CheShift 2.0: a Quantum-Mechanical-Derived 13Ca Chemical Shift Server for Protein Structure Validation

VILA, J.A.; ARNAUTOVA Y.A.; MARTIN O.A.; SCHERAGA H.A.

San Diego

Simposio; 24th Annual Symposium of the Protein Society; 2010

Protein Society (USA)

<!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --> <!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --BACKGROUND: Recently, a server (CheShift)1 has been developed to predict 13Cα chemical shifts of proteinstructures. It is based on the generation of ~700,000 conformations as a function of the φ, ψ, ω, χ1 and χ2torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at theDFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regressionformula, to reproduce the values obtained with a larger basis set.OBJECTIVE: We present an upgrade of our CheShift server,1 version 2.0, which now includes nearest-neighbor corrections due to proline-effects and a pH-dependent computation of the chemical shifts for bothtautomers of the histidine residue. A series of applications will demonstrate the improvements of the predicted13Cα chemical shifts for proteins, with respect to the original 1.0 version.BACKGROUND: Recently, a server (CheShift)1 has been developed to predict 13Cα chemical shifts of proteinstructures. It is based on the generation of ~700,000 conformations as a function of the φ, ψ, ω, χ1 and χ2torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at theDFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regressionformula, to reproduce the values obtained with a larger basis set.OBJECTIVE: We present an upgrade of our CheShift server,1 version 2.0, which now includes nearest-neighbor corrections due to proline-effects and a pH-dependent computation of the chemical shifts for bothtautomers of the histidine residue. A series of applications will demonstrate the improvements of the predicted13Cα chemical shifts for proteins, with respect to the original 1.0 versio  ds  BACKGROUND: Recently, a server (CheShift)1 has been developed to predict 13Cα chemical shifts of protein structures. It is based on the generation of ~700,000 conformations as a function of the φ, ψ, ω, χ1 and χ2 torsional angles for all 20 naturally occurring amino acids. Their 13Cα chemical shifts were computed at the DFT level of theory with a small basis set and extrapolated, with an empirically-determined linear regression formula, to reproduce the values obtained with a larger basis set.OBJECTIVE: We present an upgrade of our CheShift server,1 version 2.0, which now includes nearest-neighbor corrections due to proline-effects and a pH-dependent computation of the chemical shifts for both tautomers of the histidine residue. A series of applications will demonstrate the improvements of the predicted 13Cα chemical shifts for proteins, with respect to the original 1.0 version.