Involvement of Local, Rapid Conformational Dynamics in Binding of Flexible Recognition Motifs.
Gregory S BukowskiRachel E HornessMegan C ThielgesPublished in: The journal of physical chemistry. B (2019)
Flexible protein sequences populate ensembles of rapidly interconverting states differentiated by small-scale fluctuations; however, elucidating whether and how the ensembles determine function experimentally is challenged by the combined high spatial and temporal resolution needed to capture the states. We used carbon-deuterium (C-D) bond vibrations incorporated as infrared probes to characterize with residue-specific detail the heterogeneity of states adopted by proline-rich (PR) sequences and assess their involvement in recognition of Src homology 3 domains. The C-D absorption envelopes provided evidence for two or three sub-populations at all proline residues. The changes in the subpopulations induced by binding generally reflected recognition by conformational selection but depended on the residue and the state of the ligand to illuminate distinct mechanisms among the PR ligands. Notably, the spectral data indicate that greater adaptability among the states is associated with reduced recognition specificity and that perturbation to the ensemble populations contributes to differences in binding entropy. Broadly, the study quantifies rapidly interconverting ensembles with residue-specific detail and implicates them in function.
Keyphrases
- single molecule
- binding protein
- molecular dynamics
- molecular dynamics simulations
- amino acid
- genetic diversity
- small molecule
- single cell
- electronic health record
- optical coherence tomography
- magnetic resonance
- computed tomography
- big data
- machine learning
- living cells
- convolutional neural network
- protein protein
- fluorescent probe
- neural network