Mapping the potential energy landscape of intrinsically disordered proteins at amino acid resolution.
Intrinsically disordered regions are predicted to exist in a significant fraction of proteins encoded in eukaryotic genomes. The high levels of conformational plasticity of this class of proteins endows them with unique capacities to act in functional modes not achievable by folded proteins, but also places their molecular characterization beyond the reach of classical structural biology. New techniques are therefore required to understand the relationship between primary sequence and biological function in this class of proteins. Although dependences of some NMR parameters such as chemical shifts (CSs) or residual dipolar couplings (RDCs) on structural propensity are known, so that sampling regimes are often inferred from experimental observation, there is currently no framework that allows for a statistical mapping of the available Ramachandran space of each amino acid in terms of conformational propensity. In this study we develop such an approach, combining highly efficient conformational sampling with ensemble selection to map the backbone conformational sampling of IDPs on a residue specific level. By systematically analyzing the ability of NMR data to map the conformational landscape of disordered proteins, we identify combinations of RDCs and CSs that can be used to raise conformational degeneracies inherent to different data types, and apply these approaches to characterize the conformational behavior of two intrinsically disordered proteins, the K18 domain from Tau protein and N(TAIL) from measles virus nucleoprotein. In both cases, we identify the enhanced populations of turn and helical regions in key regions of the proteins, as well as contiguous strands that show clear and enhanced polyproline II sampling.
CEA, CNRS, and UJF-Grenoble 1, Protein Dynamics and Flexibility, Institut de Biologie Structurale Jean-Pierre Ebel, 41 Rue Jules Horowitz, Grenoble 38027, France.
Valéry
V
Ozenne
Robert
R
Schneider
Mingxi
M
Yao
Jie-rong
JR
Huang
Loïc
L
Salmon
Markus
M
Zweckstetter
Malene Ringkjøbing
MR
Jensen
Martin
M
Blackledge
D000596:Amino Acids / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D009698:Nucleoproteins / Q000737:chemistry*; D011487:Protein Conformation; D016875:tau Proteins / Q000737:chemistry*
D000596:Amino Acids; D009698:Nucleoproteins; D016875:tau Proteins