title: Classification of chemical chaperones based on their effect on protein folding landscapes.
abstract: Various small molecules present in biological systems can assist protein folding in vitro and are known as chemical chaperones. De novo design of chemical chaperones with higher activity than currently known examples is desirable to ameliorate protein misfolding and aggregation in multiple contexts. However, this development has been hindered by limited knowledge of their activities. It is thought that chemical chaperones are typically poor solvents for a protein backbone and hence facilitate native structure formation. However, it is unknown if different chemical chaperones can act differently to modulate folding energy landscapes. Using a model slow folding protein, double-mutant Maltose-binding protein (DM-MBP), we show that a canonical chemical chaperone, trimethylamine-N-oxide (TMAO), accelerates refolding by decreasing the flexibility of the refolding intermediate (RI). Among a number of small molecules that chaperone DM-MBP folding, proline and serine stabilize the transition state (TS) enthalpically, while trehalose behaves like TMAO and increases the rate of barrier crossing through nonenthalpic processes. We propose a two-group classification of chemical chaperones based upon their thermodynamic effect on RI and TS, which is also supported by single molecule Förster resonance energy transfer (smFRET) studies. Interestingly, for a different test protein, the molecular mechanisms of the two groups of chaperones are not conserved. This provides a glimpse into the complexity of chemical chaperoning activity of osmolytes. Future work would allow us to engineer synergism between the two classes to design more efficient chemical chaperones to ameliorate protein misfolding and aggregation problems.
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.|‡Academy of Scientific and Innovative Research (AcSIR), New Delhi 110001, India.
authors.forename: Rohan
authors.initials: R
authors.lastname: Dandage
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.
authors.forename: Anannya
authors.initials: A
authors.lastname: Bandyopadhyay
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.|‡Academy of Scientific and Innovative Research (AcSIR), New Delhi 110001, India.
authors.forename: Gopal Gunanathan
authors.initials: GG
authors.lastname: Jayaraj
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.
authors.forename: Kanika
authors.initials: K
authors.lastname: Saxena
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.
authors.forename: Vijit
authors.initials: V
authors.lastname: Dalal
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.
authors.forename: Aritri
authors.initials: A
authors.lastname: Das
authors.affiliation: †CSIR-Institute of Genomics and Integrative Biology, Mathura Road Campus, Delhi 110020, India.|‡Academy of Scientific and Innovative Research (AcSIR), New Delhi 110001, India.
authors.forename: Kausik
authors.initials: K
authors.lastname: Chakraborty
mesh_terms: D001419:Bacteria / Q000737:chemistry; D031541:Fluorescence Resonance Energy Transfer; D007700:Kinetics; D058619:Maltose-Binding Proteins / Q000737:chemistry*; D008744:Methylamines / Q000737:chemistry*; D008958:Models, Molecular; D011392:Proline / Q000737:chemistry*; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry; D012694:Serine / Q000737:chemistry*; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000145:classification; D013816:Thermodynamics; D014199:Trehalose / Q000737:chemistry*
chemical_list: D058619:Maltose-Binding Proteins; D008744:Methylamines; D011994:Recombinant Proteins; D054852:Small Molecule Libraries; D012694:Serine; D011392:Proline; D014199:Trehalose; C005855:trimethyloxamine