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PDBsum entry 6mla
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Protein binding
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PDB id
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6mla
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References listed in PDB file
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Key reference
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Title
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The interplay of protein-Ligand and water-Mediated interactions shape affinity and selectivity in the lao binding protein.
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Authors
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R.Vergara,
S.Romero-Romero,
I.Velázquez-López,
G.Espinoza-Pérez,
A.Rodríguez-Hernández,
N.O.Pulido,
A.Sosa-Peinado,
A.Rodríguez-Romero,
D.A.Fernández-Velasco.
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Ref.
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FEBS J, 2020,
287,
763-782.
[DOI no: ]
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PubMed id
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Abstract
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The study of binding thermodynamics is essential to understand how affinity and
selectivity are acquired in molecular complexes. Periplasmic binding proteins
(PBPs) are macromolecules of biotechnological interest that bind a broad number
of ligands and have been used to design biosensors. The
lysine-arginine-ornithine binding protein (LAO) is a PBP of 238 residues that
binds the basic amino acids l-arginine and l-histidine with nm and μm affinity,
respectively. It has been shown that the affinity difference for arginine and
histidine binding is caused by enthalpy, this correlates with the higher number
of protein-ligand contacts formed with arginine. In order to elucidate the
structural bases that determine binding affinity and selectivity in LAO, the
contribution of protein-ligand contacts to binding energetics was assessed. To
this end, an alanine scanning of the LAO-binding site residues was performed and
arginine and histidine binding were characterized by isothermal titration
calorimetry and X-ray crystallography. Although unexpected enthalpy and entropy
changes were observed in some mutants, thermodynamic data correlated with
structural information, especially, the binding heat capacity change. We found
that selectivity is conferred by several residues rather than exclusive
arginine-protein interactions. Furthermore, crystallographic structures revealed
that protein-ligand contributions to binding thermodynamics are highly
influenced by the solvent. Finally, we found a similar backbone conformation in
all the closed structures obtained, but different structures in the open state,
suggesting that the binding site residues of LAO play an important role in
stabilizing not only the holo conformation, but also the apo state. DATABASE:
Structural data are available in the Protein Data Bank database under the
accession numbers 6MLE, 6MLN, 6MLG, 6MKX, 6MLI, 6MLA, 6MKU, 6MKW, 6ML0, 6MLD,
6MLV, 6MLO, 6MLP, 6ML9, 6MLJ.
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