Minimal NMR distance information for rigidity of protein graphs

Carlile Lavor (1) , Leo Liberti (2) , Bruce Donald (3) , Thérèse Malliavin (4) , Michael Nilges (4)

1 IMECC - Instituto de Matemática, Estatística e Computação Científica [Brésil]
2 LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau]
3 Duke University [Durham]
4 Bioinformatique structurale - Structural Bioinformatics

Nuclear Magnetic Resonance (NMR) experiments provide distances between close atoms of a protein molecule and the problem is how to determine the 3D protein structure by exploiting such distances. We present a new hand-crafted order on the atoms of the protein that uses information from the chemistry of proteins and NMR experiments and allows us to formulate the problem as a combinatorial search. Additionally, this order tell us what kind of NMR distance information is crucial to understand the cardinality of the solution set of the problem and its computational complexity.

Keywords: Vertex orders; Distance geometry; Nuclear magnetic resonance; Molecular structure

Domains: Structural Biology [q-bio.BM]; Bioinformatics [q-bio.QM]; Biophysics

Carlile Lavor, Leo Liberti, Bruce Donald, Thérèse Malliavin, Michael Nilges. Minimal NMR distance information for rigidity of protein graphs. 2018. ⟨hal-01907200v1⟩