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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  [2281 journals]
• Backbone resonance assignments of the human p73 DNA binding domain
• Abstract: Abstract p53, p63, p73 family of proteins are transcription factors with crucial roles in regulating cellular processes such apoptosis, proliferation, differentiation, and DNA damage response. The three family members have both overlapping and unique biological functions. Sequence and structural homology are greatest in the DNA binding domains (DBD), which is the site of the majority of p53 mutations. Structurally unstable p53 DBD mutants can associate with themselves or p63 and p73 DBDs, impeding tumor suppressor functions. Evidence suggests that these proteins associate to form amyloid-like oligomers and fibrils through an aggregation-prone sequence within the DBDs. Despite having high sequence and structure similarities, p63 and p73 DBDs appear to have considerably lower tendencies to be incorporated into p53 aggregates, relative to p53. The backbone resonance assignments of p73 DBD reported here complement those previously reported for p53 and p63, allowing comparisons and providing molecular insights into their biological functions and roles in aggregation and tumor development.
PubDate: 2015-08-21

• 1 H, 13 C and 15 N resonance assignments and second structure information
of Fag s 1: Fagales allergen from Fagus sylvatica
• Abstract: Abstract Fagales allergens belonging to the Bet v 1 family account responsible for the majority of spring pollinosis in the temperate climate zones in the Northern hemisphere. Among them, Fag s 1 from beech pollen is an important trigger of Fagales pollen associated allergic reactions. The protein shares high similarity with birch pollen Bet v 1, the best-characterized member of this allergen family. Of note, recent work on Bet v 1 and its homologues found in Fagales pollen demonstrated that not all allergenic members of this family have the capacity to induce allergic sensitization. Fag s 1 was shown to bind pre-existing IgE antibodies most likely primarily directed against other members of this multi-allergen family. Therefore, it is especially interesting to compare the structures of Bet v 1-like pollen allergens, which have the potential to induce allergic sensitization with allergens that are mainly cross-reactive. This in the end will help to identify allergy eliciting molecular pattern on Bet v 1-like allergens. In this work, we report the 1H, 15N and 13C NMR assignment of beech pollen Fag s 1 as well as the secondary structure information based on backbone chemical shifts.
PubDate: 2015-08-20

• 1 H, 13 C and 15 N resonance assignments of a C-terminal domain of human
CHD1
• Abstract: Abstract Chromatin remodelling proteins are an essential family of eukaryotic proteins. They harness the energy from ATP hydrolysis and apply it to alter chromatin structure in order to regulate all aspects of genome biology. Chromodomain helicase DNA-binding protein 1 (CHD1) is one such remodelling protein that has specialised nucleosome organising abilities and is conserved across eukaryotes. CHD1 possesses a pair of tandem chromodomains that directly precede the core catalytic Snf2 helicase-like domain, and a C-terminal SANT-SLIDE DNA-binding domain. We have identified an additional conserved domain in the C-terminal region of CHD1. Here, we report the backbone and side chain resonance assignments for this domain from human CHD1 at pH 6.5 and 25 °C (BMRB No. 25638).
PubDate: 2015-08-19

• 1 H, 13 C and 15 N resonance assignments and secondary structure of the
human PHF6-ePHD1 domain
• Abstract: Abstract The plant homeodomain (PHD) finger 6 (PHF6) is a multidomain protein that comprises four nuclear localization signals and two extended PHD zinc finger domains (ePHD), suggesting that the PHD domains of PHF6 may have different functions compared with other PHD domains. And the PHF6 was first identified as the gene mutated associated with Börjeson–Forssman–Lehmann syndrome, an X-linked mental retardation disorder. The mutant PHF6 is also associated with T cell acute lymphoblastic leukemia and acute myeloid leukemia. But the molecular mechanism between these diseases and PHF6 are still unclear. In addition, the first conserved ePHD (ePHD1) of PHF6 is involved in its nucleolus localization, directly interacts with upstream binding factor (UBF) and suppresses rRNA transcription. Here we show the backbone resonance and side chain assignments of the PHF6-ePHD1 domain from human by heteronuclear multidimensional NMR spectroscopy and its secondary structure as predicted by the TALOS+. These assignments of PHF6-ePHD1 domain throw a light on the further structure determination, dynamics and interaction with UBF.
PubDate: 2015-08-19

• Solid-state NMR sequential assignments of the N-terminal domain of Hp DnaB
helicase
• Abstract: Abstract We present solid-state NMR assignments of the N-terminal domain of the DnaB helicase from Helicobacter pylori (153 residues) in its microcrystalline form. We use a sequential resonance assignment strategy based on three-dimensional NMR experiments. The resonance assignments obtained are compared with automated resonance assignments computed with the ssFLYA algorithm. An analysis of the 13C secondary chemical shifts determines the position of the secondary structure elements in this α-helical protein.
PubDate: 2015-08-18

• Sequence-specific 1 H, 15 N, and 13 C resonance assignments of the
autophagy-related protein LC3C
• Abstract: Abstract Autophagy is a versatile catabolic pathway for lysosomal degradation of cytoplasmic material. While the phenomenological and molecular characteristics of autophagic non-selective (bulk) decomposition have been investigated for decades, the focus of interest is increasingly shifting towards the selective mechanisms of autophagy. Both, selective as well as bulk autophagy critically depend on ubiquitin-like modifiers belonging to the Atg8 (autophagy-related 8) protein family. During evolution, Atg8 has diversified into eight different human genes. While all human homologues participate in the formation of autophagosomal membrane compartments, microtubule-associated protein light chain 3C (LC3C) additionally plays a unique role in selective autophagic clearance of intracellular pathogens (xenophagy), which relies on specific protein–protein recognition events mediated by conserved motifs. The sequence-specific 1H, 15N, and 13C resonance assignments presented here form the stepping stone to investigate the high-resolution structure and dynamics of LC3C and to delineate LC3C’s complex network of molecular interactions with the autophagic machinery by NMR spectroscopy.
PubDate: 2015-08-18

• Near-complete 1 H, 13 C, 15 N resonance assignments of
dimethylsulfoxide-denatured TGFBIp FAS1-4 A546T
• Abstract: Abstract The transforming growth factor beta induced protein (TGFBIp) is a major protein component of the human cornea. Mutations occurring in TGFBIp may cause corneal dystrophies, which ultimately lead to loss of vision. The majority of the disease-causing mutations are located in the C-terminal domain of TGFBIp, referred as the fourth fascilin-1 (FAS1-4) domain. In the present study the FAS1-4 Ala546Thr, a mutation that causes lattice corneal dystrophy, was investigated in dimethylsulfoxide using liquid-state NMR spectroscopy, to enable H/D exchange strategies for identification of the core formed in mature fibrils. Isotope-labeled fibrillated FAS1-4 A546T was dissolved in a ternary mixture 95/4/1 v/v/v% dimethylsulfoxide/water/trifluoroacetic acid, to obtain and assign a reference 2D 1H–15N HSQC spectrum for the H/D exchange analysis. Here, we report the near-complete assignments of backbone and aliphatic side chain 1H, 13C and 15N resonances for unfolded FAS1-4 A546T at 25 °C.
PubDate: 2015-08-15

• Backbone resonance assignment of N15, N30 and D10 T cell receptor β
subunits
• Abstract: Abstract The αβT Cell receptor (TCR) governs T cell immunity through its interaction with peptide bound to major histocompatibility complex molecules (pMHC). Previously, soluble ectodomain constructs have been used to elucidate the binding mode of the TCR for the MHC. However, the full heterodimeric αβTCR has proven difficult to produce reproducibly in recombinant systems to the extent seen in the routine production of novel antibodies. Particularly, the route of production in E. coli, which is most convenient for isotopic labeling of proteins, is challenging for a wide range of αβTCR, including N15αβ, N30αβ, but not D10αβ. With the aim of understanding the TCR-pMHC interaction through the use of dynamic binding measurements, we set out to produce TCRβ subunits with which we could investigate binding with pMHC. The TCRβ constructs are more readily produced and refolded than their αβ counterparts and have proven to be an effective model of preTCR in pMHC binding studies. As a first step towards characterizing potential interactions with protein ligands, we have assigned the backbone resonances of three TCRβ subunits, N15β, N30β and D10β.
PubDate: 2015-08-15

• 1 H, 13 C, and 15 N backbone resonance assignments of the full-length
40 kDa S. acidocaldarius Y-family DNA polymerase, dinB homolog
• Abstract: Abstract The dinB homolog (Dbh) is a member of the Y-family of translesion DNA polymerases, which are specialized to accurately replicate DNA across from a wide variety of lesions in living cells. Lesioned bases block the progression of high-fidelity polymerases and cause detrimental replication fork stalling; Y-family polymerases can bypass these lesions. The active site of the translesion synthesis polymerase is more open than that of a replicative polymerase; consequently Dbh polymerizes with low fidelity. Bypass polymerases also have low processivity. Short extension past the lesion allows the high-fidelity polymerase to switch back onto the site of replication. Dbh and the other Y-family polymerases have been used as structural models to investigate the mechanisms of DNA polymerization and lesion bypass. Many high-resolution crystal structures of Y-family polymerases have been reported. NMR dynamics studies can complement these structures by providing a measure of protein motions. Here we report the 15N, 1H, and 13C backbone resonance assignments at two temperatures (35 and 50 °C) for Sulfolobus acidocaldarius Dbh polymerase. Backbone resonance assignments have been obtained for 86 % of the residues. The polymerase active site is assigned as well as the majority of residues in each of the four domains.
PubDate: 2015-07-08

• 1 H, 15 N and 13 C backbone resonance assignments of the N-terminal,
tandem KH domains of human hnRNP E1
• Abstract: Abstract Heterogeneous nuclear ribonucleoproteins (hnRNPs) can be divided into subgroups based on their RNA-binding characteristics. One subgroup in mammalian cells are the Poly(C)-binding proteins (PCBPs) comprised of hnRNP K/J and hnRNP E1-4 [the latter also known as PCBP 1–4 or α-complex proteins (α-CP) 1–4]. Each subgroup member has three K homology (KH) nucleic acid-binding domains. Individual KH domains bind short single-stranded (ss), poly-pyrimidine-rich nucleic acid sequences with rather weak affinity. In this study, we report the 1H, 13C and 15N backbone resonance assignments of the first and second KH domains of hnRNP E1, which plays a pivotal role in posttranscriptional and translational regulation of RNA targets. Our NMR assignments lay the foundation for a detailed investigation of the dynamic cooperation of the tandem KH1 and KH2 domains to bind nucleic acids.
PubDate: 2015-07-05

• NMR assignment of intrinsically disordered self-processing module of the
FrpC protein of Neisseria meningitidis
• Abstract: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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

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