title: A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.
abstract: The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(β) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type.
authors.affiliation: Department of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.
authors.forename: Hoora
authors.initials: H
authors.lastname: Shaghaghi
authors.affiliation: Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Wisconsin.
authors.forename: Hossein Pasha
authors.initials: HP
authors.lastname: Ebrahimi
authors.affiliation: Department of Chemistry, Sharif University of Technology, Tehran, Iran.
authors.forename: Fariba
authors.initials: F
authors.lastname: Fathi
authors.affiliation: Department of Chemistry, Payame Noor University, Tehran, Iran.
authors.forename: Niloufar
authors.initials: N
authors.lastname: Bahrami Panah
authors.affiliation: Department of Chemistry and Biochemistry, California State University, Los Angeles, California.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Jalali-Heravi
authors.affiliation: Department of Chemistry, Sharif University of Technology, Tehran, Iran.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Tafazzoli
keywords: 13C chemical shifts; DFT; ONIOM; dihedral angle; protein; secondary structure