a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often cause population changes within these substates3,4. We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold...
Multiple myeloma (MM) remains an incurable hematological malignancy disease characterized by the progressive dysfunction of the patient’s immune system. In this context, immunotherapy for MM has emerged as a prominent area of research in recent years. V
position along the sequence, indicating that the primers used in the T-DNA flanking PCR had amplified the next best target on a homeologous chromosome which was also the same length as the intended product and therefore not able to be distinguished on the basis of size via gel ...
Multiple alignments of protein sequences are important in many applications, including phylogenetic tree estimation, secondary structure prediction and critical residue identification. Many multiple sequence alignment (MSA) algorithms have been proposed; for a recent review, see [1]. Two attributes of MSA...
Complexity is of increasing relevance due to the rapid growth of sequence databases, which now contain enough representatives of larger protein families to exceed the capacity of most current programs. Obtaining biologically accurate alignments is also a challenge, as the best methods sometimes fail to...
Total protein level of each sample was used for normalization. Data are represented as mean with SD. (B) Peptide sequences of biotinylated mouse CD3ε peptides for affinity pull-down and NMR experiments: non-phosphorylated CD3ε (Y1Y2), mono-phosphorylated CD3ε (pY1), BRS or PRS mutation...
A modified automated DNA sequencing using only one of the sequence terminators was used to genotype PCR products in single-track sequencing reactions of NAT1 and was shown to be universal for both DNA sequencing using labeled primers and labeled nucleotides. By this method we detected known SNPs...
length protein, whereas with other variants there were several-fold decreases in hydrolysis of the polysaccharides (Fig. 4E). Enzyme kinetics parameters of the truncational variants. To gain better insights to the effect of the different deletions on the catalytic activity of Ra3055 as a ...
Signatures and consequences of selection on coding sequences To gain insight into the functional basis of diversification and adaptation in Lake Malawi cichlids, we next turned our attention to protein-coding genes. We compared the mean between-species levels of non-synonymous variation\(\bar p_{\...
In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmark