Quantitative Evaluation of Experimental NMR Restraints

Nabuurs, Sander B.; Spronk, Chris A. E. M.; Krieger, Elmar; Maassen, Hans; Vriend, Gert; Vuister, Geerten W.

doi:10.1021/ja035440f

Cited by 84 publications

(104 citation statements)

References 44 publications

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“…Only NOE, dihedral angle, hydrogen bond, and 3 J HNHA potential energy terms were used as restraints during simulated annealing. Additional potential energy terms were applied during the structure refinement process: radius of gyration (Kuszewski et al 1999), conformational database (Kuszewski et al 1996), and We used the software program QUEEN to assess our NOE distance restraints during the structure calculation process (Nabuurs et al 2003(Nabuurs et al , 2006. QUEEN allowed us to sort the restraints by unique information content for systematic evaluation.…”

Section: Structure Calculationsmentioning

confidence: 99%

NMR structure of the pseudo‐receiver domain of CikA

et al. 2007

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The circadian input kinase (CikA) is a major element of the pathway that provides environmental information to the circadian clock of the cyanobacterium Synechococcus elongatus. CikA is a polypeptide of 754 residues and has three recognizable domains: GAF, histidine protein kinase, and receiver-like. This latter domain of CikA lacks the conserved phospho-accepting aspartyl residue of bona fide receiver domains and is thus a pseudo-receiver (PsR). Recently, it was shown that the PsR domain (1) attenuates the autokinase activity of CikA, (2) is necessary to localize CikA to the cell pole, and (3) is necessary for the destabilization of CikA in the presence of the quinone analog 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB). The solution structure of the PsR domain of CikA, CikAPsR, is presented here. A model of the interaction between the PsR domain and HPK portion of CikA provides a potential explanation for how the PsR domain attenuates the autokinase activity of CikA. Finally, a likely quinone-binding surface on CikAPsR is shown here.

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Section: Structure Calculationsmentioning

confidence: 99%

NMR structure of the pseudo‐receiver domain of CikA

et al. 2007

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“…Each of the 20 lowest target function conformers was energy-minimized in explicit solvent with the program AMBER-8 [17]. Table S3 reports statistics on restraint violations in the final structure together with selected quality parameters [18][19][20].…”

Section: Nmr Experiments and Structure Calculations Of Mmp-20-nngh Comentioning

confidence: 99%

Catalytic domain of MMP20 (Enamelysin) – The NMR structure of a new matrix metalloproteinase

Arendt¹,

Banci

Bertini

et al. 2007

FEBS Letters

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The solution structure of the catalytic domain of MMP-20, a member of the matrix metalloproteinases family not yet structurally characterized, complexed with N-Isobutyl-N-(4-methoxyphenylsulfonyl)glycyl hydroxamic acid (NNGH), is here reported and compared with other MMPs-NNGH adducts. The backbone dynamic has been characterized as well. We have found that, despite the same fold and very high overall similarity, the present structure experiences specific structural and dynamical similarities with some MMPs and differences with others, around the catalytic cavity. The present solution structure, not only contributes to fill the gap of structural knowledge on human MMPs, but also provides further information to design more selective and efficient inhibitors for a specific member of this class of proteins.

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“…Relationships between the restraints and the influence they can have to each other are also analyzed, as the internal consistency of RDCs [190] and of the NMR restraints [191], the relationship between the hydrogen bonds and the RDCs [192]. The internal consistency of NMR restraints was studied from the point of view of information theory [193]. The maximum likelihood model provides a frame [194] to analyze the propagation of errors from the restraints to the atomic coordinates.…”

Section: Structure Qualitymentioning

confidence: 99%

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

Malliavin

2006

COC

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Nuclear Magnetic Resonance (NMR) became during the two last decades an important method for biomolecular structure determination. NMR permits to study biomolecules in solution and gives access to the molecular flexibility at atomic level on a complete structure: in that respect, it is occupying a unique place i n structural biology. During the first years of its development, NMR was trying to meet the requirements previously defined in X-ray crystallography. But, NMR then started to determine its own criteria for the definition of a structure. Indeed, the atomic coordinates of an NMR structure are calculated using restraints on geometrical parameters (angles and distances) of the structure, which are only indirectly related to atom positions: in that respect, NMR and X-ray crystallography are very different. The indirect relation between the NMR measurements and the molecular structure and dynamics makes critical the precision and the interpretation of the NMR parameters and the development of quantitative analysis methods. The methods published since 1997 for liquid-NMR of proteins are reviewed here. First, methods for structure determination are presented, as well as methods for spectral assignment and for structure quality assessment. Second, the quantitative analysis of structure mobility i s reviewed.

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Quantitative Evaluation of Experimental NMR Restraints

Cited by 84 publications

References 44 publications

NMR structure of the pseudo‐receiver domain of CikA

NMR structure of the pseudo‐receiver domain of CikA

Catalytic domain of MMP20 (Enamelysin) – The NMR structure of a new matrix metalloproteinase

Quantitative Analysis of Biomolecular NMR Spectra: A Prerequisite for the Determination of the Structure and Dynamics of Biomolecules

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