Workflow for Protein N-terminal Acetylation and C-terminal Amidation Application using CcpNmr Analysis v2.4 Platform and Aria2.3 Structure Calculation Software

• Published in: bioRxiv
• Main Authors: Bruno De Paula Oliveira Santos, Bruno Marques Silva, Mariana Torquato Quezado De Magalhães
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 09.12.2020
• Subjects: Acetylation; Computer applications; Computer programs; Data acquisition; Data processing; NMR; Nuclear magnetic resonance; Protein structure; Proteins; Software
• DOI: 10.1101/2020.12.08.414565

Abstract Structural biology is a field that enables a better understanding of proteins from scratch. From the available techniques, solution NMR is one well established that provides structure, dynamics and protein-molecules interaction. In a NMR lab routine, from data acquisition until protein/mechanisms elucidation comes a process that can undergo months. During the past decades, different tools were developed for NMR data processing, peaks assignment, structure elucidation and data submission. Since many of these programs demand great computational skills, a few groups have tried to combine those programs and make them more friendly and useful, what can possibilite a faster process. Here we highlight CCPNMR2.4 analysis and ARIA2.3, responsible for peak assignment and structure calculation, respectively, and can work associated. Although being academic free and the possibility of working with a GUI interface, the common N-terminal acetylation and C-terminal amidation modifications are not implemented in a way that possibilities to work with them in combination, what results in a dilemma. This work brings visual data that evidences the low usability of CCPN and ARIA with N-terminal acetylated and C-terminal amidated proteins and propose a workflow to overcome this problem, which may improve the usage of both software in the mentioned versions and facilitate the lab users already used to these programs. As a proof of concept, we have chosen a N-terminal amidated peptide, L-Phenylseptin, whose structure has already been solved with other programs. Statistical data shows that no significant difference was found with the structure obtained with the new protocol. In conclusion, we exhibit a new protocol that can be used in combination with CCPNMR2.4 and ARIA2.3 for protein with the mentioned modifications and it successfully works and manipulates these molecules. Competing Interest Statement The authors have declared no competing interest. Footnotes * Synopsis During the past decades, different tools were developed for NMR data processing, peaks assignment, structure elucidation and data submission. Here we highlight CCPNMR2.4 analysis and ARIA2.3, responsible for peak assignment and structure calculation, respectively, and can work associated.