The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To ...accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.
The phosphatase of regenerating liver (PRL) family, also known as protein tyrosine phosphatase 4A (PTP4A), are dual-specificity phosphatases with largely unknown cellular functions. However, ...accumulating evidence indicates that PRLs are oncogenic across a broad variety of human cancers. PRLs are highly expressed in advanced tumors and metastases compared to early stage cancers or matched healthy tissue, and high expression of PRLs often correlates with poor patient prognosis. Consequentially, PRLs have been considered potential therapeutic targets in cancer. Persistent efforts have been made to define their role and mechanism in cancer progression and to create specific PRL inhibitors for basic research and drug development. However, targeting PRLs with small molecules remains challenging due to the highly conserved active site of protein tyrosine phosphatases and a high degree of sequence similarity between the PRL protein families. Here, we review the current PRL inhibitors, including the strategies used for their identification, their biological efficacy, potency, and selectivity, with a special focus on how PRL structure can inform future efforts to develop specific PRL inhibitors.
The surfacing of wheels and rollers with a nonuniform cross section leads to surface heating. Subsequent surface cooling produces stress and potentially disintegration of the component. To prevent ...such problems, heating of the disk and rim during surfacing is proposed, so that the temperature difference over the component is no more than 100°C.
The tendency of economically alloyed and high-chromium steel coatings to crack is compared, along with their wear resistance in various conditions. To slow the wear of the working surfaces, the ...selection of the hard coating employed in surfacing should take account of the expected operating conditions.
Transposable elements (TEs) constitute a significant part of eukaryotic genomes. Short interspersed nuclear elements (SINEs) are non-autonomous TEs, which are widely represented in mammalian genomes ...and also found in plants. After insertion in a new position in the genome, TEs quickly accumulate mutations, which complicate their identification and annotation by modern bioinformatics methods. In this study, we searched for highly divergent SINE copies in the genome of rice (Oryza sativa subsp. japonica) using the Highly Divergent Repeat Search Method (HDRSM).
The HDRSM considers correlations of neighboring symbols to construct position weight matrix (PWM) for a SINE family, which is then used to perform a search for new copies. In order to evaluate the accuracy of the method and compare it with the RepeatMasker program, we generated a set of SINE copies containing nucleotide substitutions and indels and inserted them into an artificial chromosome for analysis. The HDRSM showed better results both in terms of the number of identified inserted repeats and the accuracy of determining their boundaries. A search for the copies of 39 SINE families in the rice genome produced 14,030 hits; among them, 5704 were not detected by RepeatMasker.
The HDRSM could find divergent SINE copies, correctly determine their boundaries, and offer a high level of statistical significance. We also found that RepeatMasker is able to find relatively short copies of the SINE families with a higher level of similarity, while HDRSM is able to find more diverged copies. To obtain a comprehensive profile of SINE distribution in the genome, combined application of the HDRSM and RepeatMasker is recommended.
Phosphatase of Regenerating Liver-3 (PRL-3) is associated with cancer progression and metastasis. The mechanisms that drive PRL-3's oncogenic functions are not well understood, partly due to a lack ...of research tools available to study this protein. We have begun to address these issues by developing alpaca-derived single domain antibodies, or nanobodies, targeting PRL-3 with a KD of 30-300 nM and no activity towards highly homologous family members PRL-1 and PRL-2. We found that longer and charged N-terminal tags on PRL-3, such as GFP and FLAG, changed PRL-3 localization compared to untagged protein, indicating that the nanobodies may provide new insights into PRL-3 trafficking and function. The nanobodies perform equally, if not better, than commercially available antibodies in immunofluorescence and immunoprecipitation. Finally, hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed that the nanobodies bind partially within the PRL-3 active site and can interfere with PRL-3 phosphatase activity. Co-immunoprecipitation with a known PRL-3 active site binding partner, the CBS domain of metal transporter CNNM3, showed that the nanobodies reduced the amount of PRL-3:CBS inter-action. The potential of blocking this interaction is highly relevant in cancer, as multiple research groups have shown that PRL-3 binding to CNNM proteins is sufficient to promote metastatic growth in mouse models. The anti-PRL-3 nanobodies represent an important expansion of the research tools available to study PRL-3 function and can be used to define the role of PRL-3 in cancer progression.
PDF
