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Computational ribonucleomics of heavy metal stress tolerant Bacillus sp. strain SJ-101 16SrRNA gene has led to the identification of a novel small non-coding RNA (sRNA) and promoter-like sequences within 3' region of the gene. Using RNAz web server, a 123 bp long functional sRNA with significant thermodynamic stability (Energy contribution: -25.2) and evolutionary conservation (structure conservation...
We present an algorithmic approach for determining, in polynomial time, disulfide bonds in proteins using mass spectrometry data. The proposed technique is based on matching the set of all theoretically possible disulfide bonded structures with precursor ions derived from a tandem MS/MS experiment. For each match found, theoretical fragments from a disulfide bonded peptide structure are matched with...
Transducers used in biosensing applications are plagued by biofouling, which refers to the binding of nonspecific proteins to the device surface resulting in a compromise of the device sensitivity and selectivity. Acoustic streaming, resulting from high intensity sound waves, has the potential to address the issue of biofouling elimination in biosensors. Multi-directional transducers have the capability...
The key issues related to biosensor technology include selectivity, sensitivity, response and recovery times, and detection limit; most of these limitations stem from biofouling resulting from the binding of undesirable moieties such as non-specific proteins to the sensor surface. Thus, removal of non-specifically bound (NSB) proteins remains a significant challenge in biosensing applications. Operation...
We introduce a method for comparing protein structures using the notion of residue contexts based on protein Calpha-atom backbones. The residue context is derived from the set of vectors from a given Calpha-atom to each other Calpha-atom in the molecule. A three-dimensional histogram is generated from these vectors, containing a relative distribution of the other Calpha-atoms for each Calpha-atom...
The tertiary structure and biological function of a protein can be better understood given knowledge of the number and location of its disulfide bonds. By utilizing mass spectrometric (MS) experimental procedures that produce spectra of the protein's peptides joined by a disulfide bond, we can make initial identifications of these bonded cysteine pairings. The algorithmic problem then becomes how...
Determining the number and location of disulfide bonds within a protein provide valuable insight into the protein's three-dimensional structure. Purely computational methods that predict the bonded cysteine pairings given a protein's primary structure have limitations in both prediction correctness and the number of bonds that can be predicted. Our approach utilizes tandem mass spectrometric (MS/MS)...
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