Protein binding specificity versus promiscuity

Abstract

Interactions between macromolecules in general, and between proteins in particular, are essential for any life process. Examples include transfer of information, inhibition or activation of function, molecular recognition as in the immune system, assembly of macromolecular structures and molecular machines, and more. Proteins interact with affinities ranging from millimolar to femtomolar and, because affinity determines the concentration required to obtain 50% binding, the amount of different complexes formed is very much related to local concentrations. Although the concentration of a specific binding partner is usually quite low in the cell (nanomolar to micromolar), the total concentration of other macromolecules is very high, allowing weak and non-specific interactions to play important roles. In this review we address the question of binding specificity, that is, how do some proteins maintain monogamous relations while others are clearly polygamous. We examine recent work that addresses the molecular and structural basis for specificity versus promiscuity. We show through examples how multiple solutions exist to achieve binding via similar interfaces and how protein specificity can be tuned using both positive and negative selection (specificity by demand). Binding of a protein to numerous partners can be promoted through variation in which residues are used for binding, conformational plasticity and/or post-translational modification. Natively unstructured regions represent the extreme case in which structure is obtained only upon binding. Many natively unstructured proteins serve as hubs in protein-protein interaction networks and such promiscuity can be of functional importance in biology.

Figure 1

Overlay of β-lactamase – BLIP structures. A. cyan – TEM1-BLIP (1JTG), magenta – SHV-BLIP (2G2U), yellow – KPC2-BLIP (3E2L), pink – TEM1-BLIP1 (3GMW) and green – is BLP (3GMX) overlaid on TEM1-BLIP. B. TEM1-BLIP2 (1JTD) structure (pink over cyan) overlaid on TEM1-BLIP.

Figure 2

Interactions formed by p53 residues 367–391. In each panel, the p53 fragment is in cyan. The p53 sequence is 367-SHLKSKKGQSTSRHKKLMFKTEGPD-391, and in each structure the bold lysine residues are shown in stick representation, if unmodified. Post-translationally modified residues are shown using spheres. (A) S100 calcium-binding protein with p53 residues 367–388 (1DT7) [72], (B) Cyclin A2 with p53 residues 378–386 (1H26) [73], (C) Tumor suppressor p53-binding protein 1 with p53 dimethylated lysine residue 382 (3LGL); residues 377–381 and 383–387 did not show clear density [59], (D) 14-3-3 protein sigma with p53 residues 385–391, phosphothreonine 387 (3LW1) [60], (E) NAD-dependent deacetylase Sir2 with p53 residues 378–384 (2H2F) [74], (F) NAD-dependent deacetylase Sir2 with p53 residues 373–385; acetyllysine 382 (2H2D) [74], (G) CREB-binding protein with p53 residues 367–386; acetyllysine 382 (1JSP) [75], (H) Histone-lysine N-methyltransferase with p53 residues 369–374; N-methyl-lysine 372 (1XQH) [76].