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 Biomolecular NMR Assignments   [SJR: 0.393]   [H-I: 8]   [2 followers]  Follow         Hybrid journal (It can contain Open Access articles)    ISSN (Print) 1874-270X - ISSN (Online) 1874-2718    Published by Springer-Verlag  [2290 journals]
• NMR assignment of intrinsically disordered self-processing module of the
FrpC protein of Neisseria meningitidis
• Abstract: The self-processing module (SPM) is an internal segment of the FrpC protein (P415–F591) secreted by the pathogenic Gram-negative bacterium Neisseria meningitidis during meningococcal infection of human upper respiratory tract. SPM mediates ‘protein trans-splicing’, a unique natural mechanism for editing of proteins, which involves a calcium-dependent autocatalytic cleavage of the peptide bond between D414 and P415 and covalent linkage of the cleaved fragment through its carboxy-terminal group of D414 to $$\epsilon$$ -amino group of lysine residue within a neighboring polypeptide chain. We present an NMR resonance assignment of the calcium-free SPM, which displays characteristic features of intrinsically disordered proteins. Non-uniformly sampled 5D HN(CA)CONH, 4D HCBCACON, and HCBCANCO spectra were recorded to resolve poorly dispersed resonance frequencies of the disordered protein and 91 % of SPM residues were unambiguously assigned. Analysis of the chemical shifts revealed that two regions of the intrinsically disordered SPM (A95–S101 and R120–I127) have a tendency to form a helical structure, whereas the residues P1–D7 and G36–A40 have the propensity to adopt a $$\beta$$ -structure.
PubDate: 2015-07-03

• Chemical shift assignments of a new folded domain from yeast Pcf11
• Abstract: The yeast protein Pcf11 is a component of the cleavage/polyadenylation factor IA (CF IA) complex involved in the 3′ processing of pre-mRNA. Pcf11 interacts with RNA and the C-terminal domain (CTD) of the largest subunit of RNA polymerase II via the CTD-interaction domain (CID), and other peptide regions mediate contacts with CF IA subunits Clp1 and Rna14/Rna15. We have identified a novel domain adjacent to the CID and have determined the backbone and sidechain 1H, 13C and 15N chemical shift assignments for the bacterially produced construct. Despite the reduced sequence complexity due to numerous glutamine and leucine residues, secondary chemical shift analysis indicates that the domain is composed of three well-defined helical regions with relaxation measurements consistent with a folded independent domain. The proximity of this previously uncharacterized domain close to the N-terminal CID prompts speculation for a putative role in modulating CTD and RNA binding, or possible intermolecular contacts within CF IA.
PubDate: 2015-07-02

• NMR assignments of the C-terminal domain of human galectin-8
• Abstract: Galectins recognize β-galectosides to promote a variety of cellular functions. Despite their sequence variations, all galectins share the same carbohydrate recognition domains (CRD) and their modes of ligand recognition at a structural level are essentially identical. Human galectin 8 plays an important role in numerous cancer and immune responses. It consists of two CRDs that are connected via a flexible linker. The substrate affinities and specificities of the N- and C-terminal domains are quite different. In order to investigate the structural basis of their substrate specificities, we complete the NMR 1H, 13C, and 15N chemical shift assignments of C-terminal domain of human galectin-8 (hG8C).
PubDate: 2015-07-01

• Backbone resonance assignments of ferric human cytochrome c and the
pro-apoptotic G41S mutant in the ferric and ferrous states
• Abstract: Human cytochrome c is a multi-functional protein with key roles in both the mitochondrial electron transfer chain and in apoptosis. In the latter, a complex formed between the mitochondrial phospholipid cardiolipin and cytochrome c is crucial for instigating the release of pro-apoptotic factors, including cytochrome c, from the mitochondrion into the cytosol. The G41S mutant of human cytochrome c is the only known disease-related variant of cytochrome c and causes increased apoptotic activity in patients with autosomal dominant thrombocytopenia. NMR spectroscopy can be used to investigate the interaction of human cytochrome c with cardiolipin and the structural and dynamic factors, which may contribute to enhanced apoptotic activity for the G41S mutant. We present here essentially full backbone amide resonance assignments for ferric human cytochrome c (98 %) as well as assignments of both the ferric (92 %) and ferrous (95 %) forms of the G41S mutant. Backbone amide chemical shift differences between the wild type and G41S mutant in the ferric state reveals significant changes around the mutation site, with many other amides also affected. This suggests the possibility of increased dynamics and/or a change in the paramagnetic susceptibility tensor of the G41S mutant relative to the wild type protein.
PubDate: 2015-06-30

• Solution NMR assignment of the cryptic sixth TOG domain of mini spindles
• Abstract: TOG domains contribute to the organisation of microtubules through their ability to bind tubulin. They are found in members of the XMAP215 family of proteins, which act as microtubule polymerases and fulfill important roles in the formation of the mitotic spindle and in the assembly of kinetochore fibres. We recently identified a cryptic TOG domain in the XMAP215 family proteins, chTOG and its Drosophila homologue, mini spindles. This domain is not part of the well-established array of TOG domains involved in tubulin polymerisation. Instead it forms part of a binding site for TACC3 family proteins. This interaction is required for the assembly of kinetochore bridges in a trimeric complex with clathrin. Here we present the first NMR assignment of a sixth TOG domain from mini spindles as a first step to elucidate its structure and function.
PubDate: 2015-05-14

• Backbone and side chain NMR assignments of Geobacillus stearothermophilus
ZapA allow identification of residues that mediate the interaction of ZapA
with FtsZ
• Abstract: Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into 15N2H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.
PubDate: 2015-05-13

• Backbone chemical shift assignments for the sensor domain of the
Burkholderia pseudomallei histidine kinase RisS: “missing”
resonances at the dimer interface
• Abstract: Using a deuterated sample, all the observable backbone 1HN, 15N, 13Ca, and 13C′ chemical shifts for the dimeric, periplasmic sensor domain of the Burkholderia pseudomallei histidine kinase RisS were assigned. Approximately one-fifth of the amide resonances are “missing” in the 1H–15N HSQC spectrum and map primarily onto α-helices at the dimer interface observed in a crystal structure suggesting this region either undergoes intermediate timescale motion (μs–ms) and/or is heterogeneous.
PubDate: 2015-05-09

• H N , N, C α , C β and C′ assignments of the intrinsically
disordered C-terminus of human adenosine A 2A receptor
• Abstract: The C-terminus of the human adenosine A2A receptor differs from the other human adenosine receptors by its exceptional length and lack of a canonical cysteine residue. We have previously structurally characterized this C-terminal domain and its interaction with calmodulin. It was shown to be structurally disordered and flexible, and to bind calmodulin with high affinity in a calcium-dependent manner. Interaction with calmodulin takes place at the N-terminal end of the A2A C-terminal domain without major conformational changes in the latter. NMR was one of the biophysical methods used in the study. Here we present the HN, N, Cα, Cβ and C′ chemical shift assignments of the free form of the C-terminus residues 293–412, used in the NMR spectroscopic characterization of the domain.
PubDate: 2015-05-08

• NMR assignment of the immune mapped protein 1 (IMP1) homologue from
Plasmodium falciparum
• Abstract: Plasmodium falciparum is responsible for causing cerebral malaria in humans. IMP1 is an immunogenic protein, present in the parasite, which has been shown to induce an immune response against apicomplexan parasites in a species-specific manner. Here, we report the complete NMR assignments of PfIMP1.
PubDate: 2015-05-07

• Chemical shift assignments for S. cerevisiae Ubc13
• Abstract: The ubiquitination pathway controls several human cellular processes, most notably protein degradation. Ubiquitin, a small signaling protein, is activated by the E1 activating enzyme, transferred to an E2 conjugating enzyme, and then attached to a target substrate through a process that can be facilitated by an E3 ligase enzyme. The enzymatic mechanism of ubiquitin transfer from the E2 conjugating enzyme onto substrate is not clear. The highly conserved HPN motif in E2 catalytic domains is generally thought to help stabilize an oxyanion intermediate formed during ubiquitin transfer. However recent work suggests this motif is instead involved in a structural, non-enzymatic role. As a platform to better understand the E2 catalyzed ubiquitin transfer mechanism, we determined the chemical shift assignments of S. cerevisiae E2 enzyme Ubc13.
PubDate: 2015-05-07

• 1 H, 13 C and 15 N resonance assignments of σ S activating protein
Crl from Salmonella enterica serovar Typhimurium
• Abstract: The general stress response in Enterobacteria, like Escherichia coli or Salmonella, is controlled by the transcription factor σS, encoded by the rpoS gene, which accumulates during stationary phase growth and associates with the core RNA polymerase enzyme (E) to promote transcription of genes involved in cell survival. Tight regulation of σS is essential to preserve the balance between self-preservation under stress conditions and nutritional competence in the absence of stress. Whereas σ factors are generally inactivated upon interaction with anti-sigma proteins, σS binding by the Crl protein facilitates the formation of the holoenzyme EσS, and therefore σS-controlled transcription. Previously, critical residues in both Crl and σS were identified and assigned to the binding interface in the Crl–σS complex. However, high-resolution structural data are missing to fully understand the molecular mechanisms underlying σS activation by Crl, in particular the possible role of Crl in triggering domain rearrangements in the multi-domain protein σS. Here we provide the 1H, 13C and 15N resonance assignments of Salmonella enterica serovar Typhimurium Crl, as a starting point for CrlSTM structure determination and further structural investigation of the CrlSTM–σ STM S complex.
PubDate: 2015-05-06

• Backbone assignment and secondary structure of the PLAT domain of human
polycystin-1
• Abstract: Polycystin-1 is a large transmembrane protein mutated in the common genetic disorder autosomal dominant polycystic kidney disease. One of the predicted intracellular domains of polycystin-1 is PLAT (Polycystin-1, Lipoxygenase and Alpha Toxin), which consists of 116 amino acids and is anchored to the membrane by linkers at both ends. It is predicted to have a large number of hydrophobic residues on the surface. Assignment of the NMR spectrum was hampered by considerable line broadening, and hence a programme of site-directed mutagenesis and searching for suitable solution conditions was undertaken. The optimum construct required fusion of the GB1 domain at the N-terminus and a His tag at the C-terminus, and proved to have several additional amino acids at both ends beyond the canonical domain boundaries, as well as mutation of W3128 to alanine. Optimum solubility required 500 mM sodium chloride, and usable spectra could only be obtained by perdeuteration. Backbone assignment was made using standard triple resonance spectra and is 88 % complete. The chemical shifts obtained suggest that a loop consisting of residues 3223–3228 is mobile in solution, and that the protein is similar in structure to a prediction produced by Swiss-Model based on the structure of a homologous protein.
PubDate: 2015-05-06

• Backbone, side chain and heme resonance assignments of cytochrome OmcF
from Geobacter sulfurreducens
• Abstract: Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with 1H, 13C and 15N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.
PubDate: 2015-05-05

• 1 H, 13 C and 15 N assignments of EGF domains 8–11 of human Notch-1
• Abstract: The Notch receptor is part of a core cell–cell signaling system crucial for development and tissue homeostasis in Metazoa. Structural information is available for the negative regulatory region, the ligand-binding region and the intracellular domain of Notch, but data for the remaining portions of the extracellular region which determine its overall shape at the cell surface are still lacking. This region consists of 36 EGF-like domains arranged as multiple tandem repeats. Most EGF-like domains near the ligand-binding domains EGF11 and 12 are of the calcium-binding type, with well-described, rigid and near-linear interdomain interfaces. However, EGF10 is a conserved, non-calcium-binding domain which may confer flexibility or a non-linear organization to the receptor. To probe this, we have expressed and purified a four-domain construct, EGF8–11, from human Notch-1, and report here the 1H, 13C and 15N resonance assignments. Differences in EGF11 chemical shifts between this construct and a previously assigned construct, EGF11–13, confirm the presence of hydrophobic interdomain contacts between the hairpin turn of the major β-sheet in EGF11 and the conserved aromatic residue within the C-terminal region of EGF10. This suggests that the EGF10–11 interface is rigid.
PubDate: 2015-05-01

• Backbone assignment of the three dimers of HU from Escherichia coli at
293 K: EcHUα 2 , EcHUβ 2 and EcHUαβ
• Abstract: HU is one of the major nucleoid-associated proteins involved in bacterial chromosome structure and in all DNA-dependent cellular activities. Similarly to eukaryotic histones, this small dimeric basic protein wraps DNA in a non-sequence specific manner, promoting DNA super-structures. In most bacteria, HU is a homodimeric protein encoded by a single gene. However, in enterobacteria such as Escherichia coli, the presence of two genes coding for two peptidic chains, HUα and HUβ, lead to the coexistence of three forms: two homodimers EcHUα2 and EcHUβ2, as well as a heterodimer EcHUαβ. Genetic and biochemical investigation suggest that each EcHU dimer plays a specific physiological role in bacteria. Their relative abundance depends on the environmental conditions and is driven by an essential, yet unknown, fast outstanding chain-exchange mechanism at physiological temperature. Our goal is to understand this fundamental mechanism from a structural and kinetics standpoint using NMR. For this purpose, the first steps are the assignment of each dimer in their native and intermediate states. Here, we report the backbone assignment of each HU dimers from E. coli at 293 K in their native state.
PubDate: 2015-04-30

• Chemical shift assignments of zinc finger domain of methionine
aminopeptidase 1 (MetAP1) from Homo sapiens
• Abstract: Methionine aminopeptidase Type I (MetAP1) cleaves the initiator methionine from about 70 % of all newly synthesized proteins in almost every living cell. Human MetAP1 is a two domain protein with a zinc finger on the N-terminus and a catalytic domain on the C-terminus. Here, we report the chemical shift assignments of the amino terminal zinc binding domain (ZBD) (1–83 residues) of the human MetAP1 derived by using advanced NMR spectroscopic methods. We were able to assign the chemical shifts of ZBD of MetAP1 nearly complete, which reveal two helical fragments involving residues P44-L49 (α1) and Q59-K82 (α2). The protein structure unfolds upon complex formation with the addition of 2 M excess EDTA, indicated by the appearance of amide resonances in the random coil chemical shift region of 15NHSQC spectrum.
PubDate: 2015-04-29

• Resonance assignment of PsbP: an extrinsic protein from photosystem II of
Spinacia oleracea
• Abstract: PsbP (23 kDa) is an extrinsic eukaryotic protein of photosystem II found in the thylakoid membrane of higher plants and green algae. It has been proven to be indispensable for proper functioning of the oxygen evolving complex. By interaction with other extrinsic proteins (PsbQ, PsbO and PsbR), it modulates the concentration of two cofactors of the water splitting reaction, Ca2+ and Cl−. The crystallographic structure of PsbP from Spinacia oleracea lacks the N-terminal part as well as two inner regions which were modelled as loops. Those unresolved parts are believed to be functionally crucial for the binding of PsbP to the thylakoid membrane. In this NMR study we report 1H, 15N and 13C resonance assignments of the backbone and side chain atoms of the PsbP protein. Based on these data, an estimate of the secondary structure has been made. The structural motifs found fit the resolved parts of the crystallographic structure very well. In addition, the complete assignment set provides preliminary insight into the dynamic regions.
PubDate: 2015-04-23

• 1 H, 15 N and 13 C chemical shift assignments of the La motif and RRM1
from human LARP6
• Abstract: We report here the nearly complete 1H, 15N and 13C resonance assignment of the La motif and RNA recognition motif 1 of human LARP6, an RNA binding protein involved in regulating collagen synthesis.
PubDate: 2015-04-22

• Secondary structure and 1 H, 13 C, 15 N resonance assignments of the
endosomal sorting protein sorting nexin 3
• Abstract: Sorting nexin 3 (SNX3) belongs to a sub-family of sorting nexins that primarily contain a single Phox homology domain capable of binding phosphoinositides and membranes. We report the complete 1H, 13C and 15N resonance assignments of the full-length human SNX3 protein and identification of its secondary structure elements, revealing a canonical fold and unstructured termini.
PubDate: 2015-04-19

• Backbone and side-chain 1 H, 15 N, 13 C assignment and secondary structure
of BPSL1445 from Burkholderia pseudomallei
• Abstract: BPSL1445 is a lipoprotein produced by the Gram-negative bacterium Burkholderia pseudomallei (B. pseudomallei), the etiological agent of melioidosis. Immunodetection assays against sera patients using protein microarray suggest BPSL1445 involvement in melioidosis. Herein we report backbone, side chain NMR assignment and secondary structure for the recombinant protein.
PubDate: 2015-04-19

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