Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions

Hansen, Mark; Mueller, Luciano; Pardi, Arthur

doi:10.1038/4176

Cited by 749 publications

(757 citation statements)

References 30 publications

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“…Both samples were extensively dialyzed against the same buffer, which contained 10 mM NaCl, 10 mM potassium phosphate, and 0.02 mM EDTA in 99% D 2 O, at pH 6.8 (direct meter reading in D 2 O). One of the two samples additionally contained 22 mg/mL Pf1, which serves as the liquid crystalline alignment medium (Hansen et al, 1998). The isotropic sample also was uniformly enriched in 15 N. Using 15 N decoupling, as indicated in the pulse schemes, all described methods work equally well in the presence or absence of 15 N enrichment.…”

Section: Methodsmentioning

confidence: 99%

“…bax@nih.gov the introduction of isotopic enrichment procedures for RNA and DNA (Batey et al, 1992;Nikonowicz et al, 1992;Ono et al, 1994;Farmer et al, 1995;Zimmer and Crothers, 1995;Masse et al, 1998) and methods for weakly aligning nucleic acids relative to the magnetic field (Kung et al, 1995;Tjandra and Bax, 1997;Clore et al, 1998;Hansen et al, 1998;Ruckert and Otting, 2000;Sass et al, 2000;Tycko et al, 2000;Chou et al, 2001;Ishii et al, 2001;Meier et al, 2002;Ulmer et al, 2003), residual dipolar coupling (RDC) restraints are now also available. RDCs are particularly useful in nucleic acids, where the number of NOE restraints is typically relatively low, especially those involving long-range contacts.…”

Section: Introductionmentioning

confidence: 99%

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Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

et al. 2004

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New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond 2 D CH couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in 13 C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear 1 H-1 H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven 1 H-13 C and 13 C-13 C couplings are measured for pyrimidines (U and C), including 1 ). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than ±3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one-and two-bond J couplings cluster very tightly for each type of nucleotide.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

et al. 2004

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“…Labeled protein was obtained by growing cells in 1 L of LB to an OD of 0.7, followed by pelleting the cells and transferring them to 0.75 L of isotope labeled M9 as described [24]. 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].…”

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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“…94.3 62.6 0.0 a RDCs were measured for MBP dissolved in Pf1 bacteriophage (Hansen et al, 1998;Yang et al, 1999). b Chemical shifts used for establishing sequential connectivity.…”

Section: Alignment Tensor Determinationmentioning

confidence: 99%

Backbone assignment of proteins with known structure using residual dipolar couplings

Jung

Zweckstetter

2004

J Biomol NMR

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A prerequisite for NMR studies of protein-ligand interactions or protein dynamics is the assignment of backbone resonances. Here we demonstrate that protein assignment can significantly be enhanced when experimental dipolar couplings (RDCs) are matched to values back-calculated from a known three-dimensional structure. In case of small proteins, the program MARS allows assignment of more than 90% of backbone resonances without the need for sequential connectivity information. For bigger proteins, we show that the combination of sequential connectivity information with RDC-matching enables more residues to be assigned reliably and backbone assignment to be more robust against missing data. Structural or dynamic deviations from the employed 3D coordinates do not lead to an increased error rate in RDC-supported assignment. RDC-enhanced assignment is particularly useful when chemical shifts and sequential connectivity only provide a few reliable assignments.

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Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions

Cited by 749 publications

References 30 publications

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

Resolution-optimized NMR measurement of 1DCH, 1DCC and 2DCH residual dipolar couplings in nucleic acid bases

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

Backbone assignment of proteins with known structure using residual dipolar couplings

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