Automating unambiguous NOE data usage in NVR for NMR protein structure-based assignments

• Published in: Journal of bioinformatics and computational biology Vol. 13; no. 6; p. 1550020
• Main Authors: Akhmedov, Murodzhon, Çatay, Bülent, Apaydın, Mehmet Serkan
• Format: Journal Article
• Language: English
• Published: Singapore 01.12.2015
• Subjects: Algorithms; Computational Biology - methods; Magnetic Resonance Spectroscopy - methods; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular - methods; Protein Conformation; Proteins - chemistry; combinatorial optimization; NMR protein structure-based assignments; ant colony optimization; NOE
• ISSN: 1757-6334
• DOI: 10.1142/S0219720015500201

Nuclear Magnetic Resonance (NMR) Spectroscopy is an important technique that allows determining protein structure in solution. An important problem in protein structure determination using NMR spectroscopy is the mapping of peaks to corresponding amino acids, also known as the assignment problem. Structure-Based Assignment (SBA) is an approach to solve this problem using a template structure that is homologous to the target. Our previously developed approach Nuclear Vector Replacement-Binary Integer Programming (NVR-BIP) computed the optimal solution for small proteins, but was unable to solve the assignments of large proteins. NVR-Ant Colony Optimization (ACO) extended the applicability of the NVR approach for such proteins. One of the input data utilized in these approaches is the Nuclear Overhauser Effect (NOE) data. NOE is an interaction observed between two protons if the protons are located close in space. These protons could be amide protons, protons attached to the alpha-carbon atom in the backbone of the protein, or side chain protons. NVR only uses backbone protons. In this paper, we reformulate the NVR-BIP model to distinguish the type of proton in NOE data and use the corresponding proton coordinates in the extended formulation. In addition, the threshold value over interproton distances is set in a standard manner for all proteins by extracting the NOE upper bound distance information from the data. We also convert NOE intensities into distance thresholds. Our new approach thus handles the NOE data correctly and without manually determined parameters. We accordingly adapt NVR-ACO solution methodology to these changes. Computational results show that our approaches obtain optimal solutions for small proteins. For the large proteins our ant colony optimization-based approach obtains promising results.