Template identification. The complete MyBP-C protein sequence, which consists of 1274 amino acids and has a calculated molecular weight of 140.78 kDa, was retrieved from the UniProtKB database (http://www.uniprot.org/) (accession number Q14896). Searching the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) (http://www.rcsb.org/) confirmed that the complete tertiary structure of MyBP-C was not publicly available (40). The BLASTP search of the N-terminal region consisting of domains C0-C2 resulted in homologs with low sequence identity and subsequently suboptimal structure from prediction servers. This led us to fragment the sequence, keeping functional regions intact based on SMART (41) and PFAM (42) domain definitions. The fragmentation of the MyBP-C sequence based on functional regions showed some optimal identical structural templates for C0, C1, M-domain, and C2 regions from PDB (40).

Multi-template homology modeling of the N terminus of MyBP-C. The above structural templates were used to construct the homology model of the N terminus of MyBP-C by stitching the structures of C0, C1, M-domain, and C2 regions together. The model was constructed using the multi-template modeling method of the Modeller program (Modeller V9.20) (43). The modeled structures were energy-minimized to convergence using SYBYL software and then finally passed through the validation process using PROSA (44) and Procheck (45).

Note: The content above has been extracted from a research article, so it may not display correctly.



Q&A
Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.



We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.