Information Encoded in Non-Native States Drives Substrate-Chaperone Pairing

• Published in: Structure (London) Vol. 20; no. 9; pp. 1562 - 1573
• Main Authors: Mapa, Koyeli, Tiwari, Satyam, Kumar, Vignesh, Jayaraj, Gopal Gunanathan, Maiti, Souvik
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05.09.2012
• Subjects: Amino Acid Substitution; Bacterial Proteins - chemistry; Bacterial Proteins - isolation & purification; Chromatography, Affinity; Escherichia coli; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - isolation & purification; Heat-Shock Proteins - chemistry; HSP70 Heat-Shock Proteins - chemistry; HSP70 Heat-Shock Proteins - isolation & purification; Maltose-Binding Proteins - chemistry; Maltose-Binding Proteins - genetics; Maltose-Binding Proteins - isolation & purification; Mutagenesis, Site-Directed; Protein Binding; Protein Conformation; Protein Interaction Mapping; Protein Refolding; Substrate Specificity
• ISSN: 0969-2126; 1878-4186; 1878-4186
• DOI: 10.1016/j.str.2012.06.014

Many proteins refold in vitro through kinetic folding intermediates that are believed to be by-products of native-state centric evolution. These intermediates are postulated to play only minor roles, if any, in vivo because they lack any information related to translation-associated vectorial folding. We demonstrate that refolding intermediate of a test protein, generated in vitro, is able to find its cognate chaperone, from the whole complement of Escherichia coli soluble chaperones. Cognate chaperone-binding uniquely alters the conformation of non-native substrate. Importantly, precise chaperone targeting of substrates are maintained as long as physiological molar ratios of chaperones remain unaltered. Using a library of different chaperone substrates, we demonstrate that kinetically trapped refolding intermediates contain sufficient structural features for precise targeting to cognate chaperones. We posit that evolution favors sequences that, in addition to coding for a functional native state, encode folding intermediates with higher affinity for cognate chaperones than noncognate ones. [Display omitted] ► In vitro refolding intermediates are aptly targeted to specific chaperones ► Substrate-chaperone pairing depends on their relative affinity ► Structure of the intermediates play crucial role in precise chaperone targeting ► Substrates may be mistargeted due to large alterations in chaperone molar ratios Kinetic folding intermediates of proteins formed in vitro might play only a minor role in vivo. Here, Mapa et al. show that folding intermediates generated in vitro contain sufficient structural features for precise chaperone targeting and propose that folding intermediate structures are subject to evolution.