NMR data-driven structure determination using NMR-I-TASSER in the CASD-NMR experiment.
NMR-I-TASSER, an adaption of the I-TASSER algorithm combining NMR data for protein structure determination, recently joined the second round of the CASD-NMR experiment. Unlike many molecular dynamics-based methods, NMR-I-TASSER takes a molecular replacement-like approach to the problem by first threading the target through the PDB to identify structural templates which are then used for iterative NOE assignments and fragment structure assembly refinements. The employment of multiple templates allows NMR-I-TASSER to sample different topologies while convergence to a single structure is not required. Retroactive and blind tests of the CASD-NMR targets from Rounds 1 and 2 demonstrate that even without using NOE peak lists I-TASSER can generate correct structure topology with 15 of 20 targets having a TM-score above 0.5. With the addition of NOE-based distance restraints, NMR-I-TASSER significantly improved the I-TASSER models with all models having the TM-score above 0.5. The average RMSD was reduced from 5.29 to 2.14 Å in Round 1 and 3.18 to 1.71 Å in Round 2. There is no obvious difference in the modeling results with using raw and refined peak lists, indicating robustness of the pipeline to the NOE assignment errors. Overall, despite the low-resolution modeling the current NMR-I-TASSER pipeline provides a coarse-grained structure folding approach complementary to traditional molecular dynamics simulations, which can produce fast near-native frameworks for atomic-level structural refinement.
School of Software Engineering, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.|Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA.
Richard
R
Jang
School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.|Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA.
Yan
Y
Wang
School of Software Engineering, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China. zdxue@hust.edu.cn.|Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA. zdxue@hust.edu.cn.
Zhidong
Z
Xue
Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109-2218, USA. zhng@umich.edu.|Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA. zhng@umich.edu.
Yang
Y
Zhang
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins
CASD-NMR; I-TASSER; NMR restraints; NOE assignment; Protein structure prediction