Backbone and side-chain 1H, 13C, 15N resonance assignments of rat lipocalin2

Lipocalin2 plays an important role in the innate immune system. In this article we report the backbone and side-chain resonance assignments of rat lipocalin2 (rLcn2). These assignments provide a basis for determining the structure and dynamics of rLcn2. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Backbone 1H, 15N, and 13C resonance assignment of HP1242 from Helicobacter pylori

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone (1)H, (15)N, and (13)C resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95 % of all of the (1)HN, (15)N, (13)CO, (13)Calpha, and (13)Cbeta resonances that cover 75 non-Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.     

Backbone and side-chain 1H, 15N and 13C assignments of mouse peptide ESP4

A peptide or a small protein released from an exocrine gland or in urine is utilized as a chemosignal that elicits social or reproductive behavior in mice. Recently, we identified the male-specific peptide, exocrine gland-secreting peptide 1 (ESP1), in mouse tear fluids that enhanced female sexual receptive behavior, and determined the three dimensional structure. ESP1 appears to be a member of multigene family that consists of 38 genes in mice, which we call the ESP family. ESP4, a member of the ESP family, is expressed in various exocrine glands, and shows the highest sequence similarity with ESP1. Here, we report the NMR assignments of ESP4 which provides a basis for NMR analyses of this protein. Our results will give insight into structural relationships within the ESP family.     

Backbone and side-chain 1H, 15N, and 13C resonance assignments of Norwalk virus protease

Norovirus protease cleaves the virus-encoded polyprotein into six mature nonstructural proteins, presenting itself as an essential enzyme for the viral replication as well as an attractive target for the antiviral drug development. A deeper understanding of the structural mechanism of the protease-substrates/inhibitors interactions by means of solution NMR methods would facilitate a rational design of the virus protease inhibitor. We here report the backbone and side-chain resonance assignment of the protease from Norwalk virus, which is the prototype strain of norovirus. The assignment data has been deposited in the BMRB database under the accession number 17523.     

1H, 13C, and 15N resonance assignments of a general stress protein GSP13 from Bacillus subtilis

GSP13 encoded by gene yugI is a general stress protein in Bacillus subtilis. The NMR assignments of the protein are essential for its structure determination.     

Backbone 1H, 15N, and 13C resonance assignment and secondary structure prediction of HP0495 from Helicobacter pylori

HP0495 (Swiss-Prot ID; Y495_HELPY) is an 86-residue hypothetical protein from Helicobacter pylori strain 26695. The function of HP0495 cannot be identified based on sequence homology, and HP0495 is included in a fairly unique sequence family. Here, we report the sequence-specific backbone resonance assignments of HP0495. About 97% of all the 1HN, 15N, 13Calpha, 13Cbeta, and 13CO resonances were assigned unambiguously. We could predict the secondary structure of HP0495, by analyzing the deviation of the 13Calpha and 13Cbeta shemical shifts from their respective random coil values. Secondary structure prediction shows that HP0495 consists of two alpha-helices and four beta-strands. This study is a prerequisite for determining the solution structure of HP0495 and investigating the protein-protein interaction between HP0495 and other Helicobacter pylori proteins.     

1H, 13C and 15N resonance assignment of Urm1 from Trypanosoma brucei

Urm1 (ubiquitin-related modifier), involved in diverse biological processes in yeast, is proved to be a “molecular fossil” in ubiquitin superfamily. Here we report the resonance assignment of Urm1 from Trypanosoma brucei.     

1H, 13C, and 15N backbone and side-chain chemical shift assignment of the staphylococcal MazF mRNA interferase

MazF proteins are ribonucleases that cleave mRNA with high sequence-specificity as part of bacterial stress response and that are neutralized by the action of the corresponding antitoxin MazE. Prolonged activation of the toxin MazF leads to cell death. Several mazEF modules from Gram-negative bacteria have been characterized in terms of catalytic activity, auto-regulation mechanism and structure, but less is known about their distant relatives found in Gram-positive organisms. Currently, no solution NMR structure is available for any wild-type MazF toxin. Here we report the ¹H, ¹⁵N and ¹³C backbone and side-chain chemical shift assignments of this toxin from the pathogen bacterium Staphylococcus aureus. The BMRB accession number is 17288.     

Backbone 1H, 13C, and 15N resonance assignments for lysozyme from bacteriophage lambda

Lysozyme from lambda bacteriophage (λ lysozyme) is an 18 kDa globular protein displaying some of the structural features common to all lysozymes; in particular, λ lysozyme consists of two structural domains connected by a helix, and has its catalytic residues located at the interface between these two domains. An interesting feature of λ lysozyme, when compared to the well-characterised hen egg-white lysozyme, is its lack of disulfide bridges; this makes λ lysozyme an interesting system for studies of protein folding. A comparison of the folding properties of λ lysozyme and hen lysozyme will provide important insights into the role that disulfide bonds play in the refolding pathway of the latter protein. Here we report the ¹H, ¹³C and ¹⁵N backbone resonance assignments for λ lysozyme by heteronuclear multidimensional NMR spectroscopy. These assignments provide the starting point for detailed investigation of the refolding pathway using pulse-labelling hydrogen/deuterium exchange experiments monitored by NMR.     

Backbone 1H, 13C and 15N resonance assignment of the C-terminal EGF-cbEGF pair of LTBP1 and flanking residues

Latent TGFβ binding protein 1 (LTBP1) is a large extracellular protein that has been shown to bind covalently to the propeptide of TGFβ cytokines and form a large latent complex, which is then incapable of binding TGFβ receptors. LTBP1 has also been demonstrated to interact with a number of insoluble extracellular matrix components, such as fibrillin, which may play a role in TGFβ regulation. Here we present the backbone ¹H, ¹³C and ¹⁵N assignments for two EGF domains of human LTBP1, and flanking regions, together forming a 12 kDa protein fragment at the C-terminus of LTBP1. This region is of particular interest as it is postulated to be involved in interactions with fibrillin microfibrils.     

1H, 13C and 15N resonance assignment of truncated SUMO from Trypanosoma brucei

SUMO (small ubiquitin-like modifier) plays important roles in diverse processes by posttranslationally modifying many proteins. Here we report the resonance assignment of the truncated SUMO from Trypanosoma brucei.     

Backbone and side-chain 1H, 15N and 13C resonance assignments of S18Y mutant of ubiquitin carboxy-terminal hydrolase L1

Ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), also known as PGP9.5, is a protein of 223 amino acids. Although it was originally characterized as a deubiquitinating enzyme, recent studies indicate that it also functions as a ubiquitin (Ub) ligase and a mono-Ub stabilizer. It is highly abundant in brain, constituting up to 2% of total brain proteins. Down-regulation and extensive oxidative modification of UCH-L1 have been observed in the brains of Alzheimer’s disease (AD) and Parkinson’s disease (PD) patients. Mutations in the UCH-L1 gene have been reported to be linked to Parkinson’s disease, in particular, the I93 M variant is associated with a higher susceptibility of PD in contrast to a higher protection against PD for the S18Y variant. Hence, the structure of UCH-L1 and the underlying effects of disease associated mutations on the structure and function of UCH-L1 are of considerable interest. Here, we report the NMR spectral assignments of the S18Y human UCH-L1 mutant with the aim to obtain better understanding about the risk of Parkinson’s disease against structural and dynamical changes induced by this mutation on UCH-L1.     

Backbone and side-chain resonance assignments (1H, 15N and 13C) of the ubiquitin homology domain of mouse BAG-1

BAG-1, an important regulatory protein associates with several signaling molecules and is capable of suppressing apoptosis. A 97-amino acid segment that includes the ubiquitin homology domain of mouse BAG-1 interacts with the cytoplasmic tail domain of proHB-EGF, and this interaction is likely to have functional significance. Here we report the backbone and side-chain resonance assignments for this 97-amino acid segment of mouse BAG-1. The assignment data has been deposited in the BMRB database under the accession number 18416.     

1H, 13C, 15N backbone and side-chain resonance assignments of rat angiogenin

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.     

Backbone and side-chain 1H, 13C and 15N assignments of the ubiquitin-associated domain of human X-linked inhibitor of apoptosis protein

X-linked inhibitor of apoptosis protein (XIAP), a leading member of the family of inhibitor of apoptosis (IAP) proteins, is considered as the most potent and versatile inhibitor of caspases and apoptosis. It has been reported that XIAP is frequently overexpressed in cancer and its expression level is implicated in contributing to tumorigenesis, disease progression, chemoresistance and poor patient-survival. Therefore, XIAP is one of the leading targets in drug development for cancer therapy. Recently, based on bioinformatics study, a previously unrecognized but evolutionarily conserved ubiquitin-associated (UBA) domain in IAPs was identified. The UBA domain is found to be essential for the oncogenic potential of IAP, to maintain endothelial cell survival and to protect cells from TNF-α-induced apoptosis. Moreover, the UBA domain is required for XIAP to activate NF-κB. In the present study, we report the near complete resonance assignments of the UBA domain-containing region of human XIAP protein. Secondary structure prediction based on chemical shift index (CSI) analysis reveals that the protein is predominately α-helical, which is consistent with the structures of known UBA proteins.