmoudinobar F, Meleties M, Renfrew PD, Bonneau R, Montclare JK. Supramolecular Assembly and Small-Molecule Binding by Protein-Engineered Coiled-Coil Fibers. Biomacromolecules 2022; 23:4851-4859. [PMID: 36227640 DOI: 10.1021/acs.biomac.2c01031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to engineer a solvent-exposed surface of self-assembling coiled coils allows one to achieve a higher-order hierarchical assembly such as nano- or microfibers. Currently, these materials are being developed for a range of biomedical applications, including drug delivery systems; however, ways to mechanistically optimize the coiled-coil structure for drug binding are yet to be explored. Our laboratory has previously leveraged the functional properties of the naturally occurring cartilage oligomeric matrix protein coiled coil (C), not only for its favorable motif but also for the presence of a hydrophobic pore to allow for small-molecule binding. This includes the development of Q, a rationally designed pentameric coiled coil derived from C. Here, we present a small library of protein microfibers derived from the parent sequences of C and Q bearing various electrostatic potentials with the aim to investigate the influence of higher-order assembly and encapsulation of candidate small molecule, curcumin. The supramolecular fiber size appears to be well-controlled by sequence-imbued electrostatic surface potential, and protein stability upon curcumin binding is well correlated to relative structure loss, which can be predicted by in silico docking.
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Affiliation(s)
- Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Julia Monkovic
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Sihan Jia
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Chengliang Liu
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - Farbod Mahmoudinobar
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Michael Meleties
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, New York10010, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York11201, United States.,Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York10016, United States.,Department of Chemistry, New York University, New York, New York10012, United States.,Department of Biomaterials, New York University College of Dentistry, New York, New York10010, United States
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4
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Duro-Castano A, Rodríguez-Arco L, Ruiz-Pérez L, De Pace C, Marchello G, Noble-Jesus C, Battaglia G. One-Pot Synthesis of Oxidation-Sensitive Supramolecular Gels and Vesicles. Biomacromolecules 2021; 22:5052-5064. [PMID: 34762395 PMCID: PMC8672347 DOI: 10.1021/acs.biomac.1c01039] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/17/2021] [Indexed: 12/21/2022]
Abstract
Polypeptide-based nanoparticles offer unique advantages from a nanomedicine perspective such as biocompatibility, biodegradability, and stimuli-responsive properties to (patho)physiological conditions. Conventionally, self-assembled polypeptide nanostructures are prepared by first synthesizing their constituent amphiphilic polypeptides followed by postpolymerization self-assembly. Herein, we describe the one-pot synthesis of oxidation-sensitive supramolecular micelles and vesicles. This was achieved by polymerization-induced self-assembly (PISA) of the N-carboxyanhydride (NCA) precursor of methionine using poly(ethylene oxide) as a stabilizing and hydrophilic block in dimethyl sulfoxide (DMSO). By adjusting the hydrophobic block length and concentration, we obtained a range of morphologies from spherical to wormlike micelles, to vesicles. Remarkably, the secondary structure of polypeptides greatly influenced the final morphology of the assemblies. Surprisingly, wormlike micellar morphologies were obtained for a wide range of methionine block lengths and solid contents, with spherical micelles restricted to very short hydrophobic lengths. Wormlike micelles further assembled into oxidation-sensitive, self-standing gels in the reaction pot. Both vesicles and wormlike micelles obtained using this method demonstrated to degrade under controlled oxidant conditions, which would expand their biomedical applications such as in sustained drug release or as cellular scaffolds in tissue engineering.
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Affiliation(s)
- Aroa Duro-Castano
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
| | - Laura Rodríguez-Arco
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
- Department
of Applied Physics, University of Granada, 18071 Granada, Spain
| | - Lorena Ruiz-Pérez
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
- The
EPSRC/Jeol Centre for Liquid Phase Electron Microscopy, University College London, London WC1H 0AJ, U.K.
| | - Cesare De Pace
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
- The
EPSRC/Jeol Centre for Liquid Phase Electron Microscopy, University College London, London WC1H 0AJ, U.K.
| | - Gabriele Marchello
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
- The
EPSRC/Jeol Centre for Liquid Phase Electron Microscopy, University College London, London WC1H 0AJ, U.K.
- Institute
for Bioengineering of Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Carlos Noble-Jesus
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
| | - Giuseppe Battaglia
- Department
of Chemistry, University College London, London WC1H 0AJ, U.K.
- Institute
for the Physics of Living Systems, University
College London, London WC1E 6BT, U.K.
- The
EPSRC/Jeol Centre for Liquid Phase Electron Microscopy, University College London, London WC1H 0AJ, U.K.
- Institute
for Bioengineering of Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Catalan
Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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5
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Carter JG, Pfukwa R, Riley L, Tucker JHR, Rodger A, Dafforn TR, Klumperman B. Linear Dichroism Activity of Chiral Poly( p-Aryltriazole) Foldamers. ACS OMEGA 2021; 6:33231-33237. [PMID: 34901675 PMCID: PMC8656205 DOI: 10.1021/acsomega.1c06139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 05/04/2023]
Abstract
Controllable higher-order assembly is a central aim of macromolecular chemistry. An essential challenge to developing these molecules is improving our understanding of the structures they adopt under different conditions. Here, we demonstrate how flow linear dichroism (LD) spectroscopy is used to provide insights into the solution structure of a chiral, self-assembled fibrillar foldamer. Poly(para-aryltriazole)s fold into different structures depending on the monomer geometry and variables such as solvent and ionic strength. LD spectroscopy provides a simple route to determine chromophore alignment in solution and is generally used on natural molecules or molecular assemblies such as DNA and M13 bacteriophage. In this contribution, we show that LD spectroscopy is a powerful tool in the observation of self-assembly processes of synthetic foldamers when complemented by circular dichroism, absorbance spectroscopy, and microscopy. To that end, poly(para-aryltriazole)s were aligned in a flow field under different solvent conditions. The extended aromatic structures in the foldamer give rise to a strong LD signal that changes in sign and in intensity with varying solvent conditions. A key advantage of LD is that it only detects the large assemblies, thus removing background due to monomers and small oligomers.
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Affiliation(s)
- Jake G. Carter
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Rueben Pfukwa
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
| | - Liam Riley
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
- School
of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K.
| | - James H. R. Tucker
- School
of Chemistry, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Alison Rodger
- Department
of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Timothy R. Dafforn
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham, West Midlands B15 2TT, U.K.
| | - Bert Klumperman
- Department
of Chemistry and Polymer Sciences, Stellenbosch
University, Private Bag X1, Matieland 7602, South Africa
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6
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Abosheasha MA, Itagaki T, Ito Y, Ueda M. Tubular Assembly Formation Induced by Leucine Alignment along the Hydrophobic Helix of Amphiphilic Polypeptides. Int J Mol Sci 2021; 22:ijms222112075. [PMID: 34769498 PMCID: PMC8584449 DOI: 10.3390/ijms222112075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/01/2021] [Accepted: 11/05/2021] [Indexed: 01/01/2023] Open
Abstract
The introduction of α-helical structure with a specific helix-helix interaction into an amphipathic molecule enables the determination of the molecular packing in the assembly and the morphological control of peptide assemblies. We previously reported that the amphiphilic polypeptide SL12 with a polysarcosine (PSar) hydrophilic chain and hydrophobic α-helix (l-Leu-Aib)6 involving the LxxxLxxxL sequence, which induces homo-dimerization due to the concave-convex interaction, formed a nanotube with a uniform 80 nm diameter. In this study, we investigated the importance of the LxxxLxxxL sequence for tube formation by comparing amphiphilic polypeptide SL4A4L4 with hydrophobic α-helix (l-Leu-Aib)2-(l-Ala-Aib)2-(l-Leu-Aib)2 and SL12. SL4A4L4 formed spherical vesicles and micelles. The effect of the LxxxLxxxL sequence elongation on tube formation was demonstrated by studying assemblies of PSar-b-(l-Ala-Aib)-(l-Leu-Aib)6-(l-Ala-Aib) (SA2L12A2) and PSar-b-(l-Leu-Aib)8 (SL16). SA2L12A2 formed nanotubes with a uniform 123 nm diameter, while SL16 assembled into vesicles. These results showed that LxxxLxxxL is a necessary and sufficient sequence for the self-assembly of nanotubes. Furthermore, we fabricated a double-layer nanotube by combining two kinds of nanotubes with 80 and 120 nm diameters-SL12 and SA2L12A2. When SA2L12A2 self-assembled in SL12 nanotube dispersion, SA2L12A2 initially formed a rolled sheet, the sheet then wrapped the SL12 nanotube, and a double-layer nanotube was obtained.
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Affiliation(s)
- Mohammed A. Abosheasha
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
| | - Toru Itagaki
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
| | - Yoshihiro Ito
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
| | - Motoki Ueda
- RIKEN Cluster for Pioneering Research (CPR), Wako 351-0198, Saitama, Japan; (M.A.A.); (T.I.); (Y.I.)
- RIKEN Center for Emergent Matter Science (CEMS), Wako 351-0198, Saitama, Japan
- Correspondence:
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7
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Spectroscopy of model-membrane liposome-protein systems: complementarity of linear dichroism, circular dichroism, fluorescence and SERS. Emerg Top Life Sci 2021; 5:61-75. [PMID: 33942863 DOI: 10.1042/etls20200354] [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: 12/16/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/17/2022]
Abstract
A range of membrane models have been developed to study components of cellular systems. Lipid vesicles or liposomes are one such artificial membrane model which mimics many properties of the biological system: they are lipid bilayers composed of one or more lipids to which other molecules can associate. Liposomes are thus ideal to study the roles of cellular lipids and their interactions with other membrane components to understand a wide range of cellular processes including membrane disruption, membrane transport and catalytic activity. Although liposomes are much simpler than cellular membranes, they are still challenging to study and a variety of complementary techniques are needed. In this review article, we consider several currently used analytical methods for spectroscopic measurements of unilamellar liposomes and their interaction with proteins and peptides. Among the variety of spectroscopic techniques seeing increasing application, we have chosen to discuss: fluorescence based techniques such as FRET (fluorescence resonance energy transfer) and FRAP (fluorescence recovery after photobleaching), that are used to identify localisation and dynamics of molecules in the membrane; circular dichroism (CD) and linear dichroism (LD) for conformational and orientation changes of proteins on membrane binding; and SERS (Surface Enhanced Raman Spectroscopy) as a rapidly developing ultrasensitive technique for site-selective molecular characterisation. The review contains brief theoretical basics of the listed techniques and recent examples of their successful applications for membrane studies.
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8
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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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9
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Mannem R, Yousuf M, Sreerama L. Nanostructures Formed by Custom-Made Peptides Based on Amyloid Peptide Sequences and Their Inhibition by 2-Hydroxynaphthoquinone. Front Chem 2020; 8:684. [PMID: 32850681 PMCID: PMC7424059 DOI: 10.3389/fchem.2020.00684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/30/2020] [Indexed: 01/30/2023] Open
Abstract
Extensive research on amyloid fibril formations shows that certain core sequences within Aβ peptide play an important role in their formation. It is impossible to track these events in vivo. Many proteins and peptides with such core sequences form amyloid fibrils and such Aβ sheet mimics have become excellent tools to study amyloid fibril formation and develop therapeutic strategies. A group of peptides based on amyloid peptide sequences obtained from PDB searches, where glycine residues are substituted with alanine and isoleucine, are tested for aggregation by SEM and ThT binding assay. SEM of different peptide sequences showed morphologically different structures such as nanorods, crystalline needles and nanofibrils. The peptides were co-incubated with HNQ (a quinone) to study its effect on the process of aggregation and/or fibrillation. In conclusion, this group of peptides seem to be Aβ sheet mimics and can be very useful in understanding the different morphologies of amyloid fibrils arising from different peptide sequences and the effective strategies to inhibit or anneal them.
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Affiliation(s)
- Radhika Mannem
- Department of Chemistry and Earth Sciences, Qatar University, Doha, Qatar
| | - Mohammed Yousuf
- Central Laboratory Unit (CLU), Qatar University, Doha, Qatar
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10
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Sun H, Marelli B. Polypeptide templating for designer hierarchical materials. Nat Commun 2020; 11:351. [PMID: 31953407 PMCID: PMC6969164 DOI: 10.1038/s41467-019-14257-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 12/16/2019] [Indexed: 01/27/2023] Open
Abstract
Despite advances in directing the assembly of biomacromolecules into well-defined nanostructures, leveraging pathway complexity of molecular disorder to order transition while bridging materials fabrication from nano- to macroscale remains a challenge. Here, we present templated crystallization of structural proteins to nanofabricate hierarchically structured materials up to centimeter scale, using silk fibroin as an example. The process involves the use of ordered peptide supramolecular assemblies as templates to direct the folding and assembly of silk fibroin into nanofibrillar structures. Silk polymorphs can be engineered by varying the peptide seeds used. Modulation of the relative concentration between silk fibroin and peptide seeds, silk fibroin molecular weight and pH allows control over nanofibrils morphologies and mechanical properties. Finally, facile integration of the bottom-up templated crystallization with emerging top-down techniques enables the generation of macroscopic nanostructured materials with potential applications in information storage/encryption, surface functionalization, and printable three-dimensional constructs of customized architecture and controlled anisotropy.
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Affiliation(s)
- Hui Sun
- Laboratory for Advanced Biopolymers, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Benedetto Marelli
- Laboratory for Advanced Biopolymers, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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11
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Tunn I, Harrington MJ, Blank KG. Bioinspired Histidine⁻Zn 2+ Coordination for Tuning the Mechanical Properties of Self-Healing Coiled Coil Cross-Linked Hydrogels. Biomimetics (Basel) 2019; 4:biomimetics4010025. [PMID: 31105210 PMCID: PMC6477626 DOI: 10.3390/biomimetics4010025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Natural biopolymeric materials often possess properties superior to their individual components. In mussel byssus, reversible histidine (His)–metal coordination is a key feature, which mediates higher-order self-assembly as well as self-healing. The byssus structure, thus, serves as an excellent natural blueprint for the development of self-healing biomimetic materials with reversibly tunable mechanical properties. Inspired by byssal threads, we bioengineered His–metal coordination sites into a heterodimeric coiled coil (CC). These CC-forming peptides serve as a noncovalent cross-link for poly(ethylene glycol)-based hydrogels and participate in the formation of higher-order assemblies via intermolecular His–metal coordination as a second cross-linking mode. Raman and circular dichroism spectroscopy revealed the presence of α-helical, Zn2+ cross-linked aggregates. Using rheology, we demonstrate that the hydrogel is self-healing and that the addition of Zn2+ reversibly switches the hydrogel properties from viscoelastic to elastic. Importantly, using different Zn2+:His ratios allows for tuning the hydrogel relaxation time over nearly three orders of magnitude. This tunability is attributed to the progressive transformation of single CC cross-links into Zn2+ cross-linked aggregates; a process that is fully reversible upon addition of the metal chelator ethylenediaminetetraacetic acid. These findings reveal that His–metal coordination can be used as a versatile cross-linking mechanism for tuning the viscoelastic properties of biomimetic hydrogels.
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Affiliation(s)
- Isabell Tunn
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
| | - Matthew J Harrington
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada.
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
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12
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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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13
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Roberts EK, Wong KM, Lee EJ, Le MM, Patel DM, Paravastu AK. Post-assembly α-helix to β-sheet structural transformation within SAF-p1/p2a peptide nanofibers. SOFT MATTER 2018; 14:8986-8996. [PMID: 30375627 DOI: 10.1039/c8sm01754a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We report an unanticipated helix-to-sheet structural transformation within an assembly of SAF-p1 and SAF-p2a designer peptides. Solid-state NMR spectroscopic data support the assembled structure that was targeted by rational peptide design: an α-helical coiled-coil co-assembly of both peptides. Subsequent to assembly, however, the system converts to a β-sheet structure that continues to exhibit nearest-neighbor interactions between the two peptide components. The structural transition occurs at pH 7.4 and exhibits strongly temperature-dependent kinetics between room temperature (weeks) and 40 °C (minutes). We further observed evidence of reversibility on the timescale of months at 4 °C. The structural conversion from the anticipated structure to an unexpected structure highlights an important aspect to the challenge of designing peptide assemblies. Furthermore, the conformational switching mechanism mediated by a prerequisite α-helical nanostructure represents a previously unknown route for β-sheet designer peptide assembly.
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Affiliation(s)
- Evan K Roberts
- Department of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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14
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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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15
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Yang Y, Cornilescu G, Tal-Gan Y. Structural Characterization of Competence-Stimulating Peptide Analogues Reveals Key Features for ComD1 and ComD2 Receptor Binding in Streptococcus pneumoniae. Biochemistry 2018; 57:5359-5369. [PMID: 30125091 DOI: 10.1021/acs.biochem.8b00653] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Streptococcus pneumoniae is an important pathogen that utilizes quorum sensing (QS) to regulate genetic transformation, virulence, and biofilm formation. The competence-stimulating peptide (CSP) is a 17-amino acid signal peptide that is used by S. pneumoniae to trigger QS. S. pneumoniae strains can be divided into two main specificity groups based on the CSP signal they produce (CSP1 or CSP2) and their compatible receptors (ComD1 or ComD2, respectively). Modulation of QS in S. pneumoniae can be achieved by targeting the CSP:ComD interaction using synthetic CSP analogues. However, to rationally design CSP-based QS modulators with enhanced activities, an in-depth understanding of the structural features that are required for receptor binding is needed. Herein, we report a comprehensive in-solution three-dimensional structural characterization of eight CSP1 and CSP2 analogues with varied biological activities using nuclear magnetic resonance spectroscopy. Analysis of these structures revealed two distinct hydrophobic patches required for effective ComD1 and ComD2 binding.
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Affiliation(s)
- Yifang Yang
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States
| | - Yftah Tal-Gan
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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16
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Katyal P, Montclare JK. Design and Characterization of Fibers and Bionanocomposites Using the Coiled-Coil Domain of Cartilage Oligomeric Matrix Protein. Methods Mol Biol 2018; 1798:239-263. [PMID: 29868965 DOI: 10.1007/978-1-4939-7893-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tremendous effort has been dedicated to the design and assembly of bioinspired protein-based architectures with potential applications in drug delivery, tissue engineering, biosensing, and bioimaging. Here, we describe our strategy to generate fibers and bionanocomposites using the coiled-coil domain of cartilage oligomeric matrix protein (COMPcc). Our construct, Q, engineered by swapping particular regions of COMPcc to optimize surface charge, self-assembles to form nanofibers. The Q protein nanofibers can efficiently bind curcumin to form robust mesofibers that can be potentially used for drug delivery and biomedical applications. In addition, using the same Q protein, we describe the biotemplation of gold nanoparticles (AuNP) in the presence and absence of the hexahistidine tag (His-tag). The Q bearing His-tag·AuNP (Q·AuNP) readily deposits on electrode surfaces, while Q without His-tag·AuNP (Qx·AuNP) stabilizes the soluble protein·gold bionanocomposites for several days without aggregating.
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Affiliation(s)
- Priya Katyal
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, Tandon School of Engineering, New York University, Brooklyn, NY, USA.
- Department of Biochemistry, SUNY Downstate Medical Center, Brooklyn, NY, USA.
- Department of Biomaterials, New York University College of Dentistry, New York, NY, USA.
- Department of Chemistry, New York University, New York, NY, USA.
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17
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Dastan A, Frith WJ, Cleaver DJ. Thermal Hysteresis and Seeding of Twisted Fibers Formed by Achiral Discotic Particles. J Phys Chem B 2017; 121:9920-9928. [DOI: 10.1021/acs.jpcb.7b05316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alireza Dastan
- Materials
and Engineering Research Institute, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
| | - William J. Frith
- Unilever Discover, Colworth Laboratories, Bedfordshire MK44 1LQ, United Kingdom
| | - Douglas J. Cleaver
- Materials
and Engineering Research Institute, Sheffield Hallam University, Howard Street, Sheffield S1 1WB, United Kingdom
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18
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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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19
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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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20
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Loo Y, Goktas M, Tekinay AB, Guler MO, Hauser CAE, Mitraki A. Self-Assembled Proteins and Peptides as Scaffolds for Tissue Regeneration. Adv Healthc Mater 2015; 4:2557-86. [PMID: 26461979 DOI: 10.1002/adhm.201500402] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/24/2015] [Indexed: 12/15/2022]
Abstract
Self-assembling proteins and peptides are increasingly gaining interest for potential use as scaffolds in tissue engineering applications. They self-organize from basic building blocks under mild conditions into supramolecular structures, mimicking the native extracellular matrix. Their properties can be easily tuned through changes at the sequence level. Moreover, they can be produced in sufficient quantities with chemical synthesis or recombinant technologies to allow them to address homogeneity and standardization issues required for applications. Here. recent advances in self-assembling proteins, peptides, and peptide amphiphiles that form scaffolds suitable for tissue engineering are reviewed. The focus is on a variety of motifs, ranging from minimalistic dipeptides, simplistic ultrashort aliphatic peptides, and peptide amphiphiles to large "recombinamer" proteins. Special emphasis is placed on the rational design of self-assembling motifs and biofunctionalization strategies to influence cell behavior and modulate scaffold stability. Perspectives for combination of these "bottom-up" designer strategies with traditional "top-down" biofabrication techniques for new generations of tissue engineering scaffolds are highlighted.
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Affiliation(s)
- Yihua Loo
- Institute for Bioengineering and Nanotechnology; A* STAR; 31 Biopolis Way The Nanos 138669 Singapore
| | - Melis Goktas
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Ayse B. Tekinay
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Mustafa O. Guler
- Institute of Materials Science and Nanotechnology; National Nanotechnology Research Center (UNAM); Bilkent University; Ankara Turkey 06800
| | - Charlotte A. E. Hauser
- Institute for Bioengineering and Nanotechnology; A* STAR; 31 Biopolis Way The Nanos 138669 Singapore
| | - Anna Mitraki
- Department of Materials Science and Technology; University of Crete; Greece 70013
- Institute for Electronic Structure and Lasers (IESL); Foundation for Research and Technology Hellas (FORTH); Vassilika Vouton; Heraklion Crete Greece 70013
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21
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Burgess NC, Sharp TH, Thomas F, Wood CW, Thomson AR, Zaccai NR, Brady RL, Serpell LC, Woolfson DN. Modular Design of Self-Assembling Peptide-Based Nanotubes. J Am Chem Soc 2015. [DOI: 10.1021/jacs.5b03973] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Natasha C. Burgess
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
- Bristol Centre
for Functional Nanomaterials, University of Bristol, Tyndall Avenue, Bristol, BS8 1FD, United Kingdom
| | - Thomas H. Sharp
- Section
Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Franziska Thomas
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Christopher W. Wood
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol, BS8 1TD, United Kingdom
| | - Andrew R. Thomson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
| | - Nathan R. Zaccai
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol, BS8 1TD, United Kingdom
| | - R. Leo Brady
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol, BS8 1TD, United Kingdom
| | - Louise C. Serpell
- School
of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex, BN1 9QG, United Kingdom
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol, BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall
Avenue, Bristol, BS8 1TQ, United Kingdom
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22
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Zacco E, Anish C, Martin CE, v. Berlepsch H, Brandenburg E, Seeberger PH, Koksch B. A Self-Assembling Peptide Scaffold for the Multivalent Presentation of Antigens. Biomacromolecules 2015; 16:2188-97. [DOI: 10.1021/acs.biomac.5b00572] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Elsa Zacco
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Chakkumkal Anish
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
- Bacterial Vaccines Discovery and Early Development, Janssen Pharmaceuticals (Johnson & Johnson), Leiden, The Netherlands
| | - Christopher E. Martin
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Hans v. Berlepsch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Research
Center of Electron Microscopy and Core Facility BioSupraMol, Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße
36a, 14195 Berlin, Germany
| | - Enrico Brandenburg
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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23
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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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24
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Quinlan RA, Bromley EH, Pohl E. A silk purse from a sow's ear-bioinspired materials based on α-helical coiled coils. Curr Opin Cell Biol 2015; 32:131-7. [PMID: 25638492 DOI: 10.1016/j.ceb.2014.12.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 12/30/2014] [Accepted: 12/31/2014] [Indexed: 11/28/2022]
Abstract
This past few years have heralded remarkable times for intermediate filaments with new revelations of their structural properties that has included the first crystallographic-based model of vimentin to build on the experimental data of intra-filament interactions determined by chemical cross-linking. Now with these and other advances on their assembly, their biomechanical and their cell biological properties outlined in this review, the exploitation of the biomechanical and structural properties of intermediate filaments, their nanocomposites and biomimetic derivatives in the biomedical and private sectors has started.
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Affiliation(s)
- Roy A Quinlan
- School of Biological and Biomedical Sciences, The University of Durham, Stockton Road, Durham DH1 3LE, UK; Biophysical Sciences Institute, The University of Durham, Stockton Road, Durham DH1 3LE, UK.
| | - Elizabeth H Bromley
- Biophysical Sciences Institute, The University of Durham, Stockton Road, Durham DH1 3LE, UK; Department of Physics, The University of Durham, Stockton Road, Durham DH1 3LE, UK
| | - Ehmke Pohl
- School of Biological and Biomedical Sciences, The University of Durham, Stockton Road, Durham DH1 3LE, UK; Biophysical Sciences Institute, The University of Durham, Stockton Road, Durham DH1 3LE, UK; Department of Chemistry, The University of Durham, Stockton Road, Durham DH1 3LE, UK
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25
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Popescu MT, Liontos G, Avgeropoulos A, Tsitsilianis C. Stimuli responsive fibrous hydrogels from hierarchical self-assembly of a triblock copolypeptide. SOFT MATTER 2015; 11:331-342. [PMID: 25379651 DOI: 10.1039/c4sm02092h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, the self-assembly behavior and pH responsiveness of a triblock copolypeptide in aqueous media are demonstrated. The copolypeptide was composed of a central pH responsive poly(l-glutamic acid) (PGA), flanked by two hydrophobic poly(l-alanine) blocks (PAla) (PAla5-PGA11-PAla5). This system showed a pH-responsive transition from short tapes to spherical aggregates by increasing the pH, as a result of deprotonation of the PGA block and a conformational change from α-helix to random coil. Increasing the ionic strength to physiological conditions (0.15 M) has triggered fibrillar self-assembly through intermolecular hydrogen bonding of PAla end-blocks that form β-sheet nanostructures, in conjunction with charge screening of the central random coil PGA segments. At elevated concentrations a thermo-responsive free supporting hydrogel was obtained, consisting of rigid β-sheet based twisted superfibers, resulting from hierarchical self-assembly of the copolypeptide. Yet, morphological transformation of this nanostructure was observed upon switching the pH from physiological conditions to pH 4. An unexpected morphology constituted of α-helix-based giant nanobelts was observed as a consequence of the secondary peptide transitions.
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Bella A, Shaw M, Ray S, Ryadnov MG. Filming protein fibrillogenesis in real time. Sci Rep 2014; 4:7529. [PMID: 25519825 PMCID: PMC4269891 DOI: 10.1038/srep07529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/01/2014] [Indexed: 12/28/2022] Open
Abstract
Protein fibrillogenesis is a universal tool of nano-to-micro scale construction supporting different forms of biological function. Its exploitable potential in nanoscience and technology is substantial, but the direct observation of homogeneous fibre growth able to underpin a kinetic-based rationale for building customized nanostructures in situ is lacking. Here we introduce a kinetic model of de novo protein fibrillogenesis which we imaged at the nanoscale and in real time, filmed. The model helped to reveal that, in contrast to heterogeneous amyloid assemblies, homogeneous protein recruitment is principally characterized by uniform rates of cooperative growth at both ends of growing fibers, bi-directional growth, with lateral growth arrested at a post-seeding stage. The model provides a foundation for in situ engineering of sequence-prescribed fibrous architectures.
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Affiliation(s)
- Angelo Bella
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Michael Shaw
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Santanu Ray
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Maxim G Ryadnov
- 1] National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK [2] School of Physics and Astronomy, University of Edinburgh, UK EH9 3JZ, UK
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Hume J, Sun J, Jacquet R, Renfrew PD, Martin JA, Bonneau R, Gilchrist ML, Montclare JK. Engineered Coiled-Coil Protein Microfibers. Biomacromolecules 2014; 15:3503-10. [DOI: 10.1021/bm5004948] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jasmin Hume
- Department
of Chemical and Biomolecular Engineering, NYU Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Jennifer Sun
- Department
of Chemical and Biomolecular Engineering, NYU Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - Rudy Jacquet
- Department
of Chemical and Biomolecular Engineering, NYU Polytechnic School of Engineering, Brooklyn, New York 11201, United States
| | - P. Douglas Renfrew
- Center
for Genomics and Systems Biology, Department of Biology, New York University New York, New York 10003, United States
| | - Jesse A. Martin
- Departments
of Chemical Engineering and Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Richard Bonneau
- Center
for Genomics and Systems Biology, Department of Biology, New York University New York, New York 10003, United States
| | - M. Lane Gilchrist
- Departments
of Chemical Engineering and Biomedical Engineering, The City College of the City University of New York, New York, New York 10031, United States
| | - Jin Kim Montclare
- Department
of Chemical and Biomolecular Engineering, NYU Polytechnic School of Engineering, Brooklyn, New York 11201, United States
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Abstract
Nature produces an array of self-assembled fibres from proteins and peptides with a wide range of functionalities. This has inspired scientists to design peptides that exploit specific protein folds to form simple yet multi-functional self-assembled fibres. Of the various protein folds the most commonly used has been the β-sheet fold as it is easily accessible and produces nanoscale fibres which have a wide range of stabilities. Research has also been driven by the relationship to the various amyloid diseases, which produce β-sheet rich fibres. Here we will discuss the use of natural protein sequences as the basis of peptides that self-assemble to β-sheet rich fibres followed by peptide sequences that have been designed de novo purely based on the rules for the formation of a β-sheet. How changes in the amino acid sequence of these various peptides affects the properties of the fibres and also the macroscopic materials formed by these peptides will be discussed in each case. We will then look into how these structures have been utilized for applications as scaffolds for cell culture and tissue regeneration, followed by their use in the nanotechnology field.
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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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30
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Cryo-transmission electron microscopy structure of a gigadalton peptide fiber of de novo design. Proc Natl Acad Sci U S A 2012; 109:13266-71. [PMID: 22847414 DOI: 10.1073/pnas.1118622109] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nature presents various protein fibers that bridge the nanometer to micrometer regimes. These structures provide inspiration for the de novo design of biomimetic assemblies, both to address difficulties in studying and understanding natural systems, and to provide routes to new biomaterials with potential applications in nanotechnology and medicine. We have designed a self-assembling fiber system, the SAFs, in which two small α-helical peptides are programmed to form a dimeric coiled coil and assemble in a controlled manner. The resulting fibers are tens of nm wide and tens of μm long, and, therefore, comprise millions of peptides to give gigadalton supramolecular structures. Here, we describe the structure of the SAFs determined to approximately 8 Å resolution using cryotransmission electron microscopy. Individual micrographs show clear ultrastructure that allowed direct interpretation of the packing of individual α-helices within the fibers, and the construction of a 3D electron density map. Furthermore, a model was derived using the cryotransmission electron microscopy data and side chains taken from a 2.3 Å X-ray crystal structure of a peptide building block incapable of forming fibers. This was validated using single-particle analysis techniques, and was stable in prolonged molecular-dynamics simulation, confirming its structural viability. The level of self-assembly and self-organization in the SAFs is unprecedented for a designed peptide-based material, particularly for a system of considerably reduced complexity compared with natural proteins. This structural insight is a unique high-resolution description of how α-helical fibrils pack into larger protein fibers, and provides a basis for the design and engineering of future biomaterials.
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32
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Cohen SIA, Vendruscolo M, Welland ME, Dobson CM, Terentjev EM, Knowles TPJ. Nucleated polymerization with secondary pathways. I. Time evolution of the principal moments. J Chem Phys 2012; 135:065105. [PMID: 21842954 DOI: 10.1063/1.3608916] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Self-assembly processes resulting in linear structures are often observed in molecular biology, and include the formation of functional filaments such as actin and tubulin, as well as generally dysfunctional ones such as amyloid aggregates. Although the basic kinetic equations describing these phenomena are well-established, it has proved to be challenging, due to their non-linear nature, to derive solutions to these equations except for special cases. The availability of general analytical solutions provides a route for determining the rates of molecular level processes from the analysis of macroscopic experimental measurements of the growth kinetics, in addition to the phenomenological parameters, such as lag times and maximal growth rates that are already obtainable from standard fitting procedures. We describe here an analytical approach based on fixed-point analysis, which provides self-consistent solutions for the growth of filamentous structures that can, in addition to elongation, undergo internal fracturing and monomer-dependent nucleation as mechanisms for generating new free ends acting as growth sites. Our results generalise the analytical expression for sigmoidal growth kinetics from the Oosawa theory for nucleated polymerisation to the case of fragmenting filaments. We determine the corresponding growth laws in closed form and derive from first principles a number of relationships which have been empirically established for the kinetics of the self-assembly of amyloid fibrils.
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Affiliation(s)
- Samuel I A Cohen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Brandenburg E, Berlepsch HV, Koksch B. Specific in situ discrimination of amyloid fibrilsversus α-helical fibres by the fluorophore NIAD-4. ACTA ACUST UNITED AC 2012; 8:557-64. [DOI: 10.1039/c1mb05370a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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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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35
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Bioorthogonal dual functionalization of self-assembling peptide fibers. Biomaterials 2011; 32:3712-20. [DOI: 10.1016/j.biomaterials.2010.12.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 12/01/2010] [Indexed: 12/24/2022]
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36
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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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37
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Stedall TP, Butler MF, Woolfson DN, Hanna S. Computer simulations of the growth of synthetic peptide fibres. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:5. [PMID: 21253806 DOI: 10.1140/epje/i2011-11005-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Accepted: 11/29/2010] [Indexed: 05/30/2023]
Abstract
We present a coarse-grained computer model designed to study the growth of fibres in a synthetic self-assembling peptide system. The system consists of two 28 residue α-helical sequences, denoted AB and CD, in which the interactions between the half peptides, A, B, C and D, may be tuned individually to promote different types of growth behaviour. In the model, AB and CD are represented by double ended rods, with interaction sites distributed along their lengths. Monte Carlo simulations are performed to follow fibre growth. It is found that lateral and longitudinal growth of the fibre are governed by different mechanisms--the former is diffusion limited with a very small activation energy for the addition of units, whereas the latter occurs via a process of secondary nucleation at the fibre ends. As a result, longitudinal growth generally proceeds more slowly than lateral growth. Furthermore, it is shown that the aspect ratio of the growing fibre may be controlled by adjusting the temperature and the relative strengths of the interactions. The predictions of the model are discussed in the context of published data from real peptide systems.
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Affiliation(s)
- T P Stedall
- H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, BS81TL Bristol, UK
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38
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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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39
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Giraldo R. Amyloid Assemblies: Protein Legos at a Crossroads in Bottom-Up Synthetic Biology. Chembiochem 2010; 11:2347-57. [DOI: 10.1002/cbic.201000412] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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40
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Woolfson DN, Mahmoud ZN. More than just bare scaffolds: towards multi-component and decorated fibrous biomaterials. Chem Soc Rev 2010; 39:3464-79. [PMID: 20676443 DOI: 10.1039/c0cs00032a] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We are entering a new phase in biomaterials research in which rational design is being used to produce functionalised materials tailored to specific applications. As is evident from this Themed Issue, there are now a number of distinct types of designed, self-assembling, fibrous biomaterials. Many of these are ripe for development and application for example as scaffolds for 3D cell culture and tissue engineering, and in templating inorganic materials. Whilst a number of groups are making headway towards such applications, there is a general challenge to translate a wealth of excellent basic research into materials with a genuine future in real-life applications. Amongst other contemporary aspects of this evolving research area, a key issue is that of decorating or functionalising what are mostly bare scaffolds. There are a number of hurdles to overcome to achieve effective and controlled labelling of the scaffolds, for instance: maintaining biocompatibility, i.e., by minimising covalent chemistry, or using milder bioconjugation methods; attaining specified levels of decoration, and, in particular, high and stoichiometric labelling; introducing orthogonality, such that two or more functions can be appended to the same scaffold; and, in relevant cases, maintaining the possibility for recombinant peptide/protein production. In this critical review, we present an overview of the different approaches to tackling these challenges largely for self-assembled, peptide-based fibrous systems. We review the field as it stands by placing work within general routes to fibre functionalisation; give worked examples on our own specific system, the SAFs; and explore the potential for future developments in the area. Our feeling is that by tackling the challenges of designing multi-component and functional biomaterials, as a community we stand to learn a great deal about self-assembling biomolecular systems more broadly, as well as, hopefully, delivering new materials that will be truly useful in biotechnology and biomedical applications (107 references).
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, UKBS8 1TS.
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41
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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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42
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Hicks MR, Kowałski J, Rodger A. LD spectroscopy of natural and synthetic biomaterials. Chem Soc Rev 2010; 39:3380-93. [DOI: 10.1039/b912917k] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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