Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments
RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 341-349.

Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique to obtain structural information of a protein. In this technique, an essential step is the backbone resonance assignment and Structure Based Assignment (SBA) aims to solve this problem with the help of a template structure. Nuclear Vector Replacement (NVR) is an NMR protein SBA program, that takes as input 15 N and H N chemical shifts and unambiguous NOEs, as well as RDCs, HD-exchange and TOCSY data. NVR does not utilize 13 C chemical shifts although this data is widely available for many proteins. In addition, NVR is a proof-of-principle approach and has been run with specific and manually set parameters for some proteins. NA-NVR-ACO [M. Akhmedov, B.Çatay and M.S. Apaydın, 𝐽 . 𝐵𝑖𝑜𝑖𝑛𝑓𝑜𝑟𝑚 . 𝐶𝑜𝑚𝑝𝑢𝑡 . 𝐵𝑖𝑜𝑙 . 13 (2015) 1550020.] remedies this problem for the NOE data and standardizes NOE usage, while using an ant colony optimization based algorithm. In this paper, we standardize NA-NVR-ACO’s scoring function by using the same parameters for all the proteins and incorporating 13 C α chemical shifts. We also use a larger protein database and state-of-the-art chemical shift prediction tools, SHIFTX2 [B. Han, Y. Liu, S.W. Ginzinger and D.S. Wishart, 𝐽 . 𝐵𝑖𝑜𝑚𝑜𝑙 . 𝑁𝑀𝑅 50 (2011) 43–57.] and SPARTA+ [Y. Shen and A. Bax, 𝐽 . 𝐵𝑖𝑜𝑚𝑜𝑙 . 𝑁𝑀𝑅 48 (2010) 13–22], to extract the chemical shift statistics. Other practical improvements include automatizing data file preparation and obtaining a degree of reliability for individual peak-amino acid assignments. Our results show that our improvements bring NA-NVR-ACO closer to a practical tool, able to handle a variety of different data types.

DOI: 10.1051/ro/2015038
Classification: 90c27
Keywords: NMR structure based protein assignment, NVR, score function, triple resonance experiments, reliability of assignments
ŞeymaÇetnİkaya 1; Ekren, Şeyma Nur 1; Apaydın, Mehmet Serkan 2

1 Department of Graduate School of Natural and Applied Sciences, İstanbulŞehir University, 34662 Üsküdar, Istanbul, Turkey.
2 College of Engineering and Natural Sciences, İstanbulŞehir University, 34662 Üsküdar, Istanbul, Turkey.
     author = {\c{S}eyma\c{C}etn\.Ikaya and Ekren, \c{S}eyma Nur and Apayd{\i}n, Mehmet Serkan},
     title = {Progress in {Nuclear} {Vector} {Replacement} for {NMR} {Protein} {Structure-Based} {Assignments}},
     journal = {RAIRO - Operations Research - Recherche Op\'erationnelle},
     pages = {341--349},
     publisher = {EDP-Sciences},
     volume = {50},
     number = {2},
     year = {2016},
     doi = {10.1051/ro/2015038},
     mrnumber = {3479874},
     zbl = {1336.90070},
     language = {en},
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ŞeymaÇetnİkaya; Ekren, Şeyma Nur; Apaydın, Mehmet Serkan. Progress in Nuclear Vector Replacement for NMR Protein Structure-Based Assignments. RAIRO - Operations Research - Recherche Opérationnelle, Volume 50 (2016) no. 2, pp. 341-349. doi : 10.1051/ro/2015038.

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