Design of BRC analogous peptides based on the complex BRC8–RAD51 and the preliminary study on the peptide structures

• Published in: Amino acids 2020-05, Vol.52 (5), p.831-839
• Main Authors: Zhao, Dongxin, Lu, Kui, Liu, Guangbin, Zhu, Hanjing, Ma, Li, Qi, Jianzhao, Yuan, Libo
• Format: Article
• Language: English
• Subjects: Alanine; Amino acids; Analytical Chemistry; Biochemical Engineering; Biochemistry; Biomedical and Life Sciences; BRCA2 protein; BRCA2 Protein - chemistry; BRCA2 Protein - metabolism; Circular dichroism; Computer simulation; Deoxyribonucleic acid; Dichroism; DNA; DNA repair; Drug Design; Humans; Life Sciences; Mutagenesis; Mutation; Neurobiology; Original Article; Peptide Fragments - chemistry; Peptides; Polypeptides; Protein Conformation; Protein structure; Proteins; Proteomics; Rad51 Recombinase - chemistry; Rad51 Recombinase - metabolism; Residues; Scanning; Secondary structure; Solid phase methods; Solid phase synthesis; Solid phases; Spectroscopy; Tumor suppressor genes
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-020-02856-x

BRCA2 is an important tumor suppressor gene that plays a critical role in preserving the stability of cellular genetic information, participating in DNA repair by engaging in binding interactions with RAD51 proteins. However, the lack of structural data on BRCA2 and RAD51 makes the study of their interaction mechanism still a great challenge. We characterize the structure of the BRC8–RAD51 complex using ZDOCK protein docking software and identify the potential non-conserved active site of BRC8 via virtual alanine scanning, utilizing the obtained results to synthesize BRC8, its six analogous peptides (BRC8-1 to BRC8-6), and critical peptide fragment of RAD51 (RAD51(231–260)) by Fmoc solid-phase synthesis. The analogous peptides are found to exhibit a secondary structure significantly different from that of BRC8 by circular dichroism spectroscopy, which indicates that mutation sites determined by computer-aided simulation correspond to key amino acid residues substantially affecting polypeptide structure. On the other hand, the secondary structure of RAD51(231–260) was also considerably influenced by its interaction with BRC8 and analogs, e.g., the fraction of the α-helical structure in RAD51(231–260) increased to 23.6, 15.1, and 13.5% upon interaction with BRC8-1, BRC8-3, and BRC8-6, respectively. The results show that the properties of C-terminal amino acid residues significantly influence peptide–peptide interactions, in agreement with the results of virtual alanine scanning. Therefore, computer-aided simulation was confirmed to be a technique that is useful for narrowing down the range of sites responsible for interactions between peptides or proteins, and provides new inspirations for the design of peptides with strong interactions.