How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels

We present systematic studies for the binding of small model proteins to ligands attached to the inner walls of long nanochannels and short nanopores by polymeric tethers. Binding of proteins to specific ligands inside nanometric channels and pores leads to changes in their ionic conductance, which...

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Autores principales:	Tagliazucchi, M., Szleifer, I.
Formato:	JOUR
Materias:	Bins Biochemistry Density functional theory Ligands Nanopores Tetherlines Confined environment Ligand-receptor binding Nanometric channels Non-monotonic function Polymeric tethers Protein ligands Steric interactions Systematic study Proteins ligand macrogol nanochannel ion nanomaterial protein binding apparent dissociation constant Article chemical reaction conductance entropy geometry ion current ion transport isotherm nanopore receptor binding static electricity surface property chemistry electric conductivity particle size Electric Conductivity Ions Nanostructures Particle Size Protein Binding
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_00027863_v137_n39_p12539_Tagliazucchi
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	todo:paper_00027863_v137_n39_p12539_Tagliazucchi2023-10-03T13:54:27Z How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels Tagliazucchi, M. Szleifer, I. Bins Biochemistry Density functional theory Ligands Nanopores Tetherlines Confined environment Ligand-receptor binding Nanometric channels Non-monotonic function Polymeric tethers Protein ligands Steric interactions Systematic study Proteins ligand macrogol nanochannel ion ligand nanomaterial protein binding apparent dissociation constant Article chemical reaction conductance entropy geometry ion current ion transport isotherm nanopore protein binding receptor binding static electricity surface property chemistry electric conductivity particle size Electric Conductivity Ions Ligands Nanopores Nanostructures Particle Size Protein Binding We present systematic studies for the binding of small model proteins to ligands attached to the inner walls of long nanochannels and short nanopores by polymeric tethers. Binding of proteins to specific ligands inside nanometric channels and pores leads to changes in their ionic conductance, which have been exploited in sensors that quantify the concentration of the proteins in solution. The theoretical predictions presented in this work are aimed to provide a fundamental understanding of protein binding under geometrically confined environments and to guide the design of this kind of nanochannel-based sensors. The theory predicts that the fraction of the channel volume filled by bound proteins is a nonmonotonic function of the channel radius, the length of the tethers, the surface density of the ligands and the size of the proteins. Notably, increasing the density of ligands, decreasing the size of the channel or increasing the size of the protein may lead to a decrease of the fraction of the channel volume filled by bound proteins. These results are explained from the incomplete binding of proteins to the ligands due to repulsive protein-protein and protein-ligand steric interactions. Our work suggests strategies to optimize the change in conductance due to protein binding, for example: (i) proteins much smaller than the radius of the channel may effectively block the channel if tethers of appropriate length are used, and (ii) a large decrease in conductance upon protein binding can be achieved if the channel and the protein are oppositely charged. © 2015 American Chemical Society. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_00027863_v137_n39_p12539_Tagliazucchi
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	Bins Biochemistry Density functional theory Ligands Nanopores Tetherlines Confined environment Ligand-receptor binding Nanometric channels Non-monotonic function Polymeric tethers Protein ligands Steric interactions Systematic study Proteins ligand macrogol nanochannel ion ligand nanomaterial protein binding apparent dissociation constant Article chemical reaction conductance entropy geometry ion current ion transport isotherm nanopore protein binding receptor binding static electricity surface property chemistry electric conductivity particle size Electric Conductivity Ions Ligands Nanopores Nanostructures Particle Size Protein Binding
spellingShingle	Bins Biochemistry Density functional theory Ligands Nanopores Tetherlines Confined environment Ligand-receptor binding Nanometric channels Non-monotonic function Polymeric tethers Protein ligands Steric interactions Systematic study Proteins ligand macrogol nanochannel ion ligand nanomaterial protein binding apparent dissociation constant Article chemical reaction conductance entropy geometry ion current ion transport isotherm nanopore protein binding receptor binding static electricity surface property chemistry electric conductivity particle size Electric Conductivity Ions Ligands Nanopores Nanostructures Particle Size Protein Binding Tagliazucchi, M. Szleifer, I. How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
topic_facet	Bins Biochemistry Density functional theory Ligands Nanopores Tetherlines Confined environment Ligand-receptor binding Nanometric channels Non-monotonic function Polymeric tethers Protein ligands Steric interactions Systematic study Proteins ligand macrogol nanochannel ion ligand nanomaterial protein binding apparent dissociation constant Article chemical reaction conductance entropy geometry ion current ion transport isotherm nanopore protein binding receptor binding static electricity surface property chemistry electric conductivity particle size Electric Conductivity Ions Ligands Nanopores Nanostructures Particle Size Protein Binding
description	We present systematic studies for the binding of small model proteins to ligands attached to the inner walls of long nanochannels and short nanopores by polymeric tethers. Binding of proteins to specific ligands inside nanometric channels and pores leads to changes in their ionic conductance, which have been exploited in sensors that quantify the concentration of the proteins in solution. The theoretical predictions presented in this work are aimed to provide a fundamental understanding of protein binding under geometrically confined environments and to guide the design of this kind of nanochannel-based sensors. The theory predicts that the fraction of the channel volume filled by bound proteins is a nonmonotonic function of the channel radius, the length of the tethers, the surface density of the ligands and the size of the proteins. Notably, increasing the density of ligands, decreasing the size of the channel or increasing the size of the protein may lead to a decrease of the fraction of the channel volume filled by bound proteins. These results are explained from the incomplete binding of proteins to the ligands due to repulsive protein-protein and protein-ligand steric interactions. Our work suggests strategies to optimize the change in conductance due to protein binding, for example: (i) proteins much smaller than the radius of the channel may effectively block the channel if tethers of appropriate length are used, and (ii) a large decrease in conductance upon protein binding can be achieved if the channel and the protein are oppositely charged. © 2015 American Chemical Society.
format	JOUR
author	Tagliazucchi, M. Szleifer, I.
author_facet	Tagliazucchi, M. Szleifer, I.
author_sort	Tagliazucchi, M.
title	How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
title_short	How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
title_full	How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
title_fullStr	How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
title_full_unstemmed	How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels
title_sort	how does confinement change ligand-receptor binding equilibrium? protein binding in nanopores and nanochannels
url	http://hdl.handle.net/20.500.12110/paper_00027863_v137_n39_p12539_Tagliazucchi
work_keys_str_mv	AT tagliazucchim howdoesconfinementchangeligandreceptorbindingequilibriumproteinbindinginnanoporesandnanochannels AT szleiferi howdoesconfinementchangeligandreceptorbindingequilibriumproteinbindinginnanoporesandnanochannels
_version_	1782026385179541504

How Does Confinement Change Ligand-Receptor Binding Equilibrium? Protein Binding in Nanopores and Nanochannels

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