Integrative methods in structural biology

Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model

“…This relationship to physical units does not provide any meaningful description of the absolute time scale of characteristic dynamical processes generated by the model, due to a lost connection to the true dynamics . The present study focuses on ensemble-averaged properties of the generated ensembles and does not attempt to calibrate or interpret the generated dynamics, although previous studies with this model have demonstrated the faithful reproduction of kinetic processes for secondary-structure formation. , For each peptide, a single chain was placed in a cubic box with a volume of (20 nm) and simulated without periodic boundary conditions. Thus, no explicit cutoffs were used for the interaction functions described in the previous section.…”

“…Despite lacking stable tertiary structure under physiological conditions, intrinsically disordered proteins (IDPs) are involved in a large number of important biological functions, including intracellular signaling and regulation, and are also associated with a broad range of diseases, including cancer, neurodegenerative diseases, amylidoses, diabetes, and cardiovascular disease. , The experimental characterization of IDPs is complicated by the heterogeneous nature of their disordered conformational ensembles (i.e., conformational distributions), which challenges traditional techniques developed for folded proteins. For example, X-ray crystallography and cryo-EM, which recover high-resolution images of biomolecules in the crystalline or frozen state, are fundamentally inappropriate for characterizing the distribution of relevant IDP conformations . However, techniques including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), single-molecule Förster resonance energy transfer (FRET), dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) are capable of identifying the conformational transitions sampled by IDPs, − since they perform measurements of the protein as it fluctuates within its “natural” environment.…”

“…For example, X-ray crystallography and cryo-EM, which recover high-resolution images of biomolecules in the crystalline or frozen state, are fundamentally inappropriate for characterizing the distribution of relevant IDP conformations. 3 However, techniques including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), single-molecule Forster resonance energy transfer (FRET), dynamic light scattering (DLS), and two-focus fluorescence correlation spectroscopy (2f-FCS) are capable of identifying the conformational transitions sampled by IDPs, 4−7 since they perform measurements of the protein as it fluctuates within its "natural" environment. However, these measurements provide limited resolution in terms of the specification of a unique corresponding microscopic distribution of conformations.…”

Investigating the Conformational Ensembles of Intrinsically-Disordered Proteins with a Simple Physics-Based Model

“…The present study focuses on ensembleaveraged properties of the generated ensembles, and does not attempt to calibrate or interpret the generated dynamics, although previous studies with this model have demonstrated the faithful reproduction of kinetic processes for secondary-structure formation 30,31 . For each peptide, a single chain was placed in a cubic box with a volume of (20 nm) 3 and simulated without periodic boundary conditions. Thus, no explicit cutoffs were used for the interaction functions described in the previous section.…”

“…The experimental characterization of IDPs is complicated by the heterogeneous nature of their disordered conformational ensembles (i.e., conformational distributions), which challenges traditional techniques developed for folded proteins. For example, X-ray crystallography and cryo-EM, which recover high resolution images of biomolecules in the crystalline or frozen state, are fundamentally inappropriate for characterizing the distribution of relevant IDP conformations 3 . On the other hand, techniques including Nuclear Magnetic Resonance (NMR), Small Angle X-ray Scattering (SAXS), single-molecule Förster resonance energy transfer (FRET), dynamic light scattering (DLS) and two-focus fluorescence correlation spectroscopy (2f-FCS) are capable of identifying the conformational transitions sampled by IDPs 4-7 , since they perform measurements of the protein as it fluctuates within its "natural" environment.…”