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. 2019 Mar 15:256:91-104.
doi: 10.1016/j.dam.2018.03.071. Epub 2018 Apr 26.

Minimal NMR distance information for rigidity of protein graphs

Carlile Lavor  1 , Leo Liberti  2 , Bruce Donald  3 , Bradley Worley  4   5 , Benjamin Bardiaux  4   5 , Thérèse E Malliavin  4   5 , Michael Nilges  4   5
Affiliations

Minimal NMR distance information for rigidity of protein graphs

Carlile Lavor et al. Discrete Appl Math. .

Abstract

Nuclear Magnetic Resonance (NMR) experiments provide distances between nearby atoms of a protein molecule. The corresponding structure determination problem is to determine the 3D protein structure by exploiting such distances. We present a new order on the atoms of the protein, based on information from the chemistry of proteins and NMR experiments, which allows us to formulate the problem as a combinatorial search. Additionally, this order tells 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: Distance geometry; Molecular structure; Nuclear magnetic resonance; Vertex orders.

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Figures

Fig. 1
Fig. 1
Cartesian and internal coordinates.
Fig. 2
Fig. 2
Protein backbone.
Fig. 3
Fig. 3
Geometric interpretation of branching in BP.
Fig. 4
Fig. 4
The hc order.
Fig. 5
Fig. 5
Peptide plane.
Fig. 6
Fig. 6
Chirality property.
See this image and copyright information in PMC

References

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