title: Direct Observation of Kinetic Pathways of Biomolecular Recognition.
abstract: The pathways of molecular recognition, which is a central event in all biological processes, belong to the most important subjects of contemporary research in biomolecular science. By using fluorescence spectroscopy in a microfluidics channel, it can be determined that molecular recognition of α-chymotrypsin in hydrous surroundings at two different pH values (3.6 and 6.3) follows two distinctly different pathways. Whereas one corroborates an induced-fit model (pH 3.6), the other one (pH 6.3) is consistent with the selected-fit model of biomolecular recognition. The role of massive structural perturbations of differential recognition pathways could be ruled out by earlier XRD studies, rather was consistent with the femtosecond-resolved observation of dynamic flexibility of the protein at different pH values. At low concentrations of ligands, the selected-fit model dominates, whereas increasing the ligand concentration leads to the induced-fit model. From molecular modelling and experimental results, the timescale associated with the conformational flexibility of the protein plays a key role in the selection of a pathway in biomolecular recognition.
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India).
authors.forename: Susobhan
authors.initials: S
authors.lastname: Choudhury
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India).
authors.forename: Subrata
authors.initials: S
authors.lastname: Batabyal
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India).
authors.forename: Prasanna Kumar
authors.initials: PK
authors.lastname: Mondal
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India).
authors.forename: Priya
authors.initials: P
authors.lastname: Singh
authors.affiliation: Institute for Condensed Matter Physics and Laboratory for Emergent, Nanometrology, TU Braunschweig, Mendelssohnstrasse 3, 38106 Braunschweig (Germany). p.Lemmens@tu-bs.de.
authors.forename: Peter
authors.initials: P
authors.lastname: Lemmens
authors.affiliation: Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098 (India). skpal@bose.res.in.
authors.forename: Samir Kumar
authors.initials: SK
authors.lastname: Pal
mesh_terms: D001665:Binding Sites; D001686:Biological Phenomena; D002918:Chymotrypsin / Q000032:analysis / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D013050:Spectrometry, Fluorescence / Q000379:methods*
chemical_list: D008024:Ligands; D002918:Chymotrypsin; C117608:alpha-chymotrypsin
keywords: bioinformatics; enzymes; kinetics; molecular modeling; molecular recognition