PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode

Abstract

PixelDB, the Peptide Exosite Location Database, compiles 1966 non-redundant, high-resolution structures of protein-peptide complexes filtered to minimize the impact of crystal packing on peptide conformation. The database is organized to facilitate study of structurally conserved versus non-conserved elements of protein-peptide engagement. PixelDB clusters complexes based on the structural similarity of the peptide-binding protein, and by comparing complexes within a cluster highlights examples of domains that engage peptides using more than one binding mode. PixelDB also identifies conserved peptide core structural motifs characteristic of each binding mode. Peptide regions that flank core motifs often make non-structurally conserved interactions with the protein surface in regions we call exosites. Many examples establish that exosite contacts can be important for enhancing protein binding and interaction specificity. PixelDB provides a resource for computational and structural biologists to study, model, and predict core-motif and exosite-contacting peptide interactions. PixelDB is available to the community without restriction in a convenient flat-file format with accompanying visualization tools.Keywords: protein-peptide interactions; exosites; structural biology database; peptide binding motifs; peptide docking Abbreviations: CSV, comma separated values; ECR, exosite contacting region; ELM, eukaryotic linear motif; NISR, non-interacting surface residues; PDB, protein data bank; TM, template modeling Additional Supporting Information may be found in the online version of this article.Short Statement: The protein data bank (PDB) contains >100,000 solved structures and is a rich source of information about how proteins execute their functions. To provide a resource for scientists studying how proteins bind to peptides, the database PixelDB compiles 1966 high-quality structures of protein-peptide complexes and organizes them into related clusters. The database annotates structurally conserved and non-conserved elements in interaction interfaces and can be used to study determinants of peptide binding affinity and specificity.

Affinity and specificity of motif-based protein–protein interactions

“…For example, for disordered motifs that adopt α-helical structures upon binding, it has been found that increasing the helical propensity of the disordered region confers an increase in affinity for the binding partners [35][36][37][38]. Motif-flanking regions can also contribute with specificity determining information in terms of permissive amino acids that increase the affinity of the interaction [39][40][41][42]. Indeed, a systematic analysis of structures of motif-based interactions revealed that the local sequence context contributes about 20% of the binding and is crucial for determining specificity [40].…”

Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1

“…Peptides provide a complementary approach to targeting protein interfaces. Peptide-protein interactions are ubiquitous in nature, where there are many examples of short segments binding to large, structurally complex surfaces (Frappier et al, 2018;Tompa et al, 2014). Peptides can be delivered into cells by chemically modifying them to increase hydrophobicity and hide hydrogen bonds/negative charges (Bird et al, 2016;Rezaei Araghi et al, 2018;Walensky and Bird, 2014), conjugating them to transduction domains (such as cell-penetrating peptides) (Nischan et al, 2015;Qian et al, 2016), or delivering them using nanoparticles (Hiraki et al, 2018;Kumar et al, 2014).…”

The cell cycle regulator GpsB functions as cytosolic adaptor for multiple cell wall enzymes

“…The GpsB:PBP interaction interface notably requires no more than three sidechains from any PBP to complex with GpsB. Protein:peptide contacts involving less well-conserved exosites that flank a small core, conserved peptide motif can contribute significantly to the affinity of protein:peptide interactions 43,44 , and the contribution of exosites to affinity may explain why point mutations in Lm PBPA1 and Sp PBP2a have a significant impact using peptide fragments in vitro , but have reduced impact in vivo . For instance, the Lm PBPA1 Arg8Ala mutation had negligible effect in vivo ( Figure 2C , Supplementary Figure 2D ) yet it reduced binding by >15-fold ( Supplementary Table 1 ).…”