Exome sequencing and functional analysis identifies a novel mutation in <em>EXT1</em> gene that causes multiple osteochondromas

Multiple osteochondromas (MO) is an inherited skeletal disorder, and the molecular mechanism of MO remains elusive. Exome sequencing has high chromosomal coverage and accuracy, and has recently been successfully used to identify pathogenic gene mutations. In this study, exome sequencing followed by Sanger sequencing validation was first used to screen gene mutations in two representative MO patients from a Chinese family. After filtering the data from the 1000 Genome Project and the dbSNP database (build 132), the detected candidate gene mutations were further validated via Sanger sequencing of four other members of the same MO family and 200 unrelated healthy subjects. Immunohistochemisty and multiple sequence alignment were performed to evaluate the importance of the identified causal mutation. A novel frameshift mutation, c.1457insG at codon 486 of exon 6 of EXT1 gene, was identified, which truncated the glycosyltransferase domain of EXT1 gene. Multiple sequence alignment showed that codon 486 of EXT1 gene was highly conserved across various vertebrates. Immunohistochemisty demonstrated that the chondrocytes with functional EXT1 in MO were less than those in extragenetic solitary chondromas. The novel c.1457insG deleterious mutation of EXT1 gene reported in this study expands the causal mutation spectrum of MO, and may be helpful for prenatal genetic screening and early diagnosis of MO

The contribution of cellulosomal scaffoldins to cellulose hydrolysis by Clostridium thermocellum analyzed by using thermotargetrons

<p> Background: Clostridium thermocellum is a thermophilic anaerobic bacterium that degrades cellulose by using a highly effective cellulosome, a macromolecular complex consisting of multiple cellulose degrading enzymes organized and attached to the cell surface by non-catalytic scaffoldins. However, due largely to lack of efficient methods for genetic manipulation of C. thermocellum, it is still unclear how the different scaffoldins and their functional modules contribute to cellulose hydrolysis.</p

Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a β-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization

Compatible topologies and parameters for NMR structure determination of carbohydrates by simulated annealing

<div><p>The use of NMR methods to determine the three-dimensional structures of carbohydrates and glycoproteins is still challenging, in part because of the lack of standard protocols. In order to increase the convenience of structure determination, the topology and parameter files for carbohydrates in the program Crystallography & NMR System (CNS) were investigated and new files were developed to be compatible with the standard simulated annealing protocols for proteins and nucleic acids. Recalculating the published structures of protein-carbohydrate complexes and glycosylated proteins demonstrates that the results are comparable to the published structures which employed more complex procedures for structure calculation. Integrating the new carbohydrate parameters into the standard structure calculation protocol will facilitate three-dimensional structural study of carbohydrates and glycosylated proteins by NMR spectroscopy.</p></div

The torsion angles of carbohydrates in the original and recalculated structures.

<p>The torsion angles of carbohydrates in the original and recalculated structures.</p

The carbohydrate Ramachandran plots of original and recalculated structures.

<p>Red crosses, original structures; blue crosses, recalculated structures. <b>a</b>, The plot of α-Fuc-(1,3)-β-GlcNAc torsion angles in the structures of the CCL2-glycan complex. <b>b</b>, The plot of β-GlcNAc-(1,4)-β-GlcNAc torsion angles in the structures of the CCL2-glycan complex. <b>c</b>, The plot of α-GalNAc-Thr torsion angles in the structures of the O-linked glycoprotein GalNAcα-IFNα2a. The background plots in <b>a</b> and <b>b</b> are the maps from GlycoMapsDB (<a href="http://www.glycosciences.de/modeling/glycomapsdb/" target="_blank">http://www.glycosciences.de/modeling/glycomapsdb/</a>), while the background plot in <b>c</b> is the torsion angles from PDB (grey dots) because of no α-GalNAc-Thr map in GlycoMapsDB.</p

Enantiomeric Tartaric Acid Production Using cis-Epoxysuccinate Hydrolase: History and Perspectives

Tartaric acid is an important chiral chemical building block with broad industrial and scientific applications. The enantioselective synthesis of l(+)- and d(&minus;)-tartaric acids has been successfully achieved using bacteria presenting cis-epoxysuccinate hydrolase (CESH) activity, while the catalytic mechanisms of CESHs were not elucidated clearly until very recently. As biocatalysts, CESHs are unique epoxide hydrolases because their substrate is a small, mirror-symmetric, highly hydrophilic molecule, and their products show very high enantiomeric purity with nearly 100% enantiomeric excess. In this paper, we review over forty years of the history, process and mechanism studies of CESHs as well as our perspective on the future research and applications of CESH in enantiomeric tartaric acid production

The problem of IMPROPER term definition for the chiral carbon atom.

<p><b>a</b>, The problematic structure of the sugar ring calculated from the original carbohydrate topology file. <b>b</b>, The definition of the IMPROPER term of the sugar ring chiral carbon atom C3 in the original carbohydrate topology file. <b>c</b>, The definition of the IMPROPER term of serine CA atom in the protein topology file. <b>d</b>, The new definition of the IMPROPER term of the sugar chiral carbon atom C3.</p