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Jang YH, Raspaud E, Lansac Y. DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions. NANOSCALE ADVANCES 2023; 5:4798-4808. [PMID: 37705794 PMCID: PMC10496769 DOI: 10.1039/d2na00847e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.
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Affiliation(s)
- Yun Hee Jang
- GREMAN UMR 7347, Université de Tours, CNRS, INSA CVL 37200 Tours France
- Department of Energy Science and Engineering, DGIST Daegu 42988 Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
| | - Yves Lansac
- GREMAN UMR 7347, Université de Tours, CNRS, INSA CVL 37200 Tours France
- Department of Energy Science and Engineering, DGIST Daegu 42988 Korea
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Saclay 91405 Orsay France
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Mahajan S, Tang T. Polyethylenimine–DNA Ratio Strongly Affects Their Nanoparticle Formation: A Large-Scale Coarse-Grained Molecular Dynamics Study. J Phys Chem B 2019; 123:9629-9640. [DOI: 10.1021/acs.jpcb.9b07031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Subhamoy Mahajan
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
| | - Tian Tang
- Department of Mechanical Engineering, University of Alberta, Edmonton, AB, Canada
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3
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Nguyen TD, Olvera de la Cruz M. Manipulation of Confined Polyelectrolyte Conformations through Dielectric Mismatch. ACS NANO 2019; 13:9298-9305. [PMID: 31404496 DOI: 10.1021/acsnano.9b03900] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We demonstrate that a highly charged polyelectrolyte confined in a spherical cavity undergoes reversible transformations between amorphous conformations and a four-fold symmetry morphology as a function of dielectric mismatch between the media inside and outside the cavity. Surface polarization due to dielectric mismatch exhibits an extra "confinement" effect, which is most pronounced within a certain range of the cavity radius and the electrostatic strength between the monomers and counterions and multivalent counterions. For cavities with a charged surface, surface polarization leads to an increased amount of counterions adsorbed in the outer side, further compressing the confined polyelectrolyte into a four-fold symmetry morphology. The equilibrium conformation of the chain is dependent upon several key factors including the relative permittivities of the media inside and outside the cavity, multivalent counterion concentration, cavity radius relative to the chain length, and interface charge density. Our findings offer insights into the effects of dielectric mismatch in packaging and delivery of polyelectrolytes across media with different relative permittivities. Moreover, the reversible transformation of the polyelectrolyte conformations in response to environmental permittivity allows for potential applications in biosensing and medical monitoring.
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Affiliation(s)
- Trung Dac Nguyen
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , Illinois 60208 , United States
| | - Monica Olvera de la Cruz
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , Illinois 60208 , United States
- Department of Materials Science and Engineering , Northwestern University , Evanston , Illinois 60208 , United States
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4
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Ghosh S, T D, Baul U, Vemparala S. Aggregation dynamics of charged peptides in water: Effect of salt concentration. J Chem Phys 2019; 151:074901. [DOI: 10.1063/1.5100890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Susmita Ghosh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Devanand T
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Upayan Baul
- Institue of Physics, Albert-Ludwigs-University of Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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5
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Tom AM, Rajesh R, Vemparala S. Aggregation of flexible polyelectrolytes: Phase diagram and dynamics. J Chem Phys 2017; 147:144903. [DOI: 10.1063/1.4993684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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6
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Mima T, Kinjo T, Yamakawa S, Asahi R. Study of the conformation of polyelectrolyte aggregates using coarse-grained molecular dynamics simulations. SOFT MATTER 2017; 13:5991-5999. [PMID: 28776057 DOI: 10.1039/c7sm01196b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The conformation of polyelectrolyte aggregates as a function of the backbone rigidity is investigated by coarse-grained molecular dynamics simulation. The polyelectrolyte is represented by a bead-spring chain with charged side chains. The simulations start from the uniform distributions of the polyelectrolytes, and the resultant polyelectrolyte conformation after a few microseconds exhibits spherical self-aggregates, clusters, or bending bundle-like aggregates, depending on the backbone rigidity. The interaggregate structures on a large scale are featured by the static structure factor (SSF). The simulated SSFs of the bending bundle-like aggregates are consistent with those of the small angle X-ray scattering (SAXS) measurement so we successfully assign the microscopic structures of polyelectrolytes to the SAXS measurement. The power-law of the SSFs for the bundle conditions is steeper than that of the conventional cylinder model. The present study finds that such discrepancy in the power-law results from the bending of the bundle-like aggregates. In addition, the relaxation behavior includes slow dynamics. The present study proposes that such slow dynamics results from diffusion-limited aggregation and from gliding processes to reduce local metastable folding within the aggregates.
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Affiliation(s)
- Toshiki Mima
- Toyota Central R&D Labs., Inc., 41-1, Yokomichi, Nagakute, Aichi, Japan.
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7
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Ozgur B, Sayar M. Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation. J Phys Chem B 2016; 120:10243-10257. [PMID: 27635660 DOI: 10.1021/acs.jpcb.6b07545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.
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Affiliation(s)
| | - Mehmet Sayar
- College of Engineering, Koc University , Istanbul, Turkey.,Chemical & Biological Engineering and Mechanical Engineering Departments, Koc University , Istanbul, Turkey
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Lansac Y, Degrouard J, Renouard M, Toma AC, Livolant F, Raspaud E. A route to self-assemble suspended DNA nano-complexes. Sci Rep 2016; 6:21995. [PMID: 26912166 PMCID: PMC4766487 DOI: 10.1038/srep21995] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/27/2016] [Indexed: 11/29/2022] Open
Abstract
Highly charged polyelectrolytes can self-assemble in presence of condensing agents such as multivalent cations, amphiphilic molecules or proteins of opposite charge. Aside precipitation, the formation of soluble micro- and nano-particles has been reported in multiple systems. However a precise control of experimental conditions needed to achieve the desired structures has been so far hampered by the extreme sensitivity of the samples to formulation pathways. Herein we combine experiments and molecular modelling to investigate the detailed microscopic dynamics and the structure of self-assembled hexagonal bundles made of short dsDNA fragments complexed with small basic proteins. We suggest that inhomogeneous mixing conditions are required to form and stabilize charged self-assembled nano-aggregates in large excess of DNA. Our results should help re-interpreting puzzling behaviors reported for a large class of strongly charged polyelectrolyte systems.
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Affiliation(s)
- Yves Lansac
- GREMAN, Université François Rabelais, CNRS UMR 7347, 37200 Tours, France.,Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France.,School of Materials Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jeril Degrouard
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Madalena Renouard
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Adriana C Toma
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Françoise Livolant
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
| | - Eric Raspaud
- Laboratoire de Physique des Solides, CNRS, Université Paris-Sud, Université Paris Saclay, 91405 Orsay cedex, France
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9
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Tom AM, Rajesh R, Vemparala S. Aggregation dynamics of rigid polyelectrolytes. J Chem Phys 2016; 144:034904. [DOI: 10.1063/1.4939870] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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10
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Nguyen TD, Schultz BA, Kotov NA, Glotzer SC. Generic, phenomenological, on-the-fly renormalized repulsion model for self-limited organization of terminal supraparticle assemblies. Proc Natl Acad Sci U S A 2015; 112:E3161-8. [PMID: 26063616 PMCID: PMC4485121 DOI: 10.1073/pnas.1509239112] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Self-limited, or terminal, supraparticles have long received great interest because of their abundance in biological systems (DNA bundles and virus capsids) and their potential use in a host of applications ranging from photonics and catalysis to encapsulation for drug delivery. Moreover, soft, uniform colloidal aggregates are a promising candidate for quasicrystal and other hierarchical assemblies. In this work, we present a generic coarse-grained model that captures the formation of self-limited assemblies observed in various soft-matter systems including nanoparticles, colloids, and polyelectrolytes. Using molecular dynamics simulations, we demonstrate that the assembly process is self-limited when the repulsion between the particles is renormalized to balance their attraction during aggregation. The uniform finite-sized aggregates are further shown to be thermodynamically stable and tunable with a single dimensionless parameter. We find large aggregates self-organize internally into a core-shell morphology and exhibit anomalous uniformity when the constituent nanoparticles have a polydisperse size distribution.
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Affiliation(s)
- Trung Dac Nguyen
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | | | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109; Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Sharon C Glotzer
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109; Department of Physics, University of Michigan, Ann Arbor, MI 48109; Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
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11
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Janmey PA, Slochower DR, Wang YH, Wen Q, Cēbers A. Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids. SOFT MATTER 2014; 10:1439-49. [PMID: 24651463 PMCID: PMC4009494 DOI: 10.1039/c3sm50854d] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Anionic polyelectrolyte filaments are common in biological cells. DNA, RNA, the cytoskeletal filaments F-actin, microtubules, and intermediate filaments, and polysaccharides such as hyaluronan that form the pericellular matrix all have large net negative charge densities distributed over their surfaces. Several filamentous viruses with diameters and stiffnesses similar to those of cytoskeletal polymers also have similar negative charge densities. Extracellular protein filaments such collagen, fibrin and elastin, in contrast, have notably smaller charge densities and do not behave as highly charged polyelectrolytes in solution. This review summarizes data that demonstrate generic counterion-mediated effects on four structurally unrelated biopolymers of similar charge density: F-actin, vimentin, Pf1 virus, and DNA, and explores the possible biological and pathophysiological consequences of the polyelectrolyte properties of biological filaments.
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Affiliation(s)
- Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, 1010 Vagelos Laboratories, 3340 Smith Walk, Philadelphia, PA 19104, USA
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12
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Yao Z, Olvera de la Cruz M. Electrostatic repulsion-driven crystallization model arising from filament networks. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:042605. [PMID: 23679441 DOI: 10.1103/physreve.87.042605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/30/2013] [Indexed: 06/02/2023]
Abstract
The crystallization of bundles in filament networks interacting via long-range repulsions in confinement is described by a phenomenological model. The model demonstrates the formation of the hexagonal crystalline order via the interplay of the confinement potential and the filament-filament repulsion. Two distinct crystallization mechanisms in the short- and large- screening length regimes are discussed, and the phase diagram is obtained. Simulation of large bundles predicts the existence of topological defects within the bundled filaments. This electrostatic repulsion-driven crystallization model arising from studying filament networks can even find a more general context extending to charged colloidal systems.
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Affiliation(s)
- Zhenwei Yao
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208-3108, USA
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13
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Abstract
We present results of molecular dynamics simulations of the electrostatic interaction between two parallel charged rods in the presence of divalent counterions. Such polyelectrolytes have been considered as a simple model for understanding electrostatic interactions in highly charged biomolecules such as DNA. Since there are correlations between the free charge carriers, the phenomenon of like charge attraction appears for specific parameters. We explore the role of solvation effects and the resulting deviations from Coulomb's law on the nanoscale on this peculiar phenomenon. The behavior of the force between the charged rods in a simulation with atomistic representation of water molecules is completely different from a model in which water is modeled as a continuum dielectric. By calculating counterion-rodion pair correlation functions, we find that the presence of water molecules changes the structure of the counterion cloud and results in both qualitative and quantitative changes of the force between highly charged polyelectrolytes.
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Affiliation(s)
- Shahzad Ghanbarian
- Department of Physics and Astronomy, The University of British Columbia, 6224 Agricultural Road, Vancouver, British Columbia V6T 1Z4, Canada
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14
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Varghese A, Rajesh R, Vemparala S. Aggregation of rod-like polyelectrolyte chains in the presence of monovalent counterions. J Chem Phys 2012; 137:234901. [DOI: 10.1063/1.4771920] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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15
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Varghese A, Vemparala S, Rajesh R. Ensemble equivalence for counterion condensation on a two-dimensional charged disk. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:011119. [PMID: 22400524 DOI: 10.1103/physreve.85.011119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Indexed: 05/31/2023]
Abstract
We study the counterion condensation on a two-dimensional charged disk in the limit of infinite dilution, and compare the energy-temperature relation obtained from the canonical free energy and microcanonical entropy. The microcanonical entropy is piecewise linear in energy, and is shown to be concave for all energies. As a result, even though the interactions are long-ranged, the energy-temperature relation and hence the counterion condensation transition points are identical in both the ensembles.
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Affiliation(s)
- Anoop Varghese
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India.
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16
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Manning GS. Counterion condensation theory of attraction between like charges in the absence of multivalent counterions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:1-18. [PMID: 22197905 DOI: 10.1140/epje/i2011-11132-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/07/2011] [Indexed: 05/31/2023]
Abstract
There is abundant experimental evidence suggesting the existence of attractive interactions among identically charged polyelectrolytes in ordinary salt solutions. The presence of multivalent counterions is not required. We review the relevant literature in detail and conclude that it merits more attention than it has received. We discuss also some recent observations of a low ionic strength attraction of negatively charged DNA to the region of a negatively charged glass nanoslit where the floor of the nanoslit meets the walls, again in the absence of multivalent ions. On the theoretical side, it has become clear that purely electrostatic interactions require the presence of multivalent counterions if they are to generate like-charge attraction. Any theory of like-charge attraction in the absence of multivalent counterions must therefore contain a non-electrostatic component. We point out that counterion condensation theory, which has predicted like-charge polyelectrolyte attraction in an intermediate range of distances in ordinary 1:1 salt conditions, contains both electrostatic and non-electrostatic elements. The non-electrostatic component of the theory is the modeling constraint that the counterions fall into two explicit populations, condensed and uncondensed. As reviewed in the paper, this physically motivated constraint is supported by strong experimental evidence. We proceed to offer an explanation of the nanoslit observations by showing in an idealized model that the line of intersection of two intersecting planes is a virtual polyelectrolyte. Since we have previously developed a counterion condensation theory of attraction of two like-charged polyelectrolytes, our suggestion is that the DNA is attracted to the virtual polyelectrolytes that may be located in the nanoslit where floor meets walls. We present the detailed calculations needed to document this suggestion: an extension of previous theory to the case of polyelectrolytes with like but not identical charges; the demonstration of counterion condensation on a plane with bare charge density greater than an explicitly exhibited critical value; a calculation of the free energy of the plane; a calculation of the interaction of a line charge polyelectrolyte with a like-charged plane; and the detailed demonstration that the line of intersection of two planes is a virtual polyelectrolyte.
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Affiliation(s)
- G S Manning
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA.
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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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