Leupeptin reduces impulse noise induced hearing loss

<p>Abstract</p> <p>Background</p> <p>Exposure to continuous and impulse noise can induce a hearing loss. Leupeptin is an inhibitor of the calpains, a family of calcium-activated proteases which promote cell death. The objective of this study is to assess whether Leupeptin could reduce the hearing loss resulting from rifle impulse noise.</p> <p>Methods</p> <p>A polyethelene tube was implanted into middle ear cavities of eight fat sand rats (16 ears). Following determination of auditory nerve brainstem evoked response (ABR) threshold in each ear, the animals were exposed to the noise of 10 M16 rifle shots. Immediately after the exposure, saline was then applied to one (control) ear and non-toxic concentrations of leupeptin determined in the first phase of the study were applied to the other ear, for four consecutive days.</p> <p>Results</p> <p>Eight days after the exposure, the threshold shift (ABR) in the control ears was significantly greater (44 dB) than in the leupeptin ears (27 dB).</p> <p>Conclusion</p> <p>Leupeptin applied to the middle ear cavity can reduce the hearing loss resulting from exposure to impulse noise.</p

SiteEngines: recognition and comparison of binding sites and protein–protein interfaces

Protein surface regions with similar physicochemical properties and shapes may perform similar functions and bind similar binding partners. Here we present two web servers and software packages for recognition of the similarity of binding sites and interfaces. Both methods recognize local geometrical and physicochemical similarity, which can be present even in the absence of overall sequence or fold similarity. The first method, SiteEngine (), receives as an input two protein structures and searches the complete surface of one protein for regions similar to the binding site of the other. The second, Interface-to-Interface (I2I)-SiteEngine (), compares protein–protein interfaces, which are regions of interaction between two protein molecules. It receives as an input two structures of protein–protein complexes, extracts the interfaces and finds the three-dimensional transformation that maximizes the similarity between two pairs of interacting binding sites. The output of both servers consists of a superimposition in PDB file format and a list of physicochemical properties shared by the compared entities. The methods are highly efficient and the freely available software packages are suitable for large-scale database searches of the entire PDB

RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases

We present a new database and an on-line search engine, which store and query the protein binding pockets that interact with single-stranded RNA nucleotide bases. The database consists of a classification of binding sites derived from protein–RNA complexes. Each binding site is assigned to a cluster of similar binding sites in other protein–RNA complexes. Cluster members share similar spatial arrangements of physico–chemical properties, thus can reveal novel similarity between proteins and RNAs with different sequences and folds. The clusters provide 3D consensus binding patterns important for protein–nucleotide recognition. The database search engine allows two types of useful queries: first, given a PDB code of a protein–RNA complex, RsiteDB can detail and classify the properties of the protein binding pockets accommodating extruded RNA nucleotides not involved in local RNA base pairing. Second, given an unbound protein structure, RsiteDB can perform an on-line structural search against the constructed database of 3D consensus binding patterns. Regions similar to known patterns are predicted to serve as binding sites. Alignment of the query to these patterns with their corresponding RNA nucleotides allows making unique predictions of the protein–RNA interactions at the atomic level of detail. This database is accessable at http://bioinfo3d.cs.tau.ac.il/RsiteDB