MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data

摘要

MERA (Maximum Entropy Ramachandran map Analysis from NMR data) is a new webserver that generates residue-by-residue Ramachandran map distributions for disordered proteins or disordered regions in proteins on the basis of experimental NMR parameters. As input data, the program currently utilizes up to 12 different parameters. These include three different types of short-range NOEs, three types of backbone chemical shifts (N-15, C-13(alpha), and C-13'), six types of J couplings ((3)J(HNH alpha), (3)J(C'C'), (3)J(C'H alpha), (1)J(H alpha C alpha), (2)J(C alpha N) and (1)J(C alpha N)), as well as the N-15-relaxation derived J(0) spectral density. The Ramachandran map distributions are reported in terms of populations of their 15A degrees A xA 15A degrees voxels, and an adjustable maximum entropy weight factor is available to ensure that the obtained distributions will not deviate more from a newly derived coil library distribution than required to account for the experimental data. MERA output includes the agreement between each input parameter and its distribution-derived value. As an application, we demonstrate performance of the program for several residues in the intrinsically disordered protein alpha-synuclein, as well as for several static and dynamic residues in the folded protein GB3.