Intrinsic protein disorder uncouples affinity from binding specificity

Abstract

Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) of proteins often function by molecular recognition, in which they undergo induced folding. Based on prior generalizations, the idea prevails in the IDP field that due to the entropic penalty of induced folding, the major functional advantage associated with this binding mode is “uncoupling” specificity from binding strength. Nevertheless, both weaker binding and high specificity of IDPs/IDRs rest on limited experimental observations, making these assumptions more speculations than evidence‐supported facts. The issue is also complicated by the rather vague concept of specificity that lacks an exact measure, such as the Kd for binding strength. We addressed these issues by creating and analyzing a comprehensive dataset of well‐characterized ID/globular protein complexes, for which both the atomic structure of the complex and free energy (ΔG, Kd) of interaction is known. Through this analysis, we provide evidence that the affinity distributions of IDP/globular and globular/globular complexes show different trends, whereas specificity does not connote to weaker binding strength of IDPs/IDRs. Furthermore, protein disorder extends the spectrum in the direction of very weak interactions, which may have important regulatory consequences and suggest that, in a biological sense, strict correlation of specificity and binding strength are uncoupled by structural disorder.

De novo design of high-affinity protein binders to bioactive helical peptides

“…First, proteins designed to bind folded proteins, such as picomolar affinity hyper-stable 50-65 residue minibinders 5 , have shapes suitable for binding rigid concave targets, but not for cradling extended peptides. Second, peptides have fewer residues to interact with, and are often partially or entirely unstructured in isolation 9 ; as a result, there can be an entropic cost of structuring the peptide into a specific conformation 10 , which compromises the favorable free energy of association. Progress has been made in designing peptides that bind to extended beta strand structures 11 and polyproline II conformations conformations 12 using protein side chains to interact with the peptide backbone, but such interactions cannot be made with alpha helical peptides due to the extensive internal backbone - backbone hydrogen bonding.…”

Reply to “Intrinsic protein disorder uncouples affinity from binding specificity”

“…Second, as our work was completed later, we could collect many more examples, and could exclusively focus on cases for which high-resolution structural data were available (in Teilum et al (2015); there are 52 such ORD-ORD cases and 41 ORD-IDP cases, whereas in our study (Lazar et al, 2022), we have analyzed 144 ORD-ORD and 259 ORD-IDP complexes, respectively). As a result, our statistics shows some deviations from that reached in Teilum et al (2015), in the sense that IDPs have significantly more hydrophobic residues in their interfaces (Figure 1), as also suggested earlier (Fuxreiter et al, 2007;Meszaros et al, 2007).…”

“…As we most importantly do not know the parameters of all competing interactions, we are not in the position to tell the thermodynamic specificity of a given interaction. A closely related problem is that in principle, the authors of both papers (Lazar et al, 2022;Teilum et al, 2015) only studied "specific" interactions, without a control dataset of false positive cases. Furthermore, it is well-accepted that there are still many more true positive interactions in the proteome that still await for discovery, and this introduces another complication left undiscussed.…”

Comment on “Intrinsic protein disorder uncouples affinity from binding specificity”

“…We have elaborated on that subject in depth recently (Teilum et al, 2021) and would like to point out that there is a clear physical-chemical definition of specificity (von Hippel & Berg, 1986;Eaton et al, 1995), by which specificity and affinity cannot be uncoupled as otherwise stated in the title of the article by Lazar et al, as F I G U R E 1 Density estimates of ΔG of binding for IDP:ordered complexes (ID-OR, red) and for complexes between two globular ordered proteins (OR-OR, blue). The distributions in light colors are from the data compiled by Lazar et al (2022), whereas the distributions in darker colors are from the data compiled by Teilum et al (2015). The dashed vertical lines show the average of each distribution.…”

“…In a recent issue of Protein Science, Lazar et al published an article entitled "Intrinsic protein disorder uncouples affinity from binding specificity" (Lazar et al, 2022). In this work, the authors challenge the widespread view that intrinsically disordered proteins (IDPs) bind their interaction partners with low affinity but high specificity.…”