DIP/Dpr interactions and the evolutionary design of specificity in protein families

Abstract

<jats:title>Abstract</jats:title><jats:p>Differential binding affinities among closely related protein family members underlie many biological phenomena, including cell-cell recognition. <jats:italic>Drosophila</jats:italic> DIP and Dpr proteins mediate neuronal targeting in the fly through highly specific protein-protein interactions. We show here that DIPs/Dprs segregate into seven specificity subgroups defined by binding preferences between their DIP and Dpr members. We then describe a novel sequence-, structure- and energy-based computational approach, combined with experimental binding affinity measurements, to reveal how specificity is coded on the canonical DIP/Dpr interface. We show that binding specificity of DIP/Dpr subgroups is controlled by “negative constraints”, which interfere with binding. To achieve specificity, each subgroup utilizes a different combination of negative constraints, which are broadly distributed and cover the majority of the protein-protein interface. We discuss the structural origins of negative constraints, and potential general implications for the evolutionary origins of binding specificity in multi-protein families.</jats:p>

Adhesion Protein Structure, Molecular Affinities, and Principles of Cell-Cell Recognition

“…This work was later expanded by a comprehensive set of SPR experiments that quantified DIP/Dpr binding affinities, providing K D values for each interaction and identifying a subset of DIPs that can also engage in homophilic interactions (Cosmanescu et al, 2018). Based on measured binding preferences, phylogenetic profiles, and homology models of complexes derived from available crystal structures, DIPs and Dprs were organized into seven distinct specificity groups so that DIPs and Dprs in one group bind strongly to other proteins within the group but weakly or not at all to DIPs in other groups (Figure 5; Sergeeva et al, 2020).…”

“…DIPs and Dprs exhibit more complex specificity patterns (Carrillo et al, 2015;Cosmanescu et al, 2018;Cheng et al, 2019;Sergeeva et al, 2020). Based on the interactome shown in Figure 5, there are a total of 49 possible DIP/Dpr subfamily pairings that can be subdivided into seven ''affinity groups.''…”

“…Based on the interactome shown in Figure 5, there are a total of 49 possible DIP/Dpr subfamily pairings that can be subdivided into seven ''affinity groups.'' Although interactions are all based on a common core, there are 42 sets of negative constraints that preclude incorrect pairing (Sergeeva et al, 2020). The physical origins of these constraints include replacing a charge in an ion pair with one of an opposite sign, leading to Coulombic repulsion; replacing one member of an ion pair with a neutral group, which has the effect of burying an unsatisfied charge; and mutations in the hydrophobic core to larger amino acids that create steric clashes or to smaller ones that create cavities that lead to packing defects and to weaker hydrophobic contributions to binding.…”

Neural specification, targeting, and circuit formation during visual system assembly

“…Each DIP, which has three Ig domains, interacts with a number of Dprs, each of which possesses two Ig domains (176,177); some of these proteins are also capable of homophilic binding (177,178). As DIPs and Dprs show high sequence similarity among each other, specificity of DIP-Dpr interactions appears to be mediated via exclusion/negative constraints (177,179). RNA sequencing (RNAseq) data suggest that DIPs and Dprs are differentially expressed in some corresponding synaptic partners just prior to synaptogenesis (177,178).…”

General theory of specific binding: insights from a genetic-mechano-chemical protein model

“…10 Such undesirable interactions can, at best, lead to ine ciencies through inhibition, 14 and at worst, result in aggregation 15 or cross-talk between signals. 16 Unwanted interactions can be minimized by designing mismatch between ligands and binding pockets, 17,18 such that deformation costs energy -a form of 'conformational proofreading'. 19 Other work has suggested that residues not directly involved in binding may play a role in discrimination and allostery.…”