Roles of the Structure and Orientation of Ligands and Ligand Mimics inside the Ligand-Binding Pocket of the Vitamin D-Binding Protein†

Biochemistry ◽  
1997 ◽  
Vol 36 (24) ◽  
pp. 7432-7436 ◽  
Author(s):  
Narasimha Swamy ◽  
Alok Dutta ◽  
Rahul Ray
Keyword(s):  
Vitamin D ◽  
Ligand Binding ◽  
Binding Protein ◽  
Binding Pocket ◽  
Vitamin D Binding Protein ◽  
Ligand Binding Pocket

Tryptophan-scanning mutagenesis of the ligand binding pocket in Thermotoga maritima arginine-binding protein

Biochimie ◽  
2014 ◽  
Vol 99 ◽  
pp. 208-214 ◽  
Author(s):  
Lindsay J. Deacon ◽  
Hilbert Billones ◽  
Anne A. Galyean ◽  
Teraya Donaldson ◽  
Anna Pennacchio ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Thermotoga Maritima ◽  
Binding Protein ◽  
Binding Pocket ◽  
Ligand Binding Pocket

scholarly journals An improved reversibly dimerizing mutant of the FK506-binding protein FKBP

2016 ◽  
Author(s):  
Juan J. Barrero ◽  
Effrosyni Papanikou ◽  
Jason C. Casler ◽  
Kasey J. Day ◽  
Benjamin S. Glick
Keyword(s):  
Ligand Binding ◽  
Secretory Pathway ◽  
Binding Protein ◽  
Binding Pocket ◽  
Ligand Binding Pocket ◽  
Fk506 Binding Protein ◽  
Ligand Addition

FK506-binding protein (FKBP) is a monomer that binds to FK506, rapamycin, and related ligands. The F36M substitution, in which Phe36 in the ligand-binding pocket is changed to Met, leads to formation of antiparallel FKBP dimers, which can be dissociated into monomers by ligand binding. This FKBP(M) mutant has been employed in the mammalian secretory pathway to generate aggregates that can be dissolved by ligand addition to create cargo waves. However, when testing this approach in yeast, we found that dissolution of FKBP(M) aggregates was inefficient. An improved reversibly dimerizing FKBP formed aggregates that dissolved more readily. This FKBP(L,V) mutant carries the F36L mutation, which increases the affinity of ligand binding, and the I90V mutation, which accelerates ligand-induced dissociation of the dimers. The FKBP(L,V) mutant expands the utility of reversibly dimerizing FKBP.

scholarly journals Computational redesign of theEscherichia coliribose-binding protein ligand binding pocket for 1,3-cyclohexanediol and cyclohexanol

2019 ◽  
Author(s):  
Diogo Tavares ◽  
Artur Reimer ◽  
Shantanu Roy ◽  
Aurélie Joublin ◽  
Vladimir Sentchilo ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Computational Design ◽  
Binding Pocket ◽  
Wild Type ◽  
Ligand Binding Pocket ◽  
Mutant Proteins ◽  
Periplasmic Binding Proteins ◽  
Natural Ligands

Bacterial periplasmic-binding proteins have been acclaimed as general biosensing platform, but their range of natural ligands is too limited for optimal development of chemical compound detection. Computational redesign of the ligand-binding pocket of periplasmic-binding proteins may yield variants with new properties, but, despite earlier claims, genuine changes of specificity to non-natural ligands have so far not been achieved. In order to better understand the reasons of such limited success, we revisited here theEscherichia coliRbsB ribose-binding protein, aiming to achieve perceptible transition from ribose to structurally related chemical ligands 1,3-cyclohexanediol and cyclohexanol. Combinations of mutations were computationally predicted for nine residues in the RbsB binding pocket, then synthesized and tested in anE. colireporter chassis. Two million variants were screened in a microcolony-in-bead fluorescence-assisted sorting procedure, which yielded six mutants no longer responsive to ribose but with 1.2-1.5 times induction in presence of 1 mM 1,3-cyclohexanediol, one of which responded to cyclohexanol as well. Isothermal microcalorimetry confirmed 1,3-cyclohexanediol binding, although only two mutant proteins were sufficiently stable upon purification. Circular dichroism spectroscopy indicated discernable structural differences between these two mutant proteins and wild-type RbsB. This and further quantification of periplasmic-space abundance suggested most mutants to be prone to misfolding and/or with defects in translocation compared to wild-type. Our results thus affirm that computational design and library screening can yield RbsB mutants with recognition of non-natural but structurally similar ligands. The inherent arisal of protein instability or misfolding concomitant with designed altered ligand-binding pockets should be overcome by new experimental strategies or by improved future protein design algorithms.

Theoretical studies on the structural rearrangement of ligand binding pocket in human vitamin D receptor

2010 ◽  
Vol 111 (14) ◽  
pp. 3928-3937
Author(s):  
Jinhu Wang ◽  
Ke Tang ◽  
Qianqian Hou ◽  
Xueli Cheng ◽  
Yongjun Liu ◽  
...  
Keyword(s):  
Vitamin D ◽  
Ligand Binding ◽  
Vitamin D Receptor ◽  
Binding Pocket ◽  
Structural Rearrangement ◽  
Theoretical Studies ◽  
Ligand Binding Pocket

scholarly journals Vitamin D Receptor Agonists Specifically Modulate the Volume of the Ligand-binding Pocket

2006 ◽  
Vol 281 (15) ◽  
pp. 10516-10526 ◽  
Author(s):  
Ferdinand Molnár ◽  
Mikael Peräkylä ◽  
Carsten Carlberg
Keyword(s):  
Vitamin D ◽  
Ligand Binding ◽  
Vitamin D Receptor ◽  
Binding Pocket ◽  
Ligand Binding Pocket ◽  
Receptor Agonists
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