1aef: Difference between revisions
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==Overview== | ==Overview== | ||
Cavity complementation has been observed in many proteins, where an, appropriate small molecule binds to a cavity-forming mutant. Here, the, binding of compounds to the W191G cavity mutant of cytochrome c peroxidase, is characterized by X-ray crystallography and binding thermodynamics., Unlike cavities created by removal of hydrophobic side-chains, the W191G, cavity does not bind neutral or hydrophobic compounds, but displays a, strong specificity for heterocyclic cations, consistent with the role of, the protein to stabilize a tryptophan radical at this site. Ligand, dissociation constants for the protonated cationic state ranged from 6, microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and, binding was associated with a large enthalpy-entropy compensation. X-ray, ... | Cavity complementation has been observed in many proteins, where an, appropriate small molecule binds to a cavity-forming mutant. Here, the, binding of compounds to the W191G cavity mutant of cytochrome c peroxidase, is characterized by X-ray crystallography and binding thermodynamics., Unlike cavities created by removal of hydrophobic side-chains, the W191G, cavity does not bind neutral or hydrophobic compounds, but displays a, strong specificity for heterocyclic cations, consistent with the role of, the protein to stabilize a tryptophan radical at this site. Ligand, dissociation constants for the protonated cationic state ranged from 6, microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and, binding was associated with a large enthalpy-entropy compensation. X-ray, structures show that each of 18 compounds with binding behavior bind, specifically within the artificial cavity and not elsewhere in the, protein. The compounds make multiple hydrogen bonds to the cavity walls, using a subset of the interactions seen between the protein and solvent in, the absence of ligand. For all ligands, every atom that is capable of, making a hydrogen bond does so with either protein or solvent. The most, often seen interaction is to Asp235, and most compounds bind with a, specific orientation that is defined by their ability to interact with, this residue. Four of the ligands do not have conventional hydrogen, bonding atoms, but were nevertheless observed to orient their most polar, CH bond towards Asp235. Two of the larger ligands induce disorder in a, surface loop between Pro190 and Asn195 that has been identified as a, mobile gate to cavity access. Despite the predominance of hydrogen bonding, and electrostatic interactions, the small variation in observed binding, free energies were not correlated readily with the strength, type or, number of hydrogen bonds or with calculated electrostatic energies alone., Thus, as with naturally occurring binding sites, affinities to W191G are, likely to be due to a subtle balance of polar, non-polar, and solvation, terms. These studies demonstrate how cavity complementation and judicious, choice of site can be used to produce a protein template with an unusual, ligand-binding specificity. | ||
==About this Structure== | ==About this Structure== | ||
1AEF is a | 1AEF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with HEM and 3AP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] Structure known Active Site: AVE. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AEF OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: transit peptide]] | [[Category: transit peptide]] | ||
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 12:40:43 2007'' | ||
Revision as of 13:35, 5 November 2007
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SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (3-AMINOPYRIDINE)
OverviewOverview
Cavity complementation has been observed in many proteins, where an, appropriate small molecule binds to a cavity-forming mutant. Here, the, binding of compounds to the W191G cavity mutant of cytochrome c peroxidase, is characterized by X-ray crystallography and binding thermodynamics., Unlike cavities created by removal of hydrophobic side-chains, the W191G, cavity does not bind neutral or hydrophobic compounds, but displays a, strong specificity for heterocyclic cations, consistent with the role of, the protein to stabilize a tryptophan radical at this site. Ligand, dissociation constants for the protonated cationic state ranged from 6, microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and, binding was associated with a large enthalpy-entropy compensation. X-ray, structures show that each of 18 compounds with binding behavior bind, specifically within the artificial cavity and not elsewhere in the, protein. The compounds make multiple hydrogen bonds to the cavity walls, using a subset of the interactions seen between the protein and solvent in, the absence of ligand. For all ligands, every atom that is capable of, making a hydrogen bond does so with either protein or solvent. The most, often seen interaction is to Asp235, and most compounds bind with a, specific orientation that is defined by their ability to interact with, this residue. Four of the ligands do not have conventional hydrogen, bonding atoms, but were nevertheless observed to orient their most polar, CH bond towards Asp235. Two of the larger ligands induce disorder in a, surface loop between Pro190 and Asn195 that has been identified as a, mobile gate to cavity access. Despite the predominance of hydrogen bonding, and electrostatic interactions, the small variation in observed binding, free energies were not correlated readily with the strength, type or, number of hydrogen bonds or with calculated electrostatic energies alone., Thus, as with naturally occurring binding sites, affinities to W191G are, likely to be due to a subtle balance of polar, non-polar, and solvation, terms. These studies demonstrate how cavity complementation and judicious, choice of site can be used to produce a protein template with an unusual, ligand-binding specificity.
About this StructureAbout this Structure
1AEF is a Single protein structure of sequence from Saccharomyces cerevisiae with HEM and 3AP as ligands. Active as Cytochrome-c peroxidase, with EC number 1.11.1.5 Structure known Active Site: AVE. Full crystallographic information is available from OCA.
ReferenceReference
Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein., Musah RA, Jensen GM, Bunte SW, Rosenfeld RJ, Goodin DB, J Mol Biol. 2002 Jan 25;315(4):845-57. PMID:11812152
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