1
|
Waigh TA, Korabel N. Heterogeneous anomalous transport in cellular and molecular biology. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2023; 86:126601. [PMID: 37863075 DOI: 10.1088/1361-6633/ad058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 10/20/2023] [Indexed: 10/22/2023]
Abstract
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.
Collapse
Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics, School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Nickolay Korabel
- Department of Mathematics, The University of Manchester, Manchester M13 9PL, United Kingdom
| |
Collapse
|
2
|
Paik B, Calero-Rubio C, Lee JY, Jia X, Kiick KL, Roberts CJ. Characterizing aggregate growth and morphology of alanine-rich polypeptides as a function of sequence chemistry and solution temperature from scattering, spectroscopy, and microscopy. Biophys Chem 2020; 267:106481. [PMID: 33035751 DOI: 10.1016/j.bpc.2020.106481] [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: 06/16/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
The aggregation behavior and stability of a series of alanine-rich peptides, which are included as components of peptide-polymer conjugates, were characterized using a combination of biophysical techniques. Light scattering techniques were used to monitor changes in peptide morphology and size distributions as a function of time and temperature. The results show large particles immediately upon dissolution in buffer. At room temperature, these particles relaxed to reach a mostly monomeric peptide state, while at higher temperatures, they grew to form aggregates. Circular dichroism spectroscopy (CD) was used to monitor temperature- and time-dependent conformational changes as a function of peptide sequence and incubation time. CD measurements reveal that all of the sequences are helical at low temperatures with transitions to non-helical conformation with increased temperature. Samples incubated at room temperature were able to recover their original helicity. At increased temperature, the shorter and longer peptide sequences showed notable changes in conformation, and were not able to recover their original helicity after 72 h. After incubation for up to one week, β-sheet conformations were observed in these two cases, while only α-helical conformation loss was observed for the peptide of intermediate molecular weight. Transmission electron microscopy measurements reveal the formation of fibrils after 72 h of incubation at 60 °C for all samples, in agreement with the scattering measurements. Additional quenching experiments show that peptide aggregation can be stalled when solutions are cooled to room temperature.
Collapse
Affiliation(s)
- Bradford Paik
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Cesar Calero-Rubio
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States of America
| | - Jee Young Lee
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Xinqiao Jia
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America
| | - Kristi L Kiick
- Department of Material Science & Engineering Department, University of Delaware, Newark, DE 19716, United States of America.
| | - Christopher J Roberts
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE 19716, United States of America.
| |
Collapse
|
3
|
Georgiades P, Allan VJ, Wright GD, Woodman PG, Udommai P, Chung MA, Waigh TA. The flexibility and dynamics of the tubules in the endoplasmic reticulum. Sci Rep 2017; 7:16474. [PMID: 29184084 PMCID: PMC5705721 DOI: 10.1038/s41598-017-16570-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is a single organelle in eukaryotic cells that extends throughout the cell and is involved in a large number of cellular functions. Using a combination of fixed and live cells (human MRC5 lung cells) in diffraction limited and super-resolved fluorescence microscopy (STORM) experiments, we determined that the average persistence length of the ER tubules was 3.03 ± 0.24 μm. Removing the branched network junctions from the analysis caused a slight increase in the average persistence length to 4.71 ± 0.14 μm, and provides the tubule's persistence length with a moderate length scale dependence. The average radius of the tubules was 44.1 ± 3.2 nm. The bending rigidity of the ER tubule membranes was found to be 10.9 ± 1.2 kT (17.0 ± 1.3 kT without branch points). We investigated the dynamic behaviour of ER tubules in live cells, and found that the ER tubules behaved like semi-flexible fibres under tension. The majority of the ER tubules experienced equilibrium transverse fluctuations under tension, whereas a minority number of them had active super-diffusive motions driven by motor proteins. Cells thus actively modulate the dynamics of the ER in a well-defined manner, which is expected in turn to impact on its many functions.
Collapse
Affiliation(s)
- Pantelis Georgiades
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
| | - Victoria J Allan
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| | - Graham D Wright
- IMB Microscopy Unit, Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Republic of Singapore
| | - Philip G Woodman
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
| | - Parinya Udommai
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Manloeng A Chung
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| |
Collapse
|
4
|
Davies RPW, Liu B, Maude S, Carrick LM, Nyrkova I, McLeish TC, Harris SA. Peptide strand length controls the energetics of self-assembly and morphology of β-sheet fibrils. Biopolymers 2017; 110. [PMID: 29127706 DOI: 10.1002/bip.23073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/24/2022]
Abstract
Self-assembling peptides can be used as versatile, natural, and multifunctional building blocks to produce a variety of well-defined nanostructures, materials and devices for applications in medicine and nanotechnology. Here, we concentrate on the 1D self-assembly of de novo designed Px-2 peptide β-strands into anti-parallel β-sheet tapes and higher order aggregates. We study six members of the Px-2 family, ranging from 3 amino acids (aa) to 13 aa in length, using a range of complementary experimental techniques, computer simulation and theoretical statistical mechanics. The critical concentration for self-assembly (c*) is found to increase systematically with decreasing peptide length. The shortest peptide found to self-assemble into soluble β-tapes in water is a 5 amino acid residue peptide. These investigations help decipher the role of the peptide length in controlling self-assembly, aggregate morphology, and material properties. By extracting free energies from these data using a statistical mechanical analysis and combining the results with computer simulations at the atomistic level, we can extract the entropy of association for individual β-strands.
Collapse
Affiliation(s)
- Robert P W Davies
- Department of Oral Biology, University of Leeds, St James's University Hospital Leeds LS9 7TF
| | - Binbin Liu
- Department of Pediatrics, University of Oxford. Headington, Oxford, OX3 9DU
| | - Steven Maude
- School of Chemistry, University of Leeds, Leeds, LS2 9JT
| | - Lisa M Carrick
- School of Chemistry, University of Leeds, Leeds, LS2 9JT
| | | | - Tom C McLeish
- Department of Physics, Durham University, Durham, DH1 3LE
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT
| |
Collapse
|
5
|
Tassieri M. Dynamics of Semiflexible Polymer Solutions in the Tightly Entangled Concentration Regime. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Manlio Tassieri
- Division of Biomedical Engineering,
School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| |
Collapse
|
6
|
Waigh TA. Advances in the microrheology of complex fluids. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:074601. [PMID: 27245584 DOI: 10.1088/0034-4885/79/7/074601] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
New developments in the microrheology of complex fluids are considered. Firstly the requirements for a simple modern particle tracking microrheology experiment are introduced, the error analysis methods associated with it and the mathematical techniques required to calculate the linear viscoelasticity. Progress in microrheology instrumentation is then described with respect to detectors, light sources, colloidal probes, magnetic tweezers, optical tweezers, diffusing wave spectroscopy, optical coherence tomography, fluorescence correlation spectroscopy, elastic- and quasi-elastic scattering techniques, 3D tracking, single molecule methods, modern microscopy methods and microfluidics. New theoretical techniques are also reviewed such as Bayesian analysis, oversampling, inversion techniques, alternative statistical tools for tracks (angular correlations, first passage probabilities, the kurtosis, motor protein step segmentation etc), issues in micro/macro rheological agreement and two particle methodologies. Applications where microrheology has begun to make some impact are also considered including semi-flexible polymers, gels, microorganism biofilms, intracellular methods, high frequency viscoelasticity, comb polymers, active motile fluids, blood clots, colloids, granular materials, polymers, liquid crystals and foods. Two large emergent areas of microrheology, non-linear microrheology and surface microrheology are also discussed.
Collapse
Affiliation(s)
- Thomas Andrew Waigh
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Oxford Rd., Manchester, M13 9PL, UK. Photon Science Institute, University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
| |
Collapse
|
7
|
Du X, Zhou J, Shi J, Xu B. Supramolecular Hydrogelators and Hydrogels: From Soft Matter to Molecular Biomaterials. Chem Rev 2015; 115:13165-307. [PMID: 26646318 PMCID: PMC4936198 DOI: 10.1021/acs.chemrev.5b00299] [Citation(s) in RCA: 1258] [Impact Index Per Article: 139.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Indexed: 12/19/2022]
Abstract
In this review we intend to provide a relatively comprehensive summary of the work of supramolecular hydrogelators after 2004 and to put emphasis particularly on the applications of supramolecular hydrogels/hydrogelators as molecular biomaterials. After a brief introduction of methods for generating supramolecular hydrogels, we discuss supramolecular hydrogelators on the basis of their categories, such as small organic molecules, coordination complexes, peptides, nucleobases, and saccharides. Following molecular design, we focus on various potential applications of supramolecular hydrogels as molecular biomaterials, classified by their applications in cell cultures, tissue engineering, cell behavior, imaging, and unique applications of hydrogelators. Particularly, we discuss the applications of supramolecular hydrogelators after they form supramolecular assemblies but prior to reaching the critical gelation concentration because this subject is less explored but may hold equally great promise for helping address fundamental questions about the mechanisms or the consequences of the self-assembly of molecules, including low molecular weight ones. Finally, we provide a perspective on supramolecular hydrogelators. We hope that this review will serve as an updated introduction and reference for researchers who are interested in exploring supramolecular hydrogelators as molecular biomaterials for addressing the societal needs at various frontiers.
Collapse
Affiliation(s)
- Xuewen Du
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02454, United States
| |
Collapse
|
8
|
Aufderhorst-Roberts A, Frith WJ, Kirkland M, Donald AM. Microrheology and microstructure of Fmoc-derivative hydrogels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4483-4492. [PMID: 24684622 DOI: 10.1021/la5005819] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The viscoelasticity of hydrogel networks formed from the low-molecular-weight hydrogelator Fmoc-tyrosine (Fmoc-Y) is probed using particle-tracking microrheology. Gelation is initiated by adding glucono-δ-lactone (GdL), which gradually lowers the pH with time, allowing the dynamic properties of gelation to be examined. Consecutive plots of probe particle mean square displacement (MSD) versus lag time τ are shown to be superimposable, demonstrating the formation of a self-similar hydrogel network through a percolation transition. The analysis of this superposition yields a gel time t(gel) = 43.4 ± 0.05 min and a critical relaxation exponent n(c) = 0.782 ± 0.007, which is close to the predicted value of 3/4 for semiflexible polymer networks. The generalized Stokes-Einstein relation is applied to the master curves to find the viscoelastic moduli of the critical gel over a wide frequency range, showing that the critical gel is structurally and rheologically fragile. The scaling of G'/G″ as ω(0.795±0.099) ≈ ω(3/4) at high frequencies provides further evidence for semiflexible behavior. Cryogenic scanning electron micrographs depict a loosely connected network close to the gel point with a fibrillar persistence length that is longer than the network mesh size, further indications of semiflexible behavior. The system reported here is one of a number of synthetic systems shown to exhibit semiflexible behavior and indicates the opportunity for further rheological study of other Fmoc derivatives.
Collapse
Affiliation(s)
- Anders Aufderhorst-Roberts
- Cavendish Laboratory, Department of Physics, University of Cambridge , JJ Thomson Avenue, Cambridge, CB3 0HE U.K
| | | | | | | |
Collapse
|
9
|
Nisbet DR, Williams RJ. Self-Assembled Peptides: Characterisation and In Vivo Response. Biointerphases 2012; 7:2. [DOI: 10.1007/s13758-011-0002-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/09/2011] [Indexed: 11/25/2022] Open
|
10
|
Bowerman CJ, Nilsson BL. Self-assembly of amphipathic β-sheet peptides: insights and applications. Biopolymers 2012; 98:169-84. [PMID: 22782560 DOI: 10.1002/bip.22058] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amphipathic peptides composed of alternating polar and nonpolar residues have a strong tendency to self-assemble into one-dimensional, amyloid-like fibril structures. Fibrils derived from peptides of general (XZXZ)(n) sequence in which X is hydrophobic and Z is hydrophilic adopt a putative β-sheet bilayer. The bilayer configuration allows burial of the hydrophobic X side chain groups in the core of the fibril and leaves the polar Z side chains exposed to solvent. This architectural arrangement provides fibrils that maintain high solubility in water and has facilitated the recent exploitation of self-assembled amphipathic peptide fibrils as functional biomaterials. This article is a critical review of the development and application of self-assembling amphipathic peptides with a focus on the fundamental insight these types of peptides provide into peptide self-assembly phenomena.
Collapse
Affiliation(s)
- Charles J Bowerman
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | | |
Collapse
|
11
|
Kyle S, McPherson MJ, Aggeli A, Ingham E. WITHDRAWN: The effect of molecular design on the physical and biological properties of complementary self-assembling peptides. Biomaterials 2011:S0142-9612(11)00653-3. [PMID: 21723600 DOI: 10.1016/j.biomaterials.2011.05.082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 05/27/2011] [Indexed: 11/16/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
Collapse
Affiliation(s)
- Stuart Kyle
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; Centre for Molecular Nanoscience, School of Chemistry, Faculty of Mathematics & Physical Sciences, University of Leeds, Leeds LS2 9JT, UK; Institute of Medical & Biological Engineering, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | |
Collapse
|
12
|
Kyle S, Aggeli A, Ingham E, McPherson MJ. Recombinant self-assembling peptides as biomaterials for tissue engineering. Biomaterials 2010; 31:9395-405. [PMID: 20932572 PMCID: PMC3111806 DOI: 10.1016/j.biomaterials.2010.08.051] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Accepted: 08/23/2010] [Indexed: 12/26/2022]
Abstract
Synthetic nanostructures based on self-assembling systems that aim to mimic natural extracellular matrix are now being used as substrates in tissue engineering applications. Peptides are excellent starting materials for the self-assembly process as they can be readily synthesised both chemically and biologically. P₁₁-4 is an 11 amino acid peptide that undergoes triggered self-assembly to form a self-supporting hydrogel. It exists as unimers of random coil conformations in water above pH 7.5 but at low pH adopts an antiparallel β-sheet conformation. It also self-assembles under physiological conditions in a concentration-dependent manner. Here we describe an unimer P₁₁-4 production system and the use of a simple site-directed mutagenesis approach to generate a series of other P₁₁-family peptide expression vectors. We have developed an efficient purification strategy for these peptide biomaterials using a simple procedure involving chemical cleavage with cyanogen bromide then repeated filtration, lyophilisation and wash steps. We report peptide-fusion protein yields of ca. 4.64 g/L and we believe the highest reported recovery of a recombinant self-assembling peptide at 203 mg/L of pure recombinant P₁₁-4. This peptide forms a self-supporting hydrogel under physiological conditions with essentially identical physico-chemical properties to the chemically synthesised peptide. Critically it also displays excellent cytocompatibility when tested with primary human dermal fibroblasts. This study demonstrates that high levels of a series of recombinant self-assembling peptides can be purified using a simple process for applications as scaffolds in tissue engineering.
Collapse
Affiliation(s)
- Stuart Kyle
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
- Centre for Molecular Nanoscience, School of Chemistry, University of Leeds, LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, LS2 9JT, UK
| | - Amalia Aggeli
- Centre for Molecular Nanoscience, School of Chemistry, University of Leeds, LS2 9JT, UK
| | - Eileen Ingham
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
- Institute of Medical and Biological Engineering, University of Leeds, LS2 9JT, UK
| | - Michael J. McPherson
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| |
Collapse
|
13
|
Protopapa E, Ringstad L, Aggeli A, Nelson A. Interaction of self-assembling β-sheet peptides with phospholipid monolayers: The effect of serine, threonine, glutamine and asparagine amino acid side chains. Electrochim Acta 2010. [DOI: 10.1016/j.electacta.2010.01.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
14
|
Branco MC, Nettesheim F, Pochan DJ, Schneider JP, Wagner NJ. Fast dynamics of semiflexible chain networks of self-assembled peptides. Biomacromolecules 2009; 10:1374-80. [PMID: 19391585 DOI: 10.1021/bm801396e] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the first neutron spin echo (NSE) measurements of self-assembling peptide hydrogel networks to study the fibril dynamics on the nanometer and nanosecond length and time scales. MAX1 and MAX8 are synthetic beta-hairpin peptides that undergo triggered self-assembly at the nanoscale to form a physically cross-linked network of fibrils with a defined cross-section. When subjected to physiological pH and ionic strength (pH 7.4, 150 mM NaCl), the soluble peptides fold into a beta-hairpin and, subsequently, self-assemble to form a structurally rigid hydrogel stabilized by noncovalent cross-links. The sequence of MAX8 is identical to MAX1 with the exception of one single amino acid substitution that reduces the net charge on the peptide. As a result, faster folding and self-assembly kinetics are observed for MAX8 at the same peptide concentration and identical buffer conditions, and gels with a larger storage modulus are formed. NSE measurements of the peptide hydrogels demonstrate that the self-assembled peptide fibrils can be described as semiflexible chains on nanolength and time scales. Alteration of the peptide sequence affected the nanoscale dynamics of the hydrogels but not to an extent comparable to the large difference observed in the bulk viscoelasticity. Small angle neutron scattering (SANS) of the hydrogels reveals increased scattering for MAX8 at low wavevectors, an indication of a heterogeneous network with a tighter mesh size. Therefore, we conjecture that the difference in elastic modulus arises from differences in assembly kinetics that result in increased fibrillar branching and physical cross-links rather than a change in the fibril nanostructure or persistence length.
Collapse
Affiliation(s)
- Monica C Branco
- Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
| | | | | | | | | |
Collapse
|
15
|
Riley JM, Aggeli A, Koopmans RJ, McPherson MJ. Bioproduction and characterization of a pH responsive self-assembling peptide. Biotechnol Bioeng 2009; 103:241-51. [PMID: 19266471 DOI: 10.1002/bit.22274] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptide P(11)-4 (QQRFEWEFEQQ) was designed to self-assemble to form beta-sheets and nematic gels in the pH range 5-7 at concentrations > or =12.6 mM in water. This self-assembly is reversibly controlled by adjusting the pH of the solvent. It can also self-assemble into gels in biological media. This together with its biocompatibility and biodegradability make P(11)-4 an attractive building block for the fabrication of nanoscale materials with uses in, for example, tissue engineering. A limitation to large-scale production of such peptides is the high cost of solid phase chemical synthesis. We describe expression of peptide P(11)-4 in the bacterium Escherichia coli from constructs carrying tandem repeats of the peptide coding sequence. The vector pET31b+ was used to express P(11)-4 repeats fused to the ketosteroid isomerase protein which accumulates in easily recoverable inclusion bodies. Importantly, the use of auto-induction growth medium to enhance cell density and protein expression levels resulted in recovery of 2.5 g fusion protein/L culture in both shake flask and batch fermentation. Whole cell detergent lysis allowed recovery of inclusion bodies largely composed of the fusion protein. Cyanogen bromide cleavage followed by reverse phase HPLC allowed purification of the recombinant peptide with a C-terminal homoserine lactone (rP(11)-4(hsl)). This recombinant peptide formed pH dependent hydrogels, displayed beta-structure measured by circular dichroism and fibril formation observed by transmission electron microscopy.
Collapse
Affiliation(s)
- Jessica M Riley
- Astbury Centre for Structural Molecular Biology, Institute of Molecular and Cellular Biology, School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | |
Collapse
|
16
|
Protopapa E, Maude S, Aggeli A, Nelson A. Interaction of self-assembling beta-sheet peptides with phospholipid monolayers: the role of aggregation state, polarity, charge and applied field. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:3289-96. [PMID: 19437790 DOI: 10.1021/la803368r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Studies of beta-sheet peptide/phospholipid interactions are important for an understanding of the folding of beta-sheet-rich membrane proteins and the action of antimicrobial and toxic peptides. Further, self-assembling peptides have numerous applications in medicine and therefore an insight is required into the relation between peptide molecular structure and biomembrane activity. We previously developed one of the simplest known model peptide systems which, above a critical concentration (c*) in solution, undergoes nucleated one-dimensional self-assembly from a monomeric random coil into a hierarchy of well defined beta-sheet structures. Here we examine the effects of peptide aggregation, polarity, charge, and applied field on peptide interactions with dioleoyl phosphatidylcholine (DOPC) monolayers using electrochemical techniques. The interactions of six systematically altered 11 residue beta-sheet tape-forming peptides were investigated. The following findings with respect to 11 residue beta-sheet peptide-DOPC interaction arose from the study: (i) The solution monomer peptide species is the monolayer active moeity. (ii) Amphiphilic peptides are more monolayer active than polar peptides in the absence of applied electric field. (iii) Positive charge on amphiphilic peptides facilitates monolayer interaction in the absence of applied electric field. (iv) Negative applied electric field facilitates monolayer interaction with positively charged amphiphilic and polar peptides. (v) Neutral amphiphilic peptides permeabilize DOPC layers to ions to the greatest extent. (vi) The beta-sheet tape forming peptides are shown to be significantly less monolayer disruptive than antimicrobial peptides. These conclusions will greatly contribute to the rational design of new peptide-based biomaterials and biosensors.
Collapse
Affiliation(s)
- Elisabeth Protopapa
- Centre for Self-Organising Molecular Systems (SOMS), School of Chemistry, University of Leeds, Leeds LS2 9JT, UK
| | | | | | | |
Collapse
|
17
|
Pullara F, Emanuele A. Early stages of beta2-microglobulin aggregation and the inhibiting action of alphaB-crystallin. Proteins 2008; 73:1037-46. [PMID: 18543331 DOI: 10.1002/prot.22122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Static and dynamic light scattering experiments on extremely clean (nanofiltered) samples of the well-known amyloidogenic protein beta2-microglobulin (R3Abeta2m and WTbeta2m) evidence the self-assembly of early aggregates showing unexpected features. Further, we find that alphaB-crystallin effectively inhibits aggregation of beta2m in a far less than stoichiometric proportion, from 1:60 alphaB-crystallin monomer to beta2m monomer ratio, down to at least a 1:2 x 10(3) alphaB-crystallin oligomerto beta2m monomer ratio. Therefore, inhibition of the early stage of beta2m aggregation by alphaB-crystallin does not necessarily require a mechanicistic chaperon-like action implying one-to-one binding. This highlights the role of the free energy landscape of the system and of related modifications of solute-solvent thermodynamics caused by co-solutes, in agreement with recent work from our and other laboratories.
Collapse
Affiliation(s)
- Filippo Pullara
- Department of Physical and Astronomical Sciences, University of Palermo, 36, I-90123 Palermo, Italy
| | | |
Collapse
|
18
|
Tassieri M, Evans RML, Barbu-Tudoran L, Khaname GN, Trinick J, Waigh TA. Dynamics of semiflexible polymer solutions in the highly entangled regime. PHYSICAL REVIEW LETTERS 2008; 101:198301. [PMID: 19113316 DOI: 10.1103/physrevlett.101.198301] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Indexed: 05/27/2023]
Abstract
We present experimental evidence that the effective medium approximation (EMA), [D. C. Morse, Phys. Rev. E 63, 031502 (2001)], provides the correct scaling law of the plateau modulus G0 proportional variantrho4/3Lp(-1/3) (with rho the contour length per unit volume and Lp the persistence length) of semiflexible polymer solutions, in the highly entangled regime. Competing theories, including a binary collision approximation (BCA), instead predict G0 proportional, variantrho7/5Lp(-1/5). We have tested both predictions using F-actin solutions which permit experimental control of Lp independently of other parameters. A combination of video particle tracking microrheology and dynamic light scattering yields independent measurements of G0 and Lp, respectively. Thus we can distinguish between the two proposed laws, in contrast to previous experimental studies focused on the (less discriminating) concentration dependence.
Collapse
Affiliation(s)
- Manlio Tassieri
- School of Physics and Astronomy, University of Leeds, LS2 9JT, United Kingdom.
| | | | | | | | | | | |
Collapse
|
19
|
Glaser J, Hallatschek O, Kroy K. Dynamic structure factor of a stiff polymer in a glassy solution. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2008; 26:123-136. [PMID: 18491032 DOI: 10.1140/epje/i2007-10321-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 04/09/2008] [Indexed: 05/26/2023]
Abstract
We provide a comprehensive overview of the current theoretical understanding of the dynamic structure factor of stiff polymers in semidilute solution based on the wormlike chain (WLC) model. We extend previous work by computing exact numerical coefficients and an expression for the dynamic mean square displacement (MSD) of a free polymer and compare various common approximations for the hydrodynamic interactions, which need to be treated accurately if one wants to extract quantitative estimates for model parameters from experimental data. A recent controversy about the initial slope of the dynamic structure factor is thereby resolved. To account for the interactions of the polymer with a surrounding (sticky) polymer solution, we analyze an extension of the WLC model, the glassy wormlike chain (GWLC), which predicts near power law and logarithmic long-time tails in the dynamic structure factor.
Collapse
Affiliation(s)
- J Glaser
- Institut für Theoretische Physik, Universität Leipzig, Leipzig, Germany
| | | | | |
Collapse
|
20
|
Rogers SS, Waigh TA, Lu JR. Intracellular microrheology of motile Amoeba proteus. Biophys J 2008; 94:3313-22. [PMID: 18192370 PMCID: PMC2275677 DOI: 10.1529/biophysj.107.123851] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 11/16/2007] [Indexed: 11/18/2022] Open
Abstract
The motility of Amoeba proteus was examined using the technique of passive particle tracking microrheology, with the aid of newly developed particle tracking software, a fast digital camera, and an optical microscope. We tracked large numbers of endogeneous particles in the amoebae, which displayed subdiffusive motion at short timescales, corresponding to thermal motion in a viscoelastic medium, and superdiffusive motion at long timescales due to the convection of the cytoplasm. Subdiffusive motion was characterized by a rheological scaling exponent of 3/4 in the cortex, indicative of the semiflexible dynamics of the actin fibers. We observed shear-thinning in the flowing endoplasm, where exponents increased with increasing flow rate; i.e., the endoplasm became more fluid-like. The rheology of the cortex is found to be isotropic, reflecting an isotropic actin gel. A clear difference was seen between cortical and endoplasmic layers in terms of both viscoelasticity and flow velocity, where the profile of the latter is close to a Poiseuille flow for a Newtonian fluid.
Collapse
Affiliation(s)
- Salman S Rogers
- Biological Physics Group, School of Physics and Astronomy, University of Manchester, Manchester M60 1QD, United Kingdom
| | | | | |
Collapse
|
21
|
Tassieri M, Evans RML, Barbu-Tudoran L, Trinick J, Waigh TA. The self-assembly, elasticity, and dynamics of cardiac thin filaments. Biophys J 2008; 94:2170-8. [PMID: 18065478 PMCID: PMC2257900 DOI: 10.1529/biophysj.107.116087] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2007] [Accepted: 11/15/2007] [Indexed: 11/18/2022] Open
Abstract
Solutions of intact cardiac thin filaments were examined with transmission electron microscopy, dynamic light scattering (DLS), and particle-tracking microrheology. The filaments self-assembled in solution with a bell-shaped distribution of contour lengths that contained a population of filaments of much greater length than the in vivo sarcomere size ( approximately 1 mum) due to a one-dimensional annealing process. Dynamic semiflexible modes were found in DLS measurements at fast timescales (12.5 ns-0.0001 s). The bending modulus of the fibers is found to be in the range 4.5-16 x 10(-27) Jm and is weakly dependent on calcium concentration (with Ca2+ > or = without Ca2+). Good quantitative agreement was found for the values of the fiber diameter calculated from transmission electron microscopy and from the initial decay of DLS correlation functions: 9.9 nm and 9.7 nm with and without Ca2+, respectively. In contrast, at slower timescales and high polymer concentrations, microrheology indicates that the cardiac filaments act as short rods in solution according to the predictions of the Doi-Edwards chopsticks model (viscosity, eta approximately c(3), where c is the polymer concentration). This differs from the semiflexible behavior of long synthetic actin filaments at comparable polymer concentrations and timescales (elastic shear modulus, G' approximately c(1.4), tightly entangled) and is due to the relative ratio of the contour lengths ( approximately 30). The scaling dependence of the elastic shear modulus on the frequency (omega) for cardiac thin filaments is G' approximately omega(3/4 +/- 0.03), which is thought to arise from flexural modes of the filaments.
Collapse
Affiliation(s)
- M Tassieri
- Polymers and Complex Fluids, School of Physics and Astronomy, University of Leeds, Leeds, United Kingdom
| | | | | | | | | |
Collapse
|
22
|
Abstract
The fibrillization of peptides is relevant to many diseases based on the deposition of amyloids. The formation of fibrils is being intensively studied, especially in terms of nanotechnology applications, where fibrillar peptide hydrogels are used for cell scaffolds, as supports for functional and responsive biomaterials, biosensors, and nanowires. This Review is concerned with fundamental aspects of the self-assembly of peptides into fibrils, and discusses both natural amyloid-forming peptides and synthetic materials, including peptide fragments, copolymers, and amphiphiles.
Collapse
Affiliation(s)
- Ian W Hamley
- Department of Chemistry, University of Reading, Reading, Berkshire RG6 6AD, UK.
| |
Collapse
|
23
|
|
24
|
Carrick LM, Aggeli A, Boden N, Fisher J, Ingham E, Waigh TA. Effect of ionic strength on the self-assembly, morphology and gelation of pH responsive β-sheet tape-forming peptides. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.05.036] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Nyrkova IA, Semenov AN. Dynamic scattering of semirigid macromolecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:011802. [PMID: 17677479 DOI: 10.1103/physreve.76.011802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Indexed: 05/16/2023]
Abstract
The polarized (VV) and depolarized (VH) dynamic light scattering functions of dilute solutions of semirigid macromolecules are calculated assuming that the scattering wave vector [under q] is high compared to the chain Kuhn segment l : ql>>1. The terminal relaxation rate is Gamma proportional to q8/3. Dynamics of both uniaxial and biaxial wormlike macromolecules (filaments) are considered. Biaxial macromolecules are characterized by two persistence lengths proportional to elastic constants for bending in two perpendicular directions (easy and hard bending). We showed that biaxiality may result in a significant broadening of the relaxation spectrum. A nonmonotonous q dependence of the depolarized scattering intensity is predicted. Analyzing the short-time behavior of the dynamic structure factor for t<<1/Gamma, we show that it is characterized by two additional characteristic times: t perpendicular proportional to q(-4) and t parallel proportional to q(-8) reflecting the transverse and the longitudinal dynamics of polymer chains. The longitudinal motions (along the chain contour) increase the initial relaxation rate of the structure factor by a factor of 2. The longitudinal contribution to the dynamic structure factor is significant even for t>>t parallel.
Collapse
Affiliation(s)
- I A Nyrkova
- Institut Charles Sadron, 6 rue Boussingault, 67083 Strasbourg Cedex, France
| | | |
Collapse
|
26
|
Davies R, Aggeli A, Beevers A, Boden N, Carrick L, Fishwick C, Mcleish T, Nyrkova I, Semenov A. Self-assembling β-Sheet Tape Forming Peptides. Supramol Chem 2006. [DOI: 10.1080/10610270600665855] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- R.P.W. Davies
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - A. Aggeli
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - A.J. Beevers
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - N. Boden
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - L.M. Carrick
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - C.W.G. Fishwick
- a The University of Leeds, Centre for Self-Organising Molecular Systems, Department of Chemistry , Leeds, LS2 9JT, UK
| | - T.C.B. Mcleish
- b The University of Leeds, Department of Physics , Leeds, LS2 9JT, UK
| | - I. Nyrkova
- b The University of Leeds, Department of Physics , Leeds, LS2 9JT, UK
| | - A.N. Semenov
- b The University of Leeds, Department of Physics , Leeds, LS2 9JT, UK
| |
Collapse
|
27
|
Bell CJ, Carrick LM, Katta J, Jin Z, Ingham E, Aggeli A, Boden N, Waigh TA, Fisher J. Self-assembling peptides as injectable lubricants for osteoarthritis. J Biomed Mater Res A 2006; 78:236-46. [PMID: 16628707 DOI: 10.1002/jbm.a.30672] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The self-assembly of peptides is explored as an alternative route towards the development of new injectable joint lubricants for osteoarthritis (OA). The versatility of the peptide chemistry allows the incorporation of behavior reminiscent of hyaluronic acid (HA), while the triggered in situ self-assembly provides easy delivery of the samples by injection due to the low viscosity of the peptide solutions (that are initially monomeric). Using design criteria based on the chemical properties of HA, a range of de novo peptides were prepared with systematic alterations of charge and hydrophilicity that self-assembled into nematic fluids and gels in physiological solution conditions. The frictional characteristics of the peptides were evaluated using cartilage on cartilage sliding contacts along with their rheological characteristics. Peptide P(11)-9, whose molecular, mesoscopic, and rheological properties most closely resembled HA was found to be the most effective lubricant amongst the peptides. In healthy static and dynamic friction testing (corresponding to healthy joints) P(11)-9 at 20-40 mg/mL performed similar to HA at 10 mg/mL. In friction tests with damaged cartilage (corresponding to early stage OA) P(11)-9 was a less efficient lubricant than HA, but still the best among all the peptides tested. The results indicate that de novo self-assembling peptides could be developed as an alternate therapeutic lubricant for early stage OA.
Collapse
Affiliation(s)
- Carol J Bell
- Institute of Medical and Biological Engineering, School of Mechanical Engineering, University of Leeds, Leeds, West Yorkshire, LS2 9JT, United Kingdom
| | | | | | | | | | | | | | | | | |
Collapse
|