Looking for central tendencies in the conformational freedom of proteins using NMR measurements

DOI10.1088/1361-6420/AA54EAMaRDI QIDQ2965693zbMATH OpenOpenAlexFDO

Authors Luca Sgheri, Fabrizio Clarelli

Publication date 3 March 2017

Published in Inverse Problems (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1602.05953

zbMATH Keywords

protein foldingparamagnetic NMRunderdetermined problems

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Abstract: We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for the calculation of the Maximum Allowable Probability is proposed, which can be extended to any type of measurements. In this paper we use Pseudo Contact Shifts and Residual Dipolar Coupling. We reconstruct a single central tendency in the distribution and discuss in depth the results.

Recommendations

• Conformational freedom of proteins and the maximal probability of sets of orientations
• Efficient determination of the most favoured orientations of protein domains from paramagnetic NMR data
• Joining RDC data from flexible protein domains
• Reconstruction of orientations of a moving protein domain from paramagnetic data
• Minimal NMR distance information for rigidity of protein graphs

Cites work

• scientific article; zbMATH DE number 236854 (Why is no real title available?)
• Conformational freedom of proteins and the maximal probability of sets of orientations
• Convex hulls of orbits and orientations of a moving protein domain
• Efficient determination of the most favoured orientations of protein domains from paramagnetic NMR data
• On Information and Sufficiency
• Reconstruction of orientations of a moving protein domain from paramagnetic data
• Uniqueness and degeneracy in the localization of rigid structural elements in paramagnetic proteins

Cited in

(5)

• Reconstruction of orientations of a moving protein domain from paramagnetic data
• Conformational freedom of proteins and the maximal probability of sets of orientations
• Efficient determination of the most favoured orientations of protein domains from paramagnetic NMR data
• Sampling of conformation space in torsion angle dynamics calculations
• Joining RDC data from flexible protein domains

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