Partial alignment of biomolecules: an aid to NMR characterization

Prestegard, James H.; Kishore, A. I.

doi:10.1016/s1367-5931(00)00247-7

Cited by 94 publications

(71 citation statements)

References 65 publications

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“…In this approach, it is necessary to either demonstrate that no significant conformational changes occur upon complex formation or to localize regions where such changes may occur. This can be rapidly assessed by the measurement of residual dipolar couplings, which provide highly sensitive long range orientational information (61)(62)(63)(64)(65).…”

Section: Resultsmentioning

confidence: 99%

Solution Structure of the Phosphoryl Transfer Complex between the Cytoplasmic A Domain of the Mannitol Transporter IIMannitol and HPr of the Escherichia coliPhosphotransferase System

Cornilescu¹,

Lee²,

Cornilescu³

et al. 2002

Journal of Biological Chemistry

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The bacterial phosphoenolpyruvate:sugar phosphotransferase system (1) is a classical example of a signal transduction pathway whereby the transfer of a phosphoryl group through a series of bimolecular protein-protein complexes is coupled with the transport of sugars across the membrane (2-4). The initial events of the cascade involve a common pathway: enzyme I, which is autophosphorylated by phosphoenolpyruvate at His-189 (in Escherichia coli), transfers the phosphoryl group to His-15 (in E. coli) of the histidine-containing phosphocarrier protein (HPr).1 Subsequently, the phosphoryl group on HPr is transferred to a variety of sugar-specific carbohydrate transporters, known as enzymes II (5). The enzymes II are organized into several domains, some of which are covalently linked (5). There are two cytoplasmic domains, IIA and IIB; IIA accepts the phosphoryl group from HPr and then transfers it to IIB. The transmembrane domain IIC (and in some cases IID as well) catalyzes the translocation and phosphoryl transfer from IIB to the incoming sugar. There are five classes of enzymes II as follows: glucose-sucrose, mannitol-fructose, mannose-sorbose, lactose-cellobiose, and glucitol (3, 5). The membranebound IIC domains comprise a variable number of transmembrane helices (5). The IIA and IIB domains for the different sugar classes bear no sequence or structural similarity to one another (6 -15).The bacterial phosphoenolpyruvate:sugar phosphotransferase system provides a paradigm for understanding proteinprotein interactions and the factors governing their specificity. Thus, for example, HPr recognizes enzyme I and the various sugar-specific IIA domains, although all these target proteins are structurally dissimilar. We have recently solved the structures of the complexes between the N-terminal phosphoryl transfer domain of EI (EIN) and HPr (16) and between IIA Glucose (IIA Glc ) and HPr (17). In the present paper, we extend these studies to the solution structure determination of the complex between IIA Mannitol (IIA Mtl ) and HPr. EXPERIMENTAL PROCEDURES Expression Vector for IIAMtl -E. coli chromosomal DNA was used as a template to amplify by PCR the region corresponding to the A domain of the mannitol permease. The forward PCR primer 5Ј-GACAGCTTT-GACGATCATATGGCTAACCTGTTCAAG-3Ј contained an engineered NdeI restriction site (underlined), and the reverse primer 5Ј-TTAAC-CCCACCTTCTCCATGTCGACAGGGTGGGATTGG-3Ј contained an engineered SalI site (underlined). The NdeI-and SalI-cut PCR product was purified and cloned into the corresponding sites of the vector pRE1 * This work was supported in part by the Intramural AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (to G. M. C.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.The

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Section: Resultsmentioning

confidence: 99%

Solution Structure of the Phosphoryl Transfer Complex between the Cytoplasmic A Domain of the Mannitol Transporter IIMannitol and HPr of the Escherichia coliPhosphotransferase System

Cornilescu¹,

Lee²,

Cornilescu³

et al. 2002

Journal of Biological Chemistry

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“…The introduction of partial order to the molecular alignment, by minutely limiting their isotropic tumbling, will resurrect the RDC observable. This partial order can be introduced by either magnetic anisotropy of the molecule (Prestegard et al, 2000), a crystalline aqueous solution (Prestegard & Kishore, 2001), or incorporation of artificial tags with magnetic anisotropy susceptibility such as Lanthanide (Nitz et al, 2004). RDCs are measured relatively easily and represent an abundant source of highly precise information, such as the relative orientations of different inter-nuclear vectors within a molecule.…”

Section: Residual Dipolar Couplings (Rdcs)mentioning

confidence: 99%

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Valafar¹,

Irausquin²

2012

Protein Structure

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“…In addition, pseudoresidues comprise experimental chemical shifts and RDCs. One-bond RDCs are commonly measured from triple-resonance experiments, such as HNCO, Bax et al, 2001;Prestegard and Kishore, 2001) and it is therefore straightforward to add these RDCs to pseudoresidues. Besides the standard output provided by MARS, an alignment tensor is returned that has been optimized during the assignment process together with RDCs back-calculated from the 3D structure.…”

Section: Input and Output Datamentioning

confidence: 99%

“…In case of small proteins, they even allow simultaneous resonance assignment and structure determination (Tian et al, 2001). On the other hand, calculation of RDCs from a known 3D structure is straightforward and has been used previously for validation of protein structures Prestegard and Kishore, 2001). Therefore, an assignment method for proteins can be envisioned where dipolar couplings calculated from a known 3D structure are compared to experimental values.…”

Section: Introductionmentioning

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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Partial alignment of biomolecules: an aid to NMR characterization

Cited by 94 publications

References 65 publications

Solution Structure of the Phosphoryl Transfer Complex between the Cytoplasmic A Domain of the Mannitol Transporter IIMannitol and HPr of the Escherichia coliPhosphotransferase System

Solution Structure of the Phosphoryl Transfer Complex between the Cytoplasmic A Domain of the Mannitol Transporter IIMannitol and HPr of the Escherichia coliPhosphotransferase System

Structure and Dynamics of Proteins from Nuclear Magnetic Resonance Spectroscopy

Backbone assignment of proteins with known structure using residual dipolar couplings

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