A novel approach for assesing macromolecular complexes combining soft‐docking calculations with NMR data

Morelli, Xavier; Palma, P. Nuno; Guerlesquin, Françoise; Rigby, Alan C.

doi:10.1110/ps.07501

Cited by 52 publications

(63 citation statements)

References 48 publications

(71 reference statements)

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“…The docking algorithm BiGGER is particularly well suited for these analyses because of its ability to use NMR chemical shift perturbation results as information to filter suitable models (33,34). The BiGGER docking algorithm requires no information that constrains the orientation of the docking partners and, therefore, represents a fairly unbiased approach for using NMR data to model the tetramer interactions.…”

Section: Discussionmentioning

confidence: 99%

“…Molecular Modeling-Molecular modeling of the surfaces of interaction was accomplished using the BiGGER soft-docking algorithm (33,34) using the unbound structures of Ub (target) (35) and the hUbc13⅐hMms2 heterodimer (probe) (26). The BiGGER algorithm systematically searches the complete six-dimensional binding spaces of both target and probe and then evaluates these solutions in terms of a global scoring function consisting of geometric complementarity, electrostatic interactions, desolvation energy, and the pairwise propensities of amino acid side chains to interact across molecular interfaces.…”

Section: Methodsmentioning

confidence: 99%

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An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13

McKenna

Moraes

Pastushok

et al. 2003

Journal of Biological Chemistry

121

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A heterodimer composed of the catalytically active ubiquitin-conjugating enzyme hUbc13 and its catalytically inactive paralogue, hMms2, forms the catalytic core for the synthesis of an alternative type of multiubiquitin chain where ubiquitin molecules are tandemly linked to one another through a Lys-63 isopeptide bond. This type of linkage, as opposed to the more typical Lys-48-linked chains, serves as a non-proteolytic marker of protein targets involved in error-free postreplicative DNA repair and NF-B signal transduction. Using a two-dimensional 1 H-15 N NMR approach, we have mapped: 1) the interaction between the subunits of the human Ubc13⅐Mms2 heterodimer and 2) the interactions between each of the subunits or heterodimer with a non-covalently bound acceptor ubiquitin or a thiolesterlinked donor ubiquitin. Using these NMR-derived constraints and an unbiased docking approach, we have assembled the four components of this catalytic complex into a three-dimensional model that agrees well with its catalytic function.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13

McKenna

Moraes

Pastushok

et al. 2003

Journal of Biological Chemistry

121

View full text Add to dashboard Cite

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“…[11,12] Experimental results derived from NMR chemical-shift perturbations were used as constraints. A new algorithm was applied, which restricts the docking search from the start so that all models generated fit the constraints.…”

Section: Docking Calculationsmentioning

confidence: 99%

Pseudoazurin–Nitrite Reductase Interactions

2005

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The nitrite reductase-binding site on pseudoazurin has been determined by using NMR chemical-shift perturbations. It comprises residues in the hydrophobic patch surrounding the exposed copper ligand His81 as well as several positively charged residues. The binding site is similar for both redox states of pseudoazurin, despite differences in the binding mode. The results suggest that pseudoazurin binds in a well-defined orientation. Docking simulations provide a putative structure of the complex with a binding site on nitrite reductase that has several hydrophobic and polar residues as well as a ridge of negatively charged side chains and a copper-to-copper distance of 14 A.

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“…Recently, AIRs were supplemented with RDCs in the docking procedure [293] and the resulting complex structures were cross-validated using orientation-dependent 15 N relaxation data [286]. Similarly, structural models of a molecular complex obtained by docking of known substructures have been filtered and ranked a posteriori based on compliance with experimental CSP [294] and RDC data [295].…”

Section: Data-driven Dockingmentioning

confidence: 99%

Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules

Stangler¹,

Hartmann²,

Willbold³

et al. 2006

Zeitschrift für Physikalische Chemie

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Solution NMR / Structure / Dynamics / InteractionsHigh resolution liquid state nuclear magnetic resonance spectroscopy (NMR) is a powerful technique for in vitro studies of structure and dynamics of soluble biological macromolecules under physiological conditions. The unique combination of atomically resolved structural data with both local and global dynamic features covering the entire range of time scales from picoseconds to seconds makes NMR the method of choice in a very diverse and rapidly growing array of biochemical, biomedical, and pharmaceutical applications. After briefly introducing the basic principles of liquid state NMR we review recent methodological and instrumental advances in the field of biologically focused high resolution NMR. The main emphasis of the second part is on molecular interactions. Such interactions are fundamental for the function of proteins in living systems, e.g. for signal transduction, enzymatic catalysis, and immune defense. The tremendous opportunities of high resolution NMR in the identification and detailed characterization of the sites and modes of molecular interactions will be demonstrated.

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A novel approach for assesing macromolecular complexes combining soft‐docking calculations with NMR data

Cited by 52 publications

References 48 publications

An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13

An NMR-based Model of the Ubiquitin-bound Human Ubiquitin Conjugation Complex Mms2·Ubc13

Pseudoazurin–Nitrite Reductase Interactions

Modern High Resolution NMR for the Study of Structure, Dynamics and Interactions of Biological Macromolecules

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