Minimal NMR distance information for rigidity of protein graphs

Carlile Lavor; Leo Liberti; Bruce Donald; Bradley Worley; Benjamin Bardiaux; Thérèse E. Malliavin; Michael Nilges

doi:10.1016/j.dam.2018.03.071

Minimal NMR distance information for rigidity of protein graphs

Carlile Lavor
, Leo Liberti
, Bruce Donald
, Bradley Worley
, Benjamin Bardiaux
, Thérèse E. Malliavin
, Michael Nilges

University of Campinas (UNICAMP)
Duke University
Structural Bioinformatics Unit
Institut Pasteur, Paris
Centre national de la recherche scientifique

Research output: Contribution to journal › Article › peer-review

34 Citations (Scopus)

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.

Original language	English
Pages (from-to)	91-104
Number of pages	14
Journal	Discrete Applied Mathematics
Volume	256
DOIs	https://doi.org/10.1016/j.dam.2018.03.071
Publication status	Published - 15 Mar 2019

Keywords

Distance geometry
Molecular structure
Nuclear magnetic resonance
Vertex orders

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10.1016/j.dam.2018.03.071

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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.",

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T1 - Minimal NMR distance information for rigidity of protein graphs

AU - Lavor, Carlile

AU - Liberti, Leo

AU - Donald, Bruce

AU - Worley, Bradley

AU - Bardiaux, Benjamin

AU - Malliavin, Thérèse E.

AU - Nilges, Michael

PY - 2019/3/15

Y1 - 2019/3/15

N2 - 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.

AB - 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.

KW - Distance geometry

KW - Molecular structure

KW - Nuclear magnetic resonance

KW - Vertex orders

U2 - 10.1016/j.dam.2018.03.071

DO - 10.1016/j.dam.2018.03.071

M3 - Article

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SN - 0166-218X

VL - 256

SP - 91

EP - 104

JO - Discrete Applied Mathematics

JF - Discrete Applied Mathematics

ER -

Minimal NMR distance information for rigidity of protein graphs

Abstract

Keywords

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