Receptor-ligand rebinding kinetics in confinement
buir.contributor.author | Erbaş, Aykut | |
dc.citation.epage | 1624 | en_US |
dc.citation.issueNumber | 9 | en_US |
dc.citation.spage | 1609 | en_US |
dc.citation.volumeNumber | 116 | en_US |
dc.contributor.author | Erbaş, Aykut | en_US |
dc.contributor.author | De la Cruz, M. O. | en_US |
dc.contributor.author | Marko, F. | en_US |
dc.date.accessioned | 2020-02-07T09:48:34Z | |
dc.date.available | 2020-02-07T09:48:34Z | |
dc.date.issued | 2019 | |
dc.department | Institute of Materials Science and Nanotechnology (UNAM) | en_US |
dc.department | Nanotechnology Research Center (NANOTAM) | en_US |
dc.description.abstract | Rebinding kinetics of molecular ligands plays a key role in the operation of biomachinery, from regulatory networks to protein transcription, and is also a key factor in design of drugs and high-precision biosensors. In this study, we investigate initial release and rebinding of ligands to their binding sites grafted on a planar surface, a situation commonly observed in single-molecule experiments and that occurs in vivo, e.g., during exocytosis. Via scaling arguments and molecular dynamic simulations, we analyze the dependence of nonequilibrium rebinding kinetics on two intrinsic length scales: the average separation distance between the binding sites and the total diffusible volume (i.e., height of the experimental reservoir in which diffusion takes place or average distance between receptor-bearing surfaces). We obtain time-dependent scaling laws for on rates and for the cumulative number of rebinding events. For diffusion-limited binding, the (rebinding) on rate decreases with time via multiple power-law regimes before the terminal steady-state (constant on-rate) regime. At intermediate times, when particle density has not yet become uniform throughout the diffusible volume, the cumulative number of rebindings exhibits a novel, to our knowledge, plateau behavior because of the three-dimensional escape process of ligands from binding sites. The duration of the plateau regime depends on the average separation distance between binding sites. After the three-dimensional diffusive escape process, a one-dimensional diffusive regime describes on rates. In the reaction-limited scenario, ligands with higher affinity to their binding sites (e.g., longer residence times) delay entry to the power-law regimes. Our results will be useful for extracting hidden timescales in experiments such as kinetic rate measurements for ligand-receptor interactions in microchannels, as well as for cell signaling via diffusing molecules. | en_US |
dc.description.provenance | Submitted by Zeynep Aykut (zeynepay@bilkent.edu.tr) on 2020-02-07T09:48:34Z No. of bitstreams: 1 Receptor_ligand_rebinding_kinetics_in_confinement.pdf: 2037349 bytes, checksum: ac912abadda3fc0c097ddbef646fca28 (MD5) | en |
dc.description.provenance | Made available in DSpace on 2020-02-07T09:48:34Z (GMT). No. of bitstreams: 1 Receptor_ligand_rebinding_kinetics_in_confinement.pdf: 2037349 bytes, checksum: ac912abadda3fc0c097ddbef646fca28 (MD5) Previous issue date: 2019 | en |
dc.identifier.doi | 10.1016/j.bpj.2019.02.033 | en_US |
dc.identifier.issn | 0006-3495 | |
dc.identifier.uri | http://hdl.handle.net/11693/53160 | |
dc.language.iso | English | en_US |
dc.publisher | Biophysical Society | en_US |
dc.relation.isversionof | https://dx.doi.org/10.1016/j.bpj.2019.02.033 | en_US |
dc.source.title | Biophysical Journal | en_US |
dc.subject | Molecular ligands | en_US |
dc.subject | Rebinding kinetics | en_US |
dc.subject | Ligand-receptor interactions | en_US |
dc.subject | Receptor-ligand rebinding kinetics | en_US |
dc.title | Receptor-ligand rebinding kinetics in confinement | en_US |
dc.type | Article | en_US |
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