NDLI: Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests

Content Provider	PubMed Central
Author	Ołdziej, S. Czaplewski, C. Liwo, A. Chinchio, M. Nanias, M. Vila, J. A. Khalili, M. Arnautova, Y. A. Jagielska, A. Makowski, M. Schafroth, H. D. Kaźmierkiewicz, R. Ripoll, D. R. Pillardy, J. Saunders, J. A. Kang, Y. K. Gibson, K. D. Scheraga, H. A.
Copyright Year	2005
Abstract	Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of α and α+β proteins [60–70 residues with Cα rms deviation (rmsd) <6 Å]. However, for α+β proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two α and three α+β, with sizes of 53–235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue α+β protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-Å Cα rmsd. So far this protein is the largest α+β protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly α-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 Å rmsd, except the 32 C-terminal residues, most of which form a β-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.
Related Links	http://dx.doi.org/10.1073/pnas.0502655102
Ending Page	7552
Page Count	6
Starting Page	7547
File Format	PDF
ISSN	00278424
e-ISSN	10916490
Journal	Proceedings of the National Academy of Sciences of the United States of America
Issue Number	21
Volume Number	102
Language	English
Publisher	National Academy of Sciences
Publisher Date	2005-05-24
Access Restriction	Open
Rights Holder	National Academy of Sciences
Subject Keyword	General Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

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