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Biomolecular NMR Assignments

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ISSN (Print) 1874-270X - ISSN (Online) 1874-2718
Published by Springer-Verlag

[2216 journals]

¹H, ¹³C, ¹⁵N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus
- Abstract: Abstract Staphylococcus aureus is an opportunistic pathogen that causes skin and severe infections in mammals. Critical to S. aureus growth is its ability to scavenge iron from host cells. To this effect, S. aureus has evolved a sophisticated pathway to acquire heme from hemoglobin (Hb) as a preferred iron source. The pathway is comprised of nine iron-regulated surface determinant (Isd) proteins involved in heme capture, transport, and degradation. A key protein of the heme acquisition pathway is the surface-anchored hemoglobin receptor protein IsdB, which is comprised of two NEAr transporter (NEAT) domains that act in concert to bind Hb and extract heme for subsequent transfer to downstream acquisition pathway proteins. Despite significant advances in the structural knowledge of other Isd proteins, the structural mechanisms and molecular basis of the IsdB-mediated heme acquisition process are not well understood. In order to provide more insights into the mode of function of IsdB, we have initiated NMR structural studies of the first NEAT domain of IsdB (IsdBN1). Herein, we report the near complete 1H, 13C and 15N resonance assignments of backbone and side chain atoms, and the secondary structural topology of the 148-residue IsdB NEAT 1 domain. The NMR results are consistent with the presence of eight β-strands and one α-helix characteristic of an immunoglobulin-like fold observed in other NEAT domain family proteins. This work provides a solid framework to obtain atomic-level insights toward understanding how IsdB mediates IsdB-Hb protein–protein interactions critical for heme capture and transfer.
  PubDate: 2013-05-18
Backbone and ILV methyl resonance assignments of E. coli thymidylate synthase bound to cofactor and a nucleotide analogue
- Abstract: Abstract Thymidylate synthase (TSase) is a 62 kDa homodimeric enzyme required for de novo synthesis of thymidine monophosphate in most organisms. This makes the enzyme an excellent target for anticancer and microbial antibiotic drugs. In addition, TSase has been shown to exhibit negative cooperativity and half-the-sites reactivity. For these collective reasons, TSase is widely studied, and much is known about its kinetics and structure as it progresses through a multi-step catalytic cycle. Recently, nuclear magnetic resonance spin relaxation has been instrumental in demonstrating the critical role of dynamics in enzyme function in small model systems. These studies raise questions about how dynamics affect function in larger enzymes with more complex reaction coordinates. TSase is an ideal candidate given its size, oligomeric state, cooperativity, and status as a drug target. Here, as a pre-requisite to spin relaxation studies, we present the backbone and ILV methyl resonance assignments of TSase from Escherichia coli bound to a substrate analogue and cofactor.
  PubDate: 2013-05-09
¹H, ¹³C and ¹⁵N resonance assignments for the fibrillin-1 EGF2-EGF3-hybrid1-cbEGF1 four-domain fragment
- Abstract: Abstract Fibrillins are large extracellular glycoproteins that form the principal component of microfibrils. These perform a vital structural function in the extracellular matrix of many tissues. Fibrillins have also been implicated in mediating a number of protein–protein interactions, some of which may be significant in regulating growth factors such as transforming growth factor β. Here we present the backbone and side-chain 1H, 13C and 15N assignments for a 19 kDa protein fragment derived from the N-terminus of human fibrillin-1, encompassing four domains in total. These domains include the second and third epidermal growth factor-like (EGF) domains, the first hybrid domain (hyb1), and the first calcium-binding EGF domain of fibrillin-1. This region of fibrillin-1 is of particular interest as the hyb1 domain has been suggested to play a role in microfibril assembly, as well as several other protein–protein interactions.
  PubDate: 2013-05-07
Sequence-specific backbone ¹H, ¹³C and ¹⁵N assignments of the 34 kDa catalytic domain of PTPN5 (STEP)
- Abstract: Abstract PTPN5 is a protein tyrosine phosphatase that plays an integral role in regulating excitatory postsynaptic activity. The sequence-specific backbone assignments of the murine PTPN5 catalytic domain have been determined based on triple-resonance experiments using uniformly [2H,13C,15N]-labeled protein.
  PubDate: 2013-05-03
Backbone and side-chain ¹H, ¹³C and ¹⁵N assignments of the PPIase domain of macrophage infectivity potentiator (Mip) protein from Coxiella burnetii
- Abstract: Abstract Coxiella burnetii is an obligate intracellular gram-negative bacterium uniquely evolved to thrive in the inhospitable phagolysosome of macrophage. C. burnetii causes Q fever in humans and animals, which is emerging as a global public health concern. It is highly infectious and designated as a category B biowarfare agent because of its ubiquitous nature, abundant natural reservoirs, high resistance to environmental conditions, ease of transmission and low infectious dose. The lack of knowledge and awareness of C. burnetii leads to under-reporting and under-diagnosing of Q fever cases. Therefore, further understanding of the interactions between the infected host and the bacteria is necessary. C. burnetii macrophage infectivity potentiator (cb-Mip) is a secreted protein of 230 amino acids involving in intracellular survival of the pathogen. cb-Mip belongs to the family of FK506 binding protein, which possesses peptidyl-prolyl cis/trans isomerase (PPIase) activity. Besides acting as a PPIase, Mip protein homolog has been identified as virulence factor of many intracellular pathogenic microorganisms. In the present study, we report the near complete resonance assignments of the PPIase domain-containing region of Mip protein of C. burnetii. Secondary structure prediction based on chemical shift index analysis indicates that the protein adopts a predominately beta-strand structure, which is consistent with the crystal structure of homologous Mip protein in Legionella pneumophila.
  PubDate: 2013-04-25
¹H, ¹³C, ¹⁵N backbone and side chain NMR resonance assignments of BPSL1050 from Burkholderia pseudomallei
- Abstract: Abstract BPSL1050 is a 13.9 kDa protein produced by the Gram-negative bacterium Burkholderia pseudomallei, the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1050 involvement in melioidosis. Herein we report its backbone and side chains NMR assignment.
  PubDate: 2013-04-25
Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum
- Abstract: Abstract Vibrio anguillarum is a biofilm forming Gram-negative bacterium that survives prolonged periods in seawater and causes vibriosis in marine life. A quorum-sensing signal transduction pathway initiates biofilm formation in response to environmental stresses. The phosphotransferase protein VanU is the focal point of the quorum-sensing pathway and facilitates the regulation between independent phosphorelay systems that activate or repress biofilm formation. Here we report the 1H, 13C, and 15N backbone and side chain resonance assignments and secondary structure prediction for VanU from V. anguillarum.
  PubDate: 2013-04-21
¹H, ¹³C and ¹⁵N chemical shift assignments for the N-terminal PAS domain of the KCNH channel from Zebrafish
- Abstract: Abstract The KCNH channels are voltage-gated potassium channels that play important roles in heart and nerve cells. The N-terminal region of the KCNH channel contains a Per-Arnt-Sim (PAS) domain which is important for the channel gating through interaction with other regions of the channel. To study the solution structure of the N-terminal PAS domain of the KCNH channel from Zebrafish (zNTD), we over-expressed and purified zNTD. We report the resonance assignments for zNTD. The data will allow us to perform structural studies for this domain, which will provide insight into its structural basis for the molecular interaction with other regions of the KCNH channel.
  PubDate: 2013-04-18
¹H, ¹⁵N, and ¹³C chemical shift assignments of the calflagin Tb24 flagellar calcium binding protein of Trypanosoma brucei
- Abstract: Abstract Flagellar calcium binding proteins are expressed in a variety of trypanosomes and are potential drug targets for Chagas disease and African sleeping sickness. We report complete NMR chemical shift assignments of the flagellar calcium binding protein calflagin Tb24 of Trypanosoma brucei. (BMRB no. 18011).
  PubDate: 2013-04-01
Backbone and sidechain ¹H, ¹³C and ¹⁵N chemical shift assignments of the hydrophobin MPG1 from the rice blast fungus Magnaporthe oryzae
- Abstract: Abstract Fungal hydrophobins are secreted proteins that self-assemble at hydrophobic:hydrophilic interfaces. They are essential for a variety of processes in the fungal life cycle, including mediating interactions with surfaces and infection of hosts. The fungus Magnaporthe oryzae, the causative agent of rice blast, relies on the unique properties of hydrophobins to infect cultivated rice as well as over 50 different grass species. The hydrophobin MPG1 is highly expressed during rice blast pathogenesis and has been implicated during host infection. Here we report the backbone and sidechain assignments for the class I hydrophobin MPG1 from the rice blast fungus Magnaporthe oryzae.
  PubDate: 2013-04-01
¹H, ¹⁵N and ¹³C resonance assignments for the three LOTUS RNA binding domains of Tudor domain-containing protein TDRD7
- Abstract: Abstract The LOTUS or OST-HTH domain is a recently discovered motif of about 80 amino acids and is found in several germline-specific proteins including the Tudor domain-containing proteins TDRD5 and TDRD7, which are important for germ cell development. The LOTUS domain is an RNA binding domain but its exact function is unknown. Here, we report the 1H, 13C and 15N resonance assignments for the three LOTUS domains present in mouse TDRD7. These assignments will allow three-dimensional structure determination of the LOTUS domains and mapping of their interaction with RNA, steps toward deciphering the function of TDRD7.
  PubDate: 2013-04-01
¹H, ¹³C, and ¹⁵N backbone chemical shift assignments of StAR-related lipid transfer domain protein 5 (STARD5)
- Abstract: Abstract Steroidogenic acute regulatory (StAR)—related lipid transfer proteins possess a START (steroidogenic acute regulatory-related lipid transfer) domain. START domains are conserved protein modules involved in the non-vesicular intracellular transport of lipids and cholesterol in mammals. Fifteen mammalian proteins, divided in five subfamilies, are reported to possess a START domain. Members of the STARD4 subfamily, i.e. STARD4, 5 and 6 are essentially single START domains and are thought to be involved in the intracellular transport of cholesterol. No structure of a cholesterol-bound START domain from this family has been resolved yet. The determination of the structure of such a complex would contribute to a better understanding of the mechanism of ligand binding and transport by START domains, two unresolved aspects of their structural biology. In this context, we have undertaken the structure determination of a ligand-bound form of STARD5 by NMR. Here, we report the 1H, 13C and 15N backbone resonance assignments of the ligand-free STARD5.
  PubDate: 2013-04-01
¹H-, ¹³C- and ¹⁵N-NMR assignment of the N-terminal domain of human cerebral dopamine neurotrophic factor (CDNF)
- Abstract: Abstract Parkinson’s disease (PD) is a neurodegenerative disorder that is caused by the death of midbrain dopaminergic neurons. Current therapies for PD do not halt the neurodegeneration nor repair the affected neurons. Therefore, search for novel neurotrophic factors (NTF) for midbrain dopaminergic neurons, which could be used in novel therapeutic approaches, is highly wanted. In 2007, a potent NTF for dopaminergic neurons was described as the conserved dopamine neurotrophic factor (CDNF). Single doses of this protein protect and restore dopaminergic neurons in experimental models of PD. CDNF has two domains; an N-terminal saposin-like domain, which may bind to membranes; and a presumably intrinsically unstructured C-terminal which contains an internal cysteine bridge in a CXXC motif similar to that of thiol/disulphide oxidoreductases and isomerases, and may thus reduce the endoplasmic reticulum stress caused by incorrectly folded proteins. We show for the first time the nuclear magnetic resonance assignment of N-terminal domain of recombinant CDNF (residues 1–105) by solution 2D and 3D NMR spectroscopy. We were able to obtain a nearly complete resonance assignment, which is the first step toward the solution structure determination of this neurotrophic factor.
  PubDate: 2013-04-01
Backbone resonance assignments of the C2 domain of coagulation factor VIII
- Abstract: Abstract Factor VIII (FVIII, other clotting factors are named similarly) is a glycoprotein that circulates in the plasma bound to von Willebrand factor. During the blood coagulation cascade, activated FVIII (FVIIIa) binds to FIXa and activates FX in the presence of calcium ions and phospholipid membranes. The C1 and C2 domains mediate membrane binding that is essential for activation of the FVIIIa–FIXa complex. Here, 1H, 13C, and 15N backbone chemical shift assignments are reported for the C2 domain of FVIII, including assignments for the residues in solvent-exposed loops. The NMR resonance assignments, along with further structural studies of membrane-bound FVIII, will advance understanding of blood-clotting protein interactions.
  PubDate: 2013-04-01
Erratum to: ¹H, ¹³C and ¹⁵N NMR assignments of the C1A and C1B subdomains of PKC-delta
- PubDate: 2013-04-01
Erratum to: NMR resonance assignment of DnaE intein from Nostoc punctiforme
- PubDate: 2013-04-01
Erratum to: Resonance assignments of cohesin and dockerin domains from Clostridium acetobutylicum ATCC824
- PubDate: 2013-04-01
¹H, ¹³C and ¹⁵N resonance assignments of the periplasmic signalling domain of HasR, a TonB-dependent outer membrane heme transporter
- Abstract: Abstract TonB-dependent transporters (TBDTs) are bacterial outer membrane proteins that internalize nutrients such as vitamin B12, metal complexes, heme, some carbohydrates, etc. In addition to their transport activity, several TBDTs are also involved in a signalling cascade from the cell surface into the cytoplasm, via their periplasmic signalling domain. Here we report the backbone and side chain resonance assignments of the signalling domain of HasR, a TonB-dependent outer membrane heme transporter from Serratia marcescens as a first step towards its structural study.
  PubDate: 2013-04-01
¹H, ¹³C, ¹⁵N backbone and side-chain resonance assignments of rat angiogenin
- Abstract: Abstract Angiogenin is an unusual member of the pancreatic ribonuclease superfamily that induces formation of new blood vessels and is a promising anti-cancer target. Here we report backbone and side chain 1H, 13C, and 15N resonance assignments for rat angiogenin (residues 24–145), excluding the N-terminal signal peptide. These data allow nuclear magnetic resonance structure and inhibitor-binding studies with the aim of providing angiogenin antagonists as potential therapeutics.
  PubDate: 2013-04-01
¹H, ¹³C and ¹⁵N assignments of CdnL, an essential protein in Myxococcus xanthus
- Abstract: Abstract CdnL, an essential protein in Myxococcus xanthus and several other bacteria, is a member of the large CarD_TRCF family of bacterial proteins that interact with RNA polymerase. Structural analyses of the 164-residue M. xanthus CdnL by NMR is complicated because of broadening, and hence overlap, of the signals due to the self-association and the monomer–dimer equilibrium that occurs in solution. Here, we report 1H, 13C and 15N assignments for CdnL achieved by analyzing its NMR spectra on the basis of the complete assignment obtained in this study for the 68-residue N-terminal fragment of CdnL (CdnLNt) together with those we described previously for the stable, protease-resistant, 110-residue C-terminal domain (CdnLCt). This approach relied on our observation that many of the CdnLNt and CdnLCt chemical shifts matched closely with those of the equivalent residues in the full-length protein. Our assignments provide the crucial first step in the structural analysis of CdnL and this functionally important family of bacterial proteins.
  PubDate: 2013-04-01