PONDEROSA-C/S: client–server based software package for automated protein 3D structure determination

Peak-picking Of Noe Data Enabled by Restriction Of Shift Assignments-Client Server (PONDEROSA-C/S) builds on the original PONDEROSA software (Lee et al. in Bioinformatics 27:1727–1728. doi:10.1093/bioinformatics/btr200, 2011) and includes improved features for structure calculation and refinement. PONDEROSA-C/S consists of three programs: Ponderosa Server, Ponderosa Client, and Ponderosa Analyzer. PONDEROSA-C/S takes as input the protein sequence, a list of assigned chemical shifts, and nuclear Overhauser data sets (¹³C- and/or ¹⁵N-NOESY). The output is a set of assigned NOEs and 3D structural models for the protein. Ponderosa Analyzer supports the visualization, validation, and refinement of the results from Ponderosa Server. These tools enable semi-automated NMR-based structure determination of proteins in a rapid and robust fashion. We present examples showing the use of PONDEROSA-C/S in solving structures of four proteins: two that enable comparison with the original PONDEROSA package, and two from the Critical Assessment of automated Structure Determination by NMR (Rosato et al. in Nat Methods 6:625–626. doi:10.1038/nmeth0909-625, 2009) competition. The software package can be downloaded freely in binary format from http://pine.nmrfam.wisc.edu/download_packages.html. Registered users of the National Magnetic Resonance Facility at Madison can submit jobs to the PONDEROSA-C/S server at http://ponderosa.nmrfam.wisc.edu, where instructions, tutorials, and instructions can be found. Structures are normally returned within 1–2 days.     

Backbone resonance assignment of Alt a 1, a unique β-barrel protein and the major allergen of Alternaria alternata

Alt a 1 is the major allergen of the fungus Alternaria alternata and can be found in the cell wall of its spores. It is a cysteine linked homodimeric protein with a unique β-barrel fold as recently revealed by X-ray crystallography. Despite the elucidation of its structure, its biological function remains unknown. For Alternaria-sensitized patients, contact leads to respiratory allergy and in severe cases to asthma-related death. Here we report the sequence-specific Alt a 1 backbone ¹H, ¹⁵N and ¹³C chemical shift assignment.     

NMR assignment of backbone and side chain resonances for a putative protein–protein interaction module from a family 84 glycoside hydrolase of Clostridium perfringens

A family of Clostridium perfringens glycoside hydrolases (CpGH84A-E), with a conserved family 84 catalytic module, are thought to target the gastric mucosal layer. Chemical shift assignments have been completed for a putative protein-protein interaction X82 module from CpGH84C.     

Morphogen signaling at the vertebrate growth cone: a few cases or a general strategy?

Axon navigation relies on the competence of growth cones to sense and interpret attractive and repulsive guidance cues present along their trajectory. For most neurons, this process is mediated by a limited number of conserved families of ligand-receptor signaling systems, including Ephrin/Eph, Netrins/DCC-Unc5, Slits/Robo, and Semaphorins/Plexin-Neuropilin. Recent studies have demonstrated that some neurons respond also to well-known secreted signaling molecules, best known for their roles as morphogens, such as BMP7, SHH, FGF8, and Wnt. Thus, retina ganglion cell axon navigation is influenced by FGF, SHH, and possibly BMP signaling. Similarly, commissural neurons in the spinal cord respond sequentially to the activity of BMP, SHH, and Wnt to extend toward and away from their intermediate target, the floor plate. The data that support this conclusion will be summarized and how morphogens may signal at the growth cone will be discussed.     

NMR assignment of backbone and side chain resonances for a dockerin-containing C-terminal fragment of the putative μ-toxin from Clostridium perfringens

The μ-toxin of Clostridium perfringens, termed CpGH84A, is modular hydrolytic enzyme that contributes to the pathogenicity of this organism. Backbone and side chain ¹H, ¹³C, and ¹⁵N resonance assignments have been determined for the C-terminal 15.5 kDa FIVAR-Doc modular pair of CpGH84A.     

Complete backbone assignment of a Ca2+-binding protein of the βγ-crystallin superfamily from Methanosarcina acetivorans, at two denaturant concentrations

We report here almost complete backbone assignment of a Ca²⁺-binding protein of the βγ-crystallin superfamily from Methanosarcina acetivorans, at two denaturant (GdmCl) concentrations, using double and triple resonance experiments. These NMR assignments will be useful to understand the unfolding path of this protein. Ravi P. Barnwal and Geetika Agarwal have contributed equally.     

Ageing and the regulation of protein synthesis: a balancing act?

Ageing in diverse species ranging from yeast to humans is associated with extensive changes in both general and specific protein synthesis. Accumulating evidence now indicates that these alterations are not simply a corollary of the ageing process but, rather, they have a causative role in senescent decline. Indeed, interfering with mRNA translation significantly influences longevity. Interestingly, the mechanisms that control mRNA translation interface with intricate, conserved signalling pathways and specific conditions that regulate ageing, such as the insulin-insulin growth factor 1 signalling pathway and caloric restriction. This emerging relationship reveals that protein synthesis is a novel determinant of ageing in diverse organisms such as yeast, worms, flies and mice and can thus be considered as a universal component of the ageing process.     

Sequential assignment of the backbone nuclei (1H,15N and13C) of c-H-ras p21 (1–166).GDP using a novel 4D NMR strategy

Summary The c-H-ras p21 protein is the product of the humanras proto-oncogene, a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. These proteins play an important role in the control of cellular growth. We report here the sequential assignment of the backbone nuclei in a truncated form of the 21-kD gene product, using our recently proposed 4D NMR strategy (Boucher et al., 1992). These assignments are the first step towards a full investigation of the structure, dynamics and interactions of wild-type and oncogenicrasp21 using NMR spectroscopy. Some of the data were presented at the 33rd ENC held at Asilomar, California, U.S.A., in April 1992.Supplementary material is available from the corresponding authors: One table containing the complete resonance assignment of c-H-ras p21 (1–166).GDP.     

Comparison between Urticaceae (Parietaria) pollen count and hay fever symptoms: assessment of a «threshold-value»

Summary A comparison betweenParietaria pollen count and allergic symptoms of rhino-conjunctivitis in the early season was used in utilized to determine a «threshold-value» for this pollen. Clinical data were obtained from diary-cards of 34 allergic patients and pollen data from a volumetric sampling, carried out by means of a Hirst-Burkard pollen-trap. A significant correlation (r=0.98) was found between pollen count and symptom scores. Mild symptoms were registered with concentrations above 10–15 pollens/m³. Severe symptoms occurred when pollen count exceeded 80/m³/24 h., and over 90% of patients recorded symptoms. The importance of the late reactions and of the total allergenic airborne content are emphasized.     

δ-Aminolevulinate dehydratase: Induced expression and regional assignment of the human gene to chromosome 9q13»qter

Summary The structural gene encoding human -aminolevulinate dehydratase has been assigned to the long arm of chromosome 9 by somatic cell hybridization techniques using murine erythroleukemia-human fibroblast somatic cell hybrids. Dimethyl sulfoxide induction of erythroid differentiation in these hybrid cells resulted in a 3 to 12-fold increase in the levels of total -aminolevulinate dehydratase. Human -aminolevulinate dehydratase was detected by an immunodiscrimination assay using polyclonal mouse anti-human aminolevulinate dehydratase antibodies. Of four primary hybrid clones, each from an independent fusion, one hybrid line, XX-8, was positive for human -aminolevulinate dehydratase. Examination of 23 secondary, tertiary, and quaternary XX-8 subclones revealed that the expression of the human isozyme segregated with human chromosome 9q, confirming the provisional regional assignment made by classical linkage studies. One positive quaternary clone, XX-8-H21-H7-2, expressed human -aminolevulinate dehydratase activity and contained only human 9q13»qter. In addition, studies of tetiary and quaternary subclones from two series, XX-8-A31 and XX-8-H21-H7, indicated that murine regulatory factors increased the human as well as the murine enzymatic activity following induction of erythroid differentiation.     

1H, 13C and 15N backbone and side chain resonance assignments of a 28 kDa active mutant of maize ribosome-inactivating protein (MOD)

We report the full resonance assignments of MOD, which is an active mutant of maize ribosome-inactivating protein (mRIP). mRIP is a unique RIP which is synthesized as an inactive precursor and processed by removal of an internal inactivation region to yield an active form.     

Sequence-specific 1H, 13C, and 15N backbone assignment of the 28 kDa PDZ2/PDZ3 tandem domain of the protein tyrosine phosphatase PTP-BL

Protein tyrosine phosphatase-basophil like (PTP-BL) represents a large multi domain non-transmembrane scaffolding protein that contains five PDZ domains. Here we report the backbone assignments of the PDZ2/PDZ3 tandem domain of PTP-BL. These assignments now provide a basis for the detailed structural investigation of the interaction between the PDZ domains 2 and 3 of PTP-BL. It will lead to a better understanding of the proposed scaffolding function of this tandem domain in multi-protein complexes assembled by PTB-BL. Christian P. Fetzer, Janelle Sauvageau and Gerd Kock contributed equally to this work.     

An extended combinatorial 15N, 13Cα, and $$ ^{13} {\text{C}}^{\prime } $$ labeling approach to protein backbone resonance assignment

Solution NMR studies of α-helical membrane proteins are often complicated by severe spectral crowding. In addition, hydrophobic environments like detergent micelles, isotropic bicelles or nanodiscs lead to considerably reduced molecular tumbling rates which translates into line-broadening and low sensitivity. Both difficulties can be addressed by selective isotope labeling methods. In this publication, we propose a combinatorial protocol that utilizes four different classes of labeled amino acids, in which the three backbone heteronuclei (amide nitrogen, α-carbon and carbonyl carbon) are enriched in ¹⁵N or ¹³C isotopes individually as well as simultaneously. This results in eight different combinations of dipeptides giving rise to cross peaks in ¹H–¹⁵N correlated spectra. Their differentiation is achieved by recording a series of HN-detected 2D triple-resonance spectra. The utility of this new scheme is demonstrated with a homodimeric 142-residue membrane protein in DHPC micelles. Restricting the number of selectively labeled samples to three allowed the identification of the amino-acid type for 77 % and provided sequential information for 47 % of its residues. This enabled us to complete the backbone resonance assignment of the uniformly labeled protein merely with the help of a 3D HNCA spectrum, which can be collected with reasonable sensitivity even for relatively large, non-deuterated proteins.