Non-truncating LIFR mutation: causal for prominent congenital pain insensitivity phenotype with progressive vertebral destruction?

We present a Qatari family with two children who displayed a characteristic phenotype of congenital marked pain insensitivity with hypohidrosis and progressive aseptic destruction of joints and vertebrae resembling that of hereditary sensory and autonomic neuropathies (HSANs). The patients, aged 10 and 14, remained of uncertain genetic diagnosis until whole genome sequencing was pursued. Genome sequencing identified a novel homozygous C65S mutation in the LIFR gene that is predicted to markedly destabilize and alter the structure of a particular domain and consequently to affect the functionality of the whole multi-domain LIFR protein. The C65S mutant LIFR showed altered glycosylation and an elevated expression level that might be attributed to a slow turnover of the mutant form. LIFR mutations have been reported in Stüve-Wiedemann syndrome (SWS), a severe autosomal recessive skeletal dysplasia often resulting in early death. Our patients share some clinical features of rare cases of SWS long-term survivors; however, they also phenocopy HSAN due to the marked pain insensitivity phenotype and progressive bone destruction. Screening for LIFR mutations might be warranted in genetically unresolved HSAN phenotypes.

Sorting algorithms for single-particle imaging experiments at X-ray free-electron lasers.

Modern X-ray free-electron lasers (XFELs) operating at high repetition rates produce a tremendous amount of data. It is a great challenge to classify this information and reduce the initial data set to a manageable size for further analysis. Here an approach for classification of diffraction patterns measured in prototypical diffract-and-destroy single-particle imaging experiments at XFELs is presented. It is proposed that the data are classified on the basis of a set of parameters that take into account the underlying diffraction physics and specific relations between the real-space structure of a particle and its reciprocal-space intensity distribution. The approach is demonstrated by applying principal component analysis and support vector machine algorithms to the simulated and measured X-ray data sets.

Resonant addressing and manipulation of silicon vacancy qubits in silicon carbide.

Several systems in the solid state have been suggested as promising candidates for spin-based quantum information processing. In spite of significant progress during the last decade, there is a search for new systems with higher potential [D. DiVincenzo, Nat. Mater. 9, 468 (2010)]. We report that silicon vacancy defects in silicon carbide comprise the technological advantages of semiconductor quantum dots and the unique spin properties of the nitrogen-vacancy defects in diamond. Similar to atoms, the silicon vacancy qubits can be controlled under the double radio-optical resonance conditions, allowing for their selective addressing and manipulation. Furthermore, we reveal their long spin memory using pulsed magnetic resonance technique. All these results make silicon vacancy defects in silicon carbide very attractive for quantum applications.

DBAli: a database of protein structure alignments.

SUMMARY: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al., Nucleic Acids Res., 28, 257-259, 2000) and CE (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions. AVAILABILITY: http://guitar.rockefeller.edu/DBAli/

2.9 A crystal structure of ligand-free tryptophanyl-tRNA synthetase: domain movements fragment the adenine nucleotide binding site.

The crystal structure of ligand-free tryptophanyl-tRNA synthetase (TrpRS) was solved at 2.9 A using a combination of molecular replacement and maximum-entropy map/phase improvement. The dimeric structure (R = 23.7, Rfree = 26.2) is asymmetric, unlike that of the TrpRS tryptophanyl-5'AMP complex (TAM; Doublié S, Bricogne G, Gilmore CJ, Carter CW Jr, 1995, Structure 3:17-31). In agreement with small-angle solution X-ray scattering experiments, unliganded TrpRS has a conformation in which both monomers open, leaving only the tryptophan-binding regions of their active sites intact. The amino terminal alphaA-helix, TIGN, and KMSKS signature sequences, and the distal helical domain rotate as a single rigid body away from the dinucleotide-binding fold domain, opening the AMP binding site, seen in the TAM complex, into two halves. Comparison of side-chain packing in ligand-free TrpRS and the TAM complex, using identification of nonpolar nuclei (Ilyin VA, 1994, Protein Eng 7:1189-1195), shows that significant repacking occurs between three relatively stable core regions, one of which acts as a bearing between the other two. These domain rearrangements provide a new structural paradigm that is consistent in detail with the "induced-fit" mechanism proposed for TyrRS by Fersht et al. (Fersht AR, Knill-Jones JW, Beduelle H, Winter G, 1988, Biochemistry 27:1581-1587). Coupling of ATP binding determinants associated with the two catalytic signature sequences to the helical domain containing the presumptive anticodon-binding site provides a mechanism to coordinate active-site chemistry with relocation of the major tRNA binding determinants.

Non-polar nuclei in fungal microbial RNases.

An application of a previously proposed method for the analysis of the non-polar structure of proteins is presented. A detailed analysis of the composition and properties of non-polar nuclei and microclusters of fungal microbial ribonucleases has been performed on the basis of the 3-D structures of RNase T1 and related proteins. Three hydrophobic nuclei were found in these structures. It has been shown that all residues in non-polar nuclei have high homology (approximately 89%). Residues in the nuclei are practically fully buried in the interior of a molecule. Detailed analysis of non-polar nuclei properties shows that these nuclei determine the hydrophobic core of a protein and the location and role of each residue in the non-polar interior of proteins. In addition it was found that there are variable residues not only on the surface of a protein but on the surface of the nuclei inside the protein and between the nuclei and that there is a consistent region in all proteins, the hydrophobic gamma-nuclei. An evaluation of the stability of non-polar nuclei, the conservation of their compositions and their positions in the protein globule, allows one to assume that these three nuclei play an important functional role in the stability and folding of molecules of RNases and possibly can be considered as independent structural elements of 3-D structures of these proteins.

Analysis of non-polar regions in proteins.

A new method for finding hydrophobic nuclei and microclusters in protein structure is proposed. The method uses simple and clear-cut criteria based on an analysis of distances between the hydrocarbon groups of all residues. A detailed analysis of the composition and properties of hydrophobic nucleic and microclusters for proteins of different types has been carried out. This approach reveals that a hydrophobic nucleus can be composed not merely of classical hydrophobic amino acids, but also of dicarboxylic acids, their amides, arginine, lysine, histidine and tyrosine. The hydrophobic nucleus defined by this method should be considered as an individual structural unit along with such elements of the secondary structure as alpha-helices, beta-turns and beta-sheets.