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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  [2335 journals]
• 1 H, 15 N and 13 C resonance assignments of the C-terminal domain of
Vibrio cholerae TolA protein
• Abstract: Abstract Vibrio cholerae is the bacterial causative agent of the human disease cholera. Non-pathogenic bacterium can be converted to pathogenic following infection by a filamentous phage, CTXΦ, that carries the cholera toxin encoding genes. A crucial step during phage infection requires a direct interaction between the CTXΦ minor coat protein (pIIICTX) and the C-terminal domain of V. cholerae TolA protein (TolAIIIvc). In order to get a better understanding of TolA function during the infection process, we have initiated a study of the V. cholerae TolAIII domain by 2D and 3D heteronuclear NMR. With the exception of the His-tag (H123–H128), 97 % of backbone 1H, 15N and 13C resonances were assigned and the side chain assignments for 92 % of the protein were obtained (BMRB deposit with accession number 25689).
PubDate: 2016-07-19

• 1 H, 15 N, 13 C resonance assignments for pyrazinoic acid binding domain
of ribosomal protein S1 from Mycobacterium tuberculosis
• Abstract: Abstract Ribosomal protein S1 of Mycobacterium tuberculosis (MtRpsA) binds to ribosome and mRNA, and plays significant role in the regulation of translation initiation, conventional protein synthesis and transfer-messenger RNA (tmRNA) mediated trans-translation. It has been identified as the target of pyrazinoic acid (POA), a bactericidal moiety from hydrolysis of pyrazinamide, which is a mainstay of combination therapy for tuberculosis. POA prevented the interactions between the C-terminal S1 domain of MtRpsA (residues 280–368, MtRpsACTD_S1) and tmRNA; so that POA can inhibit the trans-translation, which is a key component of multiple quality control pathways in bacteria. However, the details of molecular mechanism and dynamic characteristics for MtRpsACTD_S1 interactions with POA, tmRNA or mRNA are still unclear. Here we present the 1H, 15N, 13C resonance assignments of MtRpsACTD_S1 as well as the secondary structure information based on backbone chemical shifts, which lay foundation for further solution structure determination, dynamic properties characterization and interactions investigation between MtRpsACTD_S1 and tmRNA, RNA or POA.
PubDate: 2016-07-13

• 1 H, 13 C and 15 N backbone resonance assignments and dynamic properties
of the PDZ tandem of Whirlin
• Abstract: Abstract Mammals perceive sounds thanks to mechanosensory hair cells located in the inner ear. The stereocilia of these cells are tightly bound together in bundles by a network of cadherins and scaffolding proteins. Stereocilia deflection induces stretching of this network and is responsible for hair cell depolarization that triggers the neuronal message, transducing the mechanical signal into an electric signal transmissible to the brain. Nearly all proteins involved in this mechano-electrical transduction network contain short C-terminal motifs of interaction with PDZ domains (PSD-95, Discs Large, ZO-1). Interestingly only two of these proteins encompass PDZ domains: Harmonin and Whirlin. As our first step towards a comprehensive structural study of Whirlin, we have assigned the 1H, 13C and 15N backbone resonances of a tandem formed by the first two PDZ domains of Whirlin, reported the secondary structure elements of this tandem as predicted by the TALOS+ server and evaluated its dynamics from 15N relaxation measurements.
PubDate: 2016-07-09

• Backbone and side chain assignments of human cell cycle regulatory protein
S-phase kinase-associated protein 1
• Abstract: Abstract Ubiquitination of proteins is required to regulate several cellular mechanisms in cells. Skp1-Cullin-1-F-box (SCF), the largest family of the RING E3 ligases, recognizes and carries out the poly-ubiquitination of many substrate proteins. SCF E3 ligase is a multi-component protein complex, and the human S-phase kinase-associated protein 1 (Skp1) is the adapter protein, which binds and presents the substrate binding protein F-box (FBP) to the rest of the E3 ligase. Several crystallographic studies have solved the partial structure of Skp1 in complex with various FBPs, but there is no structure of standalone Skp1. Understanding the conformational and structural properties of Skp1 with and without FBPs is required to understand the complete mechanism of poly-ubiquitination. Here, we report ~90 % backbone and 64 % side chain 1H, 13C, 15N assignments of Skp1 protein using various double and triple resonance NMR experiments.
PubDate: 2016-07-09

• Resonance assignments of a VapC family toxin from Clostridium thermocellum
• Abstract: Abstract Toxin–antitoxin (TA) systems widely exist in bacterial plasmids, phages, and chromosomes and play important roles in growth persistence and host-pathogen interaction. Virulence associated protein BC (VapBC) family TAs are the most abundant TAs in bacteria and many pathogens contain a large number of vapBC loci in the genome which have been extensively studied. Clostridium thermocellum, a cellulolytic anaerobic gram-positive bacterium with promising applications in biofuel production, also contains a VapBC TA in the genome. Despite the structures of several VapBC family TAs have been determined, the toxin and anti-toxin components of C. thermocellum VapBC have very low sequence identity to the proteins in PDB. Therefore, the structure and functional mechanism of this TA is largely unknown. Here we reported the NMR resonance assignments of the VapC toxin from C. thermocellum as a basis for further structural and functional studies.
PubDate: 2016-07-08

• 1 H, 13 C and 15 N backbone resonance assignment for the 40.5 kDa
catalytic domain of Ubiquitin Specific Protease 7 (USP7)
• Abstract: Abstract The deubiquitinase Ubiquitin Specific Protease 7 (USP7) is part of the regulatory cascade of proteins that modulates the activity of the tumor suppressor protein p53. Deubiquitination of its target Murine Double Minute 2 (MDM2) leads to increased proteosomal degradation of p53. Consequently, USP7 has emerged as an attractive oncology target because its inhibition stabilizes p53, thereby promoting p53-dependent apoptosis in cancer cells. Here we report the backbone resonance assignment for the 40.5 kDa catalytic domain of USP7.
PubDate: 2016-07-08

• Chemical shift assignments of the homodimer protein SP_0782 (7–79)
from Streptococcus pneumoniae
• Abstract: Abstract The protein SP_0782 from Streptococcus pneumonia is a small homodimeric protein that belongs to a protein family containing representative members with single-stranded DNA (ssDNA) binding functions. The ssDNA binding of the homolog YdbC from Lactococcus lactis was previously characterized when bound to a 20-mer of pyridine-rich ssDNA, sharing an overall similar structural fold with the human transcription coactivator PC4. We report that SP_0782 exhibits distinct differences in ssDNA binding properties from YdbC as revealed by NMR titration experiments. Unlike the binding of the ssDNA dT19G1 to PC4 and YdbC, SP_0782 resulted in aggregation. In addition, SP_0782 exhibits favorable binding to shorter ssDNA such as dT6. The reason is unclear, and the SP_0782 structure–function relationship remains to be elucidated. Here, we report the complete 1H, 13C, and 15N backbone and side chain NMR assignments of SP_0782, residues 7–79.
PubDate: 2016-07-07

• 1 H, 15 N, and 13 C resonance assignments of Staphylococcus aureus
• Abstract: Abstract The pathogenic bacterium Staphylococcus aureus has evolved to actively evade many aspects of the human innate immune system by expressing a series of secreted inhibitory proteins. Among these, the extracellular adherence protein (Eap) has been shown to inhibit the classical and lectin pathways of the complement system. By binding to complement component C4b, Eap is able to inhibit formation of the CP/LP C3 pro-convertase. Secreted full-length, mature Eap consists of four ~98 residue domains, all of which adopt a similar beta-grasp fold, and are connected through a short linker region. Through multiple biochemical approaches, it has been determined that the third and fourth domains of Eap are responsible for C4b binding. Here we report the backbone and side-chain resonance assignments of the 11.3 kDa fourth domain of Eap. The assignment data has been deposited in the BMRB database under the accession number 26726.
PubDate: 2016-07-02

• Backbone resonance assignments for the SET domain of the human
methyltransferase NSD2
• Abstract: Abstract Aberrant NSD2 methyltransferase activity is implicated as the oncogenic driver in multiple myeloma, suggesting opportunities for novel therapeutic intervention. The methyltransferase activity of NSD2 resides in its catalytic SET domain, which is conserved among most lysine methyltransferases. Here we report the backbone $$\hbox {H}^{\mathrm{N}}$$ , N, C $$^{\prime }$$ , $$\hbox {C}^\alpha$$ and side-chain $$\hbox {C}^\beta$$ assignments of a 25 kDa NSD2 SET domain construct, spanning residues 991–1203. A chemical shift analysis of C $$^{\prime }$$ , $$\hbox {C}^\alpha$$ and $$\hbox {C}^\beta$$ resonances predicts a secondary structural pattern that is in agreement with homology models.
PubDate: 2016-07-01

• NMR backbone resonance assignment and solution secondary structure
determination of human NSD1 and NSD2
• Abstract: Abstract Proteins of the NSD family are histone-methyl transferases with critical functions in the regulation of chromatin structure and function. NSD1 and NSD2 are homologous proteins that function as epigenetic regulators of transcription through their abilities to catalyse histone methylation. Misregulation of NSD1 and NSD2 expression or mutations in their genes are linked to a number of human diseases such as Sotos syndrome, and cancers including acute myeloid leukemia, multiple myeloma, and lung cancer. The catalytic domain of both proteins contains a conserved SET domain which is involved in histone methylation. Here we report the backbone resonance assignments and secondary structure information of the catalytic domains of human NSD1 and NSD2.
PubDate: 2016-06-29

• Chemical shift assignments and secondary structure prediction for Q4DY78,
a conserved kinetoplastid-specific protein from Trypanosoma cruzi
• Abstract: Abstract Trypanosoma cruzi, Trypanosma brucei and Leishmania spp. are kinetoplastid protozoa causative agents of Chagas disease, sleeping sickness and leishmaniasis, respectively, neglected tropical diseases estimated to infect millions of people worldwide. Their genome sequencing has revealed approximately 50 % of genes encoding hypothetical proteins of unknown function, opening possibilities for novel target identification and drug discovery. Q4DY78 is a putative essential protein from T. cruzi conserved in the related kinetoplastids and divergent from mammalian host proteins. Here we report the 1H, 15N, and 13C chemical shift assignments and secondary structure analysis of the Q4DY78 protein as basis for NMR structure determination, functional analysis and drug screening.
PubDate: 2016-06-29

• 1 H, 13 C, and 15 N resonance assignments for the pro-inflammatory
cytokine interleukin-36α
• Abstract: Abstract Interleukin-36α (IL-36α) is a recently characterised member of the interleukin-1 superfamily. It is involved in the pathogenesis of inflammatory arthritis in one third of psoriasis patients. By binding of IL-36α to its receptor IL-36R via the NF-κB pathway other cytokines involved in inflammatory and apoptotic cascade are activated. The efficacy of complex formation is controlled by N-terminal processing. To obtain a more detailed view on the structure function relationship we performed a heteronuclear multidimensional NMR investigation and here report the 1H, 13C, and 15N resonance assignments for the backbone and side chain nuclei of the pro-inflammatory cytokine interleukin-36α.
PubDate: 2016-06-28

• 1 H N , 13 C, and 15 N resonance assignments of the CDTb-interacting
domain (CDTaBID) from the Clostridium difficile binary toxin catalytic
component (CDTa, residues 1–221)
• Abstract: Abstract Once considered a relatively harmless bacterium, Clostridium difficile has become a major concern for healthcare facilities, now the most commonly reported hospital-acquired pathogen. C. difficile infection (CDI) is usually contracted when the normal gut microbiome is compromised by antibiotic therapy, allowing the opportunistic pathogen to grow and produce its toxins. The severity of infection ranges from watery diarrhea and abdominal cramping to pseudomembranous colitis, sepsis, or death. The past decade has seen a marked increase in the frequency and severity of CDI among industrialized nations owing directly to the emergence of a highly virulent C. difficile strain, NAP1. Along with the large Clostridial toxins expressed by non-epidemic strains, C. difficile NAP1 produces a binary toxin, C. difficile transferase (CDT). As the name suggests, CDT is a two-component toxin comprised of an ADP-ribosyltransferase (ART) component (CDTa) and a cell-binding/translocation component (CDTb) that function to destabilize the host cytoskeleton by covalent modification of actin monomers. Central to the mechanism of binary toxin-induced pathogenicity is the formation of CDTa/CDTb complexes at the cell surface. From the perspective of CDTa, this interaction is mediated by the N-terminal domain (residues 1–215) and is spatially and functionally independent of ART activity, which is located in the C-terminal domain (residues 216–420). Here we report the 1HN, 13C, and 15N backbone resonance assignments of a 221 amino acid, ~26 kDa N-terminal CDTb-interacting domain (CDTaBID) construct by heteronuclear NMR spectroscopy. These NMR assignments represent the first component coordination domain for a family of Clostridium or Bacillus species harboring ART activity. Our assignments lay the foundation for detailed solution state characterization of structure–function relationships, toxin complex formation, and NMR-based drug discovery efforts.
PubDate: 2016-06-28

• Backbone 1 H, 13 C and 15 N resonance assignments of the OB domain of the
single stranded DNA-binding protein hSSB1 (NABP2/OBFC2B) and chemical
shift mapping of the DNA-binding interface
• Abstract: Abstract Single-stranded DNA-binding proteins (SSBs) are highly important in DNA metabolism and play an essential role in all major DNA repair pathways. SSBs are generally characterised by the presence of an oligonucleotide binding (OB) fold which is able to recognise single-stranded DNA (ssDNA) with high affinity. We discovered two news SSBs in humans (hSSB1 and hSSB2) that both contain a single OB domain followed by a divergent spacer region and a charged C-terminus. We have extensively characterised one of these, hSSB1 (NABP2/OBFC2B), in numerous important DNA processing events such as, in DNA double-stranded break repair and in the response to oxidative DNA damage. Although the structure of hSSB1 bound to ssDNA has recently been determined using X-ray crystallography, the detailed atomic level mechanism of the interaction of hSSB1 with ssDNA in solution has not been established. In this study we report the solution-state backbone chemical shift assignments of the OB domain of hSSB1. In addition, we have utilized NMR to map the DNA-binding interface of hSSB1, revealing major differences between recognition of ssDNA under physiological conditions and in the recently determined crystal structure. Our NMR data in combination with further biophysical and biochemical experiments will allow us to address these discrepancies and shed light onto the structural basis of DNA-binding by hSSB1 in solution.
PubDate: 2016-05-18

• 1 H, 15 N, 13 C resonance assignments for Saccharomyces cerevisiae Rad23
UBL domain
• Abstract: Abstract Rad23 functions in nucleotide excision repair and proteasome-mediated protein degradation. It has four distinct structural domains that are connected by flexible linker regions, including an N-terminal ubiquitin-like (UBL) domain that binds proteasomes. We report in this NMR study the 1H, 15N and 13C resonance assignments for the backbone and side chain atoms of the Rad23 UBL domain (Rad23UBL) with BioMagResBank accession number 25825. We find that a Rad23 proline amino acid (P20) located in a loop undergoes isomerization. The secondary structural elements predicted from the NMR data fit well to that of the Rad23UBL when complexed with E4 ubiquitin ligase Ufd2, as reported in a crystallographic structure. These complete assignments can be used to study the protein dynamics of the Rad23UBL and its interaction of with other ubiquitin receptors or proteasome subunits.
PubDate: 2016-05-17

• NMR resonance assignments of the major apple allergen Mal d 1
• Abstract: Abstract The major apple allergen Mal d 1 is the predominant cause of apple (Malus domestica) allergies in large parts of Europe and Northern America. Allergic reactions against this 17.5 kDa protein are the consequence of initial sensitization to the structurally homologous major allergen from birch pollen, Bet v 1. Consumption of apples can subsequently provoke immunologic cross-reactivity of Bet v 1-specific antibodies with Mal d 1 and trigger severe oral allergic syndroms, affecting more than 70 % of all individuals that are sensitized to birch pollen. While the accumulated immunological data suggest that Mal d 1 has a three-dimensional fold that is similar to Bet v 1, experimental structural data for this protein are not available to date. In a first step towards structural characterization of Mal d 1, backbone and side chain 1H, 13C and 15N chemical shifts of the isoform Mal d 1.0101 were assigned. The NMR-chemical shift data show that this protein is composed of seven β-strands and three α-helices, which is in accordance with the reported secondary structure of the major birch pollen allergen, indicating that Mal d 1 and Bet v 1 indeed have similar three-dimensional folds. The next stage in the characterization of Mal d 1 will be to utilize these resonance assignments in solving the solution structure of this protein.
PubDate: 2016-05-11

• Solid-state NMR sequential assignment of an Amyloid-β(1–42)
fibril polymorph
• Abstract: Abstract The formation of fibrils of the amyloid-β (Aβ) peptide is considered to be a key event in the pathology of Alzheimer’s disease (AD). The determination of a high-resolution structure of these fibrils is relevant for the understanding of the molecular basis of AD. In this work, we present the sequential resonance assignment of one of the polymorphs of Aβ(1–42) fibrils. We show that most of the protein is rigid, while a stretch of 4 residues (11–14) is not visible by solid-state NMR spectroscopy due to dynamics.
PubDate: 2016-05-10

• Solid-state NMR sequential assignment of the β-endorphin peptide in
its amyloid form
• Abstract: Abstract Insights into the three-dimensional structure of hormone fibrils are crucial for a detailed understanding of how an amyloid structure allows the storage of hormones in secretory vesicles prior to hormone secretion into the blood stream. As an example for various hormone amyloids, we have studied the endogenous opioid neuropeptide β-endorphin in one of its fibril forms. We have achieved the sequential assignment of the chemical shifts of the backbone and side-chain heavy atoms of the fibril. The secondary chemical shift analysis revealed that the β-endorphin peptide adopts three β-strands in its fibril state. This finding fosters the amyloid nature of a hormone at the atomic level.
PubDate: 2016-05-10

• Backbone and side-chain chemical shift assignments for the C-terminal
domain of Tcb2, a cytoskeletal calcium-binding protein from Tetrahymena
thermophila
• Abstract: Abstract Tcb2 is a putative calcium-binding protein from the membrane-associated cytoskeleton of the ciliated protozoan Tetrahymena thermophila. It has been hypothesized to participate in several calcium-mediated processes in Tetrahymena, including ciliary movement, cell cortex signaling, and pronuclear exchange. Sequence analysis suggests that the protein belongs to the calmodulin family, with N- and C-terminal domains connected by a central linker, and two helix-loop-helix motifs in each domain. However, its calcium-binding properties, structure and precise biological function remain unknown. Interestingly, Tcb2 is a major component of unique contractile fibers isolated from the Tetrahymena cytoskeleton; in these fibers, addition of calcium triggers an ATP-independent type of contraction. Here we report the 1H, 13C and 15N backbone and side-chain chemical shift assignments of the C-terminal domain of the protein (Tcb2-C) in the absence and presence of calcium ions. 1H–15N HSQC spectra show that the domain is well folded both in the absence and presence of calcium, and undergoes a dramatic conformational change upon calcium addition. Secondary structure prediction from chemical shifts reveals an architecture encountered in other calcium-binding proteins, with paired EF-hand motifs connected by a flexible linker. These studies represent a starting point for the determination of the high-resolution solution structure of Tcb2-C at both low and high calcium levels, and, together with additional structural studies on the full-length protein, will help establish the molecular basis of Tcb2 function and unique contractile properties.
PubDate: 2016-05-07

• Backbone and side-chain 1 H, 13 C, and 15 N chemical shift assignments for
the apo -form of the lytic polysaccharide monooxygenase Nc LPMO9C
• Abstract: Abstract The apo-form of the 23.3 kDa catalytic domain of the AA9 family lytic polysaccharide monooxygenase NcLPMO9C from Neurospora crassa has been isotopically labeled and recombinantly expressed in Pichia pastoris. In this paper, we report the 1H, 13C, and 15N chemical shift assignments of this LPMO.
PubDate: 2016-05-04

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