Periodicity, planarity, and pixel (3P): a program using the intrinsic residual dipolar coupling periodicity-to-peptide plane correlation and phi/psi angles to derive protein backbone structures.
We present a detailed description of a theory and a program called 3P. "3P" stands for periodicity, planarity, and pixel. The 3P program is based on the intrinsic periodic correlations between residual dipolar couplings (RDCs) and in-plane internuclear vectors, and between RDCs and the orientation of peptide planes relative to an alignment tensor. The program extracts accurate rhombic, axial components of the alignment tensor without explicit coordinates, and discrete peptide plane orientations, which are utilized in combination with readily available phi/psi angles to determine the three-dimensional backbone structures of proteins. The 3P program uses one alignment tensor. We demonstrate the utility and robustness of the program, using both experimental and synthetic data sets, which were added with different levels of noise or were incomplete. The program is interfaced to Xplor-NIH via a "3P" module and is available to the public. The limitations and differences between our program and existing methods are also discussed.
Wang
Jinbu
J
Protein Nucleic Acid Interaction Section, Structural Biophysics Laboratory, NCI-Frederick, NIH, Frederick, MD 21702, USA.
Walsh
Joseph D
JD
Kuszewski
John
J
Wang
Yun-Xing
YX
D000465:Algorithms; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry / Q000235:genetics; D008962:Models, Theoretical; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D025801:Ubiquitin / Q000737:chemistry
D010455:Peptides; D011506:Proteins; D025801:Ubiquitin; D002265:Carboxylic Ester Hydrolases; C019952:cutinase