FuzDB: a new phase in understanding fuzzy interactions

Abstract

Fuzzy interactions are specific, variable contacts between proteins and other biomolecules (proteins, DNA, RNA, small molecules) formed in accord to the cellular context. Fuzzy interactions have recently been demonstrated to regulate biomolecular condensates generated by liquid-liquid phase separation. The FuzDB v4.0 database (https://fuzdb.org) assembles experimentally identified examples of fuzzy interactions, where disordered regions mediate functionally important, context-dependent contacts between the partners in stoichiometric and higher-order assemblies. The new version of FuzDB establishes cross-links with databases on structure (PDB, BMRB, PED), function (ELM, UniProt) and biomolecular condensates (PhaSepDB, PhaSePro, LLPSDB). FuzDB v4.0 is a source to decipher molecular basis of complex cellular interaction behaviors, including those in protein droplets.

Figure 1.

FuzDB Browse page. A Table of Entries (by default 20 entries/page) is shown with the following columns: FuzDB identifier, protein name as reported in the corresponding UniProt entry, the UniProt identifier, definition of the fuzzy region(s), structure identifier in the PDB, LLPS identifier in specific dataset of biomolecular condensates, and the key references for structure and function. By clicking on each FuzDB identifier the user can access the Entry page (Figure 2). The Search can be performed for free text in all fields, entry ID, protein name, UniProt identifier, structure identifier, detection method, partner protein, LLPS and ELM reference, and biological description. The Download on the top-right side is available for whole database or a selected subset of protein(s) in JSON, TSV, FASTA, XML and TXT formats.

Figure 2.

FuzDB Entry page. The page is organized in different sections which are summarized in the right side (top). The top of the page shows the entry identifier and title as reported in UniProt. The feature viewer displays the fuzzy region/s, short linear motifs (SLiMs) and posttranslational modification sites (PTMs) mapped on the UniProt protein sequence. Sequence viewer highlights the amino acids involved in the fuzzy region/s. The Function section provides information on the biological activity based on the UniProt database. The Functional sites section lists the evolutionary conserved protein domains and short linear motifs (SLiMs) located in the fuzzy region/s. The boundaries of the functional regions, database cross-links and PubMed identifiers are also displayed. The Posttranslational modification site section displays the PTMs in the fuzzy region. Only the first 5 are shown, and the list can be expanded. The Condensate section lists the evidence to form biomolecular condensate either as driver or client and provide cross-links to the PhaSepDB, PhaSePro and LLPSDB databases. The Structure section lists the region/s that remain heterogeneous in the bound state based on experimental structure-determination. The table shows cross-links to PDB, PED and DisProt databases and the corresponding PubMed identifier/s. The Significance section summarizes the biological impact of fuzzy interactions on the biological activity.

Figure 3.

Fuzzy interactions by KRAS control the signaling outcome of the MAPK pathway (FC00179). Activation of RAF by KRAS is achieved via shifting its conformation equilibrium in the membrane-bound form (50). In state A (PDB:6pts), α4-α5 of KRAS and the RAF cystein-rich domain (CRD, green) interacts with the membrane surface, while the RAF RAS-binding domain (RBD, blue) is distant from the membrane. In state B (PDB:6ptw), the RAF RBD approaches the membrane surface, enabling KRAS α4-α5 separation. The exposed KRAS α4-α5 induces dimerization leading to enhanced MAPK signaling activity. Cancer mutations stabilize state B resulting in more active MAPK signaling. KRAS residues involved in fuzzy interactions are shown by orange, RAF residues are cyan. Loop residues ¹⁰⁶KGKKAR¹¹¹ distinguished in the conformational transition are shown in red.