title: Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction.
abstract: A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of (15)N, (13)C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.
authors: Campus Chemical Instrumentation Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States.
authors: Da-Wei
authors: DW
authors: Li
authors: Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States.
authors: Dan
authors: D
authors: Meng
authors: Campus Chemical Instrumentation Center, The Ohio State University, Columbus, OH 43210, United States; Department of Chemistry & Biochemistry, The Ohio State University, Columbus, OH 43210, United States; Chemical Sciences Laboratory, Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32306, United States. Electronic address: bruschweiler.1@osu.edu.
authors: Rafael
authors: R
authors: Brüschweiler
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000032:analysis; D001331:Automation; D002250:Carbon Radioisotopes; D018360:Crystallography, X-Ray; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009590:Nitrogen Radioisotopes; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results
chemical_list: D000596:Amino Acids; D002250:Carbon Radioisotopes; D009590:Nitrogen Radioisotopes; D011506:Proteins
keywords: Chemical shift prediction; Protein structure based NMR resonance assignments