Order Matrix Analysis of Residual Dipolar Couplings Using Singular Value Decomposition

Losonczi, Judit; Andrec, Michael; Fischer, Mark W. F.; Prestegard, James H.

doi:10.1006/jmre.1999.1754

Cited by 555 publications

(630 citation statements)

References 29 publications

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“…A set of such couplings provides orientational constraints that allow the determination of a preferred orientation of molecules or domains in the anisotropic medium. Comparing the alignment tensors of individual domains in domain pairs provides a sensitive measure of interdomain orientation (44).…”

Section: Sh3 and Sh2 Domain Communication By Ligand-bindingmentioning

confidence: 99%

Binding, Domain Orientation, and Dynamics of the Lck SH3−SH2 Domain Pair and Comparison with Other Src-Family Kinases

et al. 2005

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The catalytic activity of Src-family kinases is regulated by association with its SH3 and SH2 domains. Activation requires displacement of intermolecular contacts by SH3/SH2 binding ligands resulting in dissociation of the SH3 and SH2 domains from the kinase domain. To understand the contribution of the SH3-SH2 domain pair to this regulatory process, the binding of peptides derived from physiologically relevant SH2 and SH3 interaction partners was studied for Lck and its relative Fyn by NMR spectroscopy. In contrast to Fyn, activating ligands do not induce communication between SH2 and SH3 domains in Lck. This can be attributed to the particular properties of the Lck SH3-SH2 linker which is shown to be extremely flexible thus effectively decoupling the behavior of the SH3 and SH2 domains. Measurements on the SH32 tandem from Lck further revealed a relative domain orientation that is distinctly different from that found in the Lck SH32 crystal structure and in other Src kinases. These data suggest that flexibility between SH2 and SH3 domains contributes to the adaptation of Src-family kinases to specific environments and distinct functions.

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Section: Sh3 and Sh2 Domain Communication By Ligand-bindingmentioning

confidence: 99%

Binding, Domain Orientation, and Dynamics of the Lck SH3−SH2 Domain Pair and Comparison with Other Src-Family Kinases

et al. 2005

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“…Isotopically labeled M9 contained either 15 in 12 mg/mL pf1 phage [41]. Tensor parameters were determined from histogram plots of the couplings [42] and values based on intermediate structures [43,44]. The magnitude of the alignment tensor and rhombicity were set to -13.…”

Section: Methodsmentioning

confidence: 99%

NMR structure of the N-terminal domain of the replication initiator protein DnaA

Lowery

Chandonia

Kim

et al. 2007

J Struct Funct Genomics

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DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1 -100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/-0.2 Å based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.Keywords: replication, DnaB, DiaA, ATPase, initiation Page 2 12/12/06The bacterial protein DnaA plays a central role in the initiation of chromosomal replication and is involved in the activation and repression of several genes, including its own gene (dnaA) in E.coli. Replication begins with the formation of oligomers of DnaA on recognition sites at the origin of replication (OriC). The DnaA complex unwinds and opens several AT-rich segments of doublestranded DNA within the origin and stabilizes the resulting single-strands. DnaA then recruits the DnaB helicase with help from DnaC to form the "prepriming complex" [1]. After priming of the singlestranded DNA, replication occurs by the action of DNA Polymerase III. ATP hydrolysis acts as the switch between active (ATP-bound) and inactive (ADP-bound) forms of DnaA. Initiation begins only with the ATP-bound form (for reviews see [2][3][4] , as well as domain IV bound to DNA [8] showed that domain III resembles other members of the AAA+ family of ATPases, and that domain IV adopts a helix-turn-helix DNA-binding fold. In contrast, the secondary structure of domain I has been predicted based on multiple sequence alignments [5,9,10], however, little is known about its tertiary structure.DnaA recognizes five high affinity 9 base pair sites as well as several lower affinity 6 base pair sites within OriC via the C-terminal helix-turn-helix DNA-binding domain (domain IV) [11,12]. In addition to direct binding, the formation of oligomers containing 20 to 30 molecules of DnaA at the origin has been demonstrated by electron microscopy [13,14]. The mechanism of oligomer formation has been studied extensively [3,15], but the nature of the complex remains poorly understood.Replacement of the dimerization domain of the lambda cI repressor with the N-terminal domain of DnaA resulted in a functional chimeric protein, suggesting direct interactions between the N-terminal ...

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“…27 The actual number of equations depends on the experimentally available number of residual dipolar couplings in which corresponding internuclear vectors are not collinear. …”

Section: Order Tensor Approachmentioning

confidence: 99%

Determining the Stereochemistry of Molecules from Residual Dipolar Couplings (RDCs)

Böttcher

Thiele

2012

Encyclopedia of Magnetic Resonance

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Residual dipolar couplings (RDCs) have recently revolutionized the structure determination of biological macromolecules by NMR spectroscopy. Their utility in the structure determination of small/medium-sized organic compounds is more and more recognized. The questions arising in organic compounds are completely different from biomolecular NMR. Especially, the determination of the stereochemistry (relative configuration and diastereotopic assignments) is the focus of this article. A short overview on how to introduce the anisotropic environment necessary to measure RDCs and the applications for the determination of relative configurations in rigid and moderately flexible compounds are given together with the description of the theoretical background for interpreting the data. Since the area of alignment media for organic compounds and the applications to flexible compounds are developing extremely fast, this article can be viewed as momentary picture only.

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Order Matrix Analysis of Residual Dipolar Couplings Using Singular Value Decomposition

Cited by 555 publications

References 29 publications

Binding, Domain Orientation, and Dynamics of the Lck SH3−SH2 Domain Pair and Comparison with Other Src-Family Kinases

Binding, Domain Orientation, and Dynamics of the Lck SH3−SH2 Domain Pair and Comparison with Other Src-Family Kinases

NMR structure of the N-terminal domain of the replication initiator protein DnaA

Determining the Stereochemistry of Molecules from Residual Dipolar Couplings (RDCs)

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