[2] Measurement of homo- and heteronuclear J couplings from quantitative J correlation

Bax, Ad; Vuister, Geerten W.; Grzesiek, Stephan; Delaglio, Frank; Wang, Andy C.; Tschudin, Rolf; Zhu, Guang

doi:10.1016/s0076-6879(94)39004-5

Cited by 420 publications

(315 citation statements)

References 27 publications

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“…The cDNA encoding the mature form of DEN2C (amino acids 1-100) from the PR-159S1 strain of DEN2 (11) was cloned into the pET30a (Novagen) expression plasmid. Expression of uniformly 15 N͞ 13 C and 15 N-labeled proteins were accomplished by growth in M9 minimal media containing 15 NH 4 Cl (1 g͞liter) with or without 13 C 6 -glucose (2 g͞liter, Spectra Stable Isotopes, Columbia MD), respectively. Purification of DEN2C was performed as described (10).…”

Section: Methodsmentioning

confidence: 99%

“…All NMR spectra were acquired at 300 K (unless stated otherwise) on a Varian Inova 600 spectrometer equipped with 5-mm [ 1 H, 15 N, 13 C] triple-resonance z axis pulsed-field gradient probes. Backbone assignments were made by using standard triple-resonance experiments 3D HNCACB, CBCA(CO)NH, C(CO)NH, HC(CO)NH, and 2D 15 N heteronuclear single quantum coherence, 2D constant time 13 C heteronuclear single quantum coherence recorded on uniformly 15 N͞ 13 C-labeled DEN2C. Side-chain assignments were obtained from 3D HCCH-TOCSY spectrum.…”

Section: Methodsmentioning

confidence: 99%

“…Proton-proton distance constraints were derived from 3D 13 (13,14). Restraints for torsion angles were derived from 3 J HNH ␣ measured from a 3D HNHA-J spectrum (15). NMR data were processed with NMRPIPE (16) and were analyzed in SPARKY (T. D. Goddard and D. G. Kneller, University of California, San Francisco).…”

Section: Methodsmentioning

confidence: 99%

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Solution structure of dengue virus capsid protein reveals another fold

Jones

Groesch

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

302

419

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Dengue virus is responsible for Ϸ50 -100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.D engue virus, a member of the flavivirus genus of enveloped RNA viruses, is one of the most significant mosquito-borne viral pathogens, given the impact of the recent resurgence of dengue fever and dengue hemorrhagic fever (1). Other members of the flavivirus genus are also important human pathogens and include such viruses as yellow fever, West Nile virus, and Japanese encephalitis (2). The structure of dengue virus was recently described by using cryo-electron microscopy, which permitted visualization of certain viral protein components (3). The organization of the major envelope glycoprotein (E) in the virion was obtained by fitting the atomic structure of the ectodomain from the related tick-borne encephalitis (TBE) E protein into the outermost layer of density (4). Density internal to the E ectodomain demonstrated a host-derived lipid bilayer with transmembrane helices from E and the small structural protein M (5). Interior to the bilayer is the nucleocapsid core that comprises multiple copies of the capsid, or core, protein (C) and a single 10.7-kb genome RNA. Surprisingly, the organization of the C protein within the nucleocapsid core layer is not discernable. The lack of strong density for C may suggest a rather unique architecture of the flavivirus nucleocapsid core that is distinct from the structural organization of morphologically related viruses such as alphaviruses, a genus in the Togaviridae family of mosquito-borne viruses.The dengue C protein is essential in virus assembly to ensure specific encapsidation of the viral genome. The critical role of C is evident from the existence of subviral particles that are released from infected cells but lack C protein and genome RNA (6). The me...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Solution structure of dengue virus capsid protein reveals another fold

Jones

Groesch

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

302

419

View full text Add to dashboard Cite

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“…The 2D HNCG arom, HN(CO)CG arom, and HNCG were used to determine intraresidue 3 J NC␥ and 3 J CЈC␥ (22,26). Other 3 J couplings involved in a methyl group were measured by using quantitative J correlation experiments (27). The measured coupling constants were used to derive torsion angle constraints.…”

Section: Methodsmentioning

confidence: 99%

Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein

Feng

Zeng

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

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Werner syndrome (WS) is an autosomal recessive disease that results in premature aging. Mutations in the WS gene (WRN) result in a loss of expression of the WRN protein and predispose WS patients to accelerated aging. As a helicase and a nuclease, WRN is unique among the five human RecQ helicase family members and is capable of multiple functions involved in DNA replication, repair, recombination, and telomere maintenance. A 144-residue fragment of WRN was previously determined to be a multifunctional DNA-and protein-binding domain (DPBD) that interacts with structure-specific DNA and a variety of DNA-processing proteins. In addition, DPBD functions as a nucleolar targeting sequence of WRN. The solution structure of the DPBD, the first of a WRN fragment, has been solved by NMR. DPBD consists of a winged helix-like motif and an unstructured C-terminal region of Ϸ20 aa. The putative DNA-binding surface of DPBD has been identified by using known structural and biochemical data. Based on the structural data and on the biochemical data, we suggest a surface on the DPBD for interacting with other proteins. In this structural model, a single winged helix domain binds to both DNA and other proteins. Furthermore, we propose that DPBD functions as a regulatory domain to regulate the enzymatic activity of WRN and to direct cellular localization of WRN through protein-protein interaction.DNA-and protein-binding domain ͉ functional regulation ͉ NMR structure ͉ winged helix

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“…NOE interproton distance restraints were derived from three-dimensional 15 N-, 13 C-, and 13 C/ 13 C-separated NOE and four-dimensional 13 C/ 13 C-separated NOE experiments. Three-bond J couplings ( 3 J HNH␣ , 3 J NC␥ , and 3 J CЈ-C␥ couplings) were measured using quantitative J correlation spectroscopy (36). Stereospecific assignment of valine and leucine methyl groups were derived from an analysis of cross-peak multiplet patterns in a high resolution 1 H-13 C correlation spectrum recorded on a fractionally (10%) 13 C-labeled sample of IIB mtl (37).…”

Section: Methodsmentioning

confidence: 99%

Three-dimensional Solution Structure of the Cytoplasmic B Domain of the Mannitol Transporter IIMannitol of the Escherichia coli Phosphotransferase System

Legler

Cai

Peterkofsky

et al. 2004

Journal of Biological Chemistry

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The solution structure of the cytoplasmic B domain of the mannitol (Mtl) transporter (II Mtl ) from the mannitol branch of the Escherichia coli phosphotransferase system has been solved by multidimensional NMR spectroscopy with extensive use of residual dipolar couplings. The ordered IIB Mtl domain (residues 375-471 of II Mtl ) consists of a four-stranded parallel ␤-sheet flanked by two helices (␣ 1 and ␣ 3 ) on one face and helix ␣ 2 on the opposite face with a characteristic Rossmann fold comprising two right-handed ␤ 1 ␣ 1 ␤ 2 and ␤ 3 ␣ 2 ␤ 4 motifs. The active site loop is structurally very similar to that of the eukaryotic protein tyrosine phosphatases, with the active site cysteine (Cys-384) primed in the thiolate state (pK a < 5.6) for nucleophilic attack at the phosphorylated histidine (His-554) of the IIA Mtl domain through stabilization by hydrogen bonding interactions with neighboring backbone amide groups at positions i ؉ 2/3/4 from Cys-384 and with the hydroxyl group of Ser-391 at position i ؉ 7. Modeling of the phosphorylated state of IIB Mtl suggests that the phosphoryl group can be readily stabilized by hydrogen bonding interactions with backbone amides in the i ؉ 2/4/5/6/7 positions as well as with the hydroxyl group of Ser390 at position i ؉ 6. Despite the absence of any significant sequence identity, the structure of IIB Mtl is remarkably similar to the structures of bovine protein tyrosine phosphatase (which contains two long insertions relative to IIB Mtl ) and the cytoplasmic B component of enzyme II Chb , which fulfills an analogous role to IIB Mtl in the N,N -diacetylchitobiose branch of the phosphotransferase system. All three proteins utilize a cysteine residue in the nucleophilic attack of a phosphoryl group covalently bound to another protein.In bacteria, the translocation of sugars across the cytoplasmic membrane is coupled to concomitant phosphorylation, a process that is mediated by the phosphoenolpyruvate:sugar phosphotransferase system (PTS) 1 signal transduction pathway (1). The initial steps of the PTS are common to all sugars in that enzyme I transfers a phosphoryl group from phosphoenolpyruvate to the histidine phosphocarrier protein (HPr). Thereafter, the phosphoryl group is transferred from HPr to the sugar-specific enzymes II. There are four general classes of enzymes II (2-4), namely glucose, mannitol (Mtl), mannose, and lactose/chitobiose (Chb). The domain organization of the sugar-specific enzymes II are similar, and the domains may or may not be covalently linked to one another. There are two cytoplasmic domains, IIA and IIB, and a transmembrane IIC domain (and in some cases IID as well). IIA accepts the phosphoryl group from HPr and subsequently donates it to IIB; IIC catalyzes the translocation of the sugar across the cytoplasmic membrane and its phosphorylation by IIB. The IIA and IIB cytoplasmic domains for the different sugar classes bear no sequence similarity to one another and, in the case of those whose structures have been solved, no structural resemblance ei...

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[2] Measurement of homo- and heteronuclear J couplings from quantitative J correlation

Cited by 420 publications

References 27 publications

Solution structure of dengue virus capsid protein reveals another fold

Solution structure of dengue virus capsid protein reveals another fold

Solution structure of a multifunctional DNA- and protein-binding motif of human Werner syndrome protein

Three-dimensional Solution Structure of the Cytoplasmic B Domain of the Mannitol Transporter IIMannitol of the Escherichia coli Phosphotransferase System

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