title: When the Scaffold Cannot Be Ignored: The Role of the Hydrophobic Core in Ligand Binding and Specificity.
abstract: The traditional view of protein-ligand binding treats a protein as comprising distinct binding epitopes on the surface of a degenerate structural scaffold, largely ignoring the impact of a protein's energy landscape. To determine the robustness of this simplification, we compared two small helix-turn-helix transcription factors with different energy landscapes. λ-Repressor is stable and well folded, while MarA appears to be marginally stable with multiple native conformations (molten). While λ-repressor is known to tolerate any hydrophobic mutation in the core, we find MarA drastically less tolerant to core mutation. Moreover, core mutations in MarA (distant from the DNA-binding interface) change the relative affinities of its binding partners, altering ligand specificity. These results can be explained by taking into account the effects of mutations on the entire energy landscape and not just the native state. Thus, for proteins with multiple conformations that are close in energy, such as many intrinsically disordered proteins, residues distant from the active site can alter both binding affinity and specificity.
authors: California Institute for Quantitative Biosciences- Berkeley, University of California, Berkeley, CA 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA.
authors: Diana A
authors: DA
authors: Koulechova
authors: Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA.
authors: Katherine W
authors: KW
authors: Tripp
authors: California Institute for Quantitative Biosciences- Berkeley, University of California, Berkeley, CA 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA.
authors: Geoffrey
authors: G
authors: Horner
authors: California Institute for Quantitative Biosciences- Berkeley, University of California, Berkeley, CA 94720-3220, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220, USA. Electronic address: marqusee@berkeley.edu.
authors: Susan
authors: S
authors: Marqusee
mesh_terms: D002942:Circular Dichroism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D057927:Hydrophobic and Hydrophilic Interactions; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D013816:Thermodynamics; D054334:Viral Regulatory and Accessory Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D008024:Ligands; C080002:MarA protein, E coli; D012097:Repressor Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins
keywords: DNA binding; energy landscape; hydrophobic core; ligand binding