Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts

  title={Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts},
  author={Stephen Neal and Alex M. Nip and Haiyan Zhang and David Scott Wishart},
  journal={Journal of Biomolecular NMR},
A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates… 

Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script, which should be useful in protein structure determination.

Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins. 2. Level of Theory, Basis Set, and Solvents Model Dependence.

The systematic investigation performed here on the influences of the level of theory, basis set size, inclusion or exclusion of an implicit solvent model, and the use of partial charges to describe additional parts of the macromolecule on the accuracy of NMR chemical shifts demonstrates that using a valence triple-ζ basis set leads to large improvement compared to the results given in the previous publication.

Predicting 13Cα chemical shifts for validation of protein structures

Application of this methodology to 5,735 residues from 74 conformations of the three remaining proteins that differ in their number of amino acid residues, sequence and three-dimensional structure, together with a new scoring function, enables it to provide evidence confirming the presence of dynamics for proteins in solution, and hence showing that an ensemble of conformations is a better representation of the structure in solution than any single conformation.

Protein Chemical Shift Prediction

The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures

Structure-based prediction of methyl chemical shifts in proteins

The CH3Shift method of performing structure-based predictions of methyl chemical shifts is presented and an accuracy range is shown that ranges from 0.133 to 0.198 ppm for 1H chemical shifts for Ala, Thr, Val, Leu and Ile methyl groups.

Computational Assignment of Chemical Shifts for Protein Residues

Chemshift is presented, a module for handling chemical shift assignments, implemented in the protein structure determination program Phaistos, which treats both the assignment of experimental data, as well as the weighing compared to physical terms, in a probabilistic framework where no data is discarded.

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%, and addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%.

Determining valine side-chain rotamer conformations in proteins from methyl 13C chemical shifts: application to the 360 kDa half-proteasome.

The utility of the methodology and the importance of NMR approaches for the study of high molecular weight complexes that can be recalcitrant to high resolution X-ray analysis are emphasized.

SHIFTX2: significantly improved protein chemical shift prediction

A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data and will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation.



Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database

An algorithm for prediction of 15N and 13C shifts in proteins from their structure based on density functional calculations on peptides is incorporated into a program called SHIFTS, which should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement.


We have investigated the carbon-13 solution nuclear magnetic resonance (NMR) chemical shifts of Cα, Cβ, and Cγ carbons of 19 valine residues in a vertebrate calmodulin, a nuclease from Staphylococcus

Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal

Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach.

The ability to predict chemical shifts in proteins from known or test structures opens new avenues to structure refinement or determination, especially for condensed systems.

Probing multiple effects on 15N, 13Cα, 13Cβ, and 13C′ chemical shifts in peptides using density functional theory

We have used density functional calculations on model peptides to study conformational effects on (15)N, (13)C alpha, (13)C beta, and (13)C' chemical shifts, associated with hydrogen bonding,

Protein Structure Refinement and Prediction via NMR Chemical Shifts and Quantum Chemistry

An approach utilizing Bayesian probability and NMR chemical shifts to derive structural information about proteins is presented. The method is based on measurement of a spectroscopic parameter, P

Protein chemical shift analysis: a practical guide

Proper protein chemical shift analysis requires careful experimental measurements and the implementation of standardized referencing procedures. In this article we outline the steps necessary to

Peptide group chemical shift computation

It is shown that the expression accounts for the main physical effects of the protein peptide group on the proton chemical shifts, and explains the main characteristics of the C‐α, H and amide NH chemical shifts in proteins.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence, and these averages can reliably be used as angular restraints for the protein whose structure is being studied.