Orienting molecular fragments and molecules with residual dipolar couplings

Nikolai R. Skrynnikov

doi:10.1016/j.crhy.2004.02.006

Orienting molecular fragments and molecules with residual dipolar couplings
[Orienter des fragments moléculaires et des molécules grâce aux couplages dipolaires résiduels]

Présenté par : Guy Laval

Nikolai R. Skrynnikov ¹

¹ Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA

Comptes Rendus. Physique, Volume 5 (2004) no. 3, pp. 359-375.

Résumé
Abstract

Les protéines et les acides nucléiques, tout comme leurs complexes, sont constitués de différents domaines dont la structure est souvent connue. Toutefois, la connaissance de la position relative de ces éléments reste souvent peu précise. Une bonne solution à ce problème consiste à exploiter les couplages dipolaires résiduels (RDCs) mesurés par des techniques de RMN en solution, en utilisant des échantillons faiblement orientés. En s'appuyant sur une approche basée sur des fragments rigides, l'orientation relative des différents éléments structuraux peut être optimisée afin d'être en accord avec les données de RDCs. Cet article explique pourquoi cette approche est bien adaptée à leur exploitation et discute son implémentation. Des exemples d'une telle approche appliquée à des fragments de protéines, à des hélices d'ARN, à des protéines multidomaines, à des systèmes ligand-protéine ou encore à des complexes de protéines sont décrits en détails. La discussion comprend également le cas des systèmes en équilibre conformationnel. Les différentes dégénérescences inhérentes aux couplages dipolaires résiduels sont considérées ainsi que les méthodes permettant de lever ces ambiguités.

Many proteins and nucleic acids, as well as their complexes, consist of structural units with a known internal structure. However, relative position of these units within the entity is often a subject of uncertainty. This problem can be effectively addressed with the help of residual dipolar couplings (RDCs) measured by solution-state NMR in weakly oriented samples. Using a rigid-body approach, the relative orientation of the structural units can be adjusted to match the experimental RDC data. This paper explains why the rigid-body approach is well suited for application with the RDC data and discusses the general algorithm suitable for such studies. The examples of RDC-based rigid-body treatment involving protein backbone fragments, RNA helices, multidomain proteins, protein-ligand systems, and protein complexes are described in detail. The discussion includes systems where multiple structures co-exist in a dynamic equilibrium. Various degeneracies associated with the RDC data are considered and the methods that can assist in resolving the ambiguities are described.

Publié le : 2004-04-01

DOI : 10.1016/j.crhy.2004.02.006

Keywords: Residual dipolar couplings, Solution-state NMR
Mot clés : Couplages dipolaires résiduels, RMN en solution

Affiliations des auteurs :

Nikolai R. Skrynnikov ¹

¹ Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084, USA

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     author = {Nikolai R. Skrynnikov},
     title = {Orienting molecular fragments and molecules with residual dipolar couplings},
     journal = {Comptes Rendus. Physique},
     pages = {359--375},
     publisher = {Elsevier},
     volume = {5},
     number = {3},
     year = {2004},
     doi = {10.1016/j.crhy.2004.02.006},
     language = {en},
}

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Nikolai R. Skrynnikov. Orienting molecular fragments and molecules with residual dipolar couplings. Comptes Rendus. Physique, Volume 5 (2004) no. 3, pp. 359-375. doi : 10.1016/j.crhy.2004.02.006. https://comptes-rendus.academie-sciences.fr/physique/articles/10.1016/j.crhy.2004.02.006/

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