Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement.
Summary of "Rapid calculation of protein chemical shifts using bond polarization theory and its application to protein structure refinement."
Although difficult to analyze, NMR chemical shifts provide detailed information on protein structure. We have adapted the semi-empirical bond polarization theory (BPT) to protein chemical shift calculation and chemical shift driven protein structure refinement. A new parameterization for BPT amide nitrogen chemical shift calculation has been derived from MP2 ab initio calculations and successfully evaluated using crystalline tripeptides. We computed the chemical shifts of the small globular protein ubiquitin, demonstrating that BPT calculations can match the results obtained at the DFT level of theory at very low computational cost. In addition to the calculation of chemical shift tensors, BPT allows the calculation of chemical shift gradients and consequently chemical shift driven geometry optimizations. We applied chemical shift driven protein structure refinement to the conformational analysis of a set of Trypanosoma brucei (the causative agent of African sleeping sickness) tryparedoxin peroxidase Px III structures. We found that the interaction of Px III with its reaction partner Tpx seems to be governed by conformational selection rather than by induced fit.
Affiliation
Institute for Biological Interfaces (IBG2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany. ulrich.sternberg@kit.edu.
Journal Details
This article was published in the following journal.
Name: Physical chemistry chemical physics : PCCP
ISSN: 1463-9084
Pages: 12263-76
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/22868284
- DOI: http://dx.doi.org/10.1039/c2cp41726j
Medical and Biotech [MESH] Definitions
Work Schedule Tolerance
Physiological or psychological effects of periods of work which may be fixed or flexible such as flexitime, work shifts, and rotating shifts.
Fluorescence Polarization
Measurement of the polarization of fluorescent light from solutions or microscopic specimens. It is used to provide information concerning molecular size, shape, and conformation, molecular anisotropy, electronic energy transfer, molecular interaction, including dye and coenzyme binding, and the antigen-antibody reaction.
Fluid Shifts
Translocation of body fluids from one compartment to another, such as from the vascular to the interstitial compartments. Fluid shifts are associated with profound changes in vascular permeability and WATER-ELECTROLYTE IMBALANCE. The shift can also be from the lower body to the upper body as in conditions of weightlessness.
Fluorescence Polarization Immunoassay
Fluoroimmunoassay where detection of the hapten-antibody reaction is based on measurement of the increased polarization of fluorescence-labeled hapten when it is combined with antibody. The assay is very useful for the measurement of small haptenic antigens such as drugs at low concentrations.
Photolysis
Chemical bond cleavage reactions resulting from absorption of radiant energy.
PubMed Articles
Fragment density functional theory (DFT) calculation of NMR chemical shifts for several proteins (Trp-cage, Pin1 WW domain, the third IgG-binding domain of Protein G (GB3) and human ubiquitin) has bee...
An approach towards accurate NMR measurements of deuterium isotope effects on the chemical shifts of all backbone nuclei in proteins ((15)N, (13)Cα, (13)CO, (1)Hα) and (13)Cβ nuclei arising from (1...
An empirical correlation between the fluorine isotropic chemical shifts, measured by (19)F NMR spectroscopy, and the type of fluorine-protein interactions observed in crystal structures is presented...
Using Chemical Shifts to Determine Structural Changes in Proteins upon Complex Formation.
Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the...
The (1)H and (13)C NMR spectra of 17 OHN hydrogen-bonded complexes formed by CH(3)(13)COOH(D) with 14 substituted pyridines, 2 amines, and N-methylimidazole have been measured in the temperature regio...
Clinical Trials
Validation of Brief Objective Neurobehavioral Detectors (BOND) in Mild TBI
The Veterans Health Administration (VHA) has stated the need for a brief screening instrument that can assist with the triage of the enormous number of returning OEF/OIF veterans with conc...
Clinical Evaluation of Three Dental Adhesive Systems in Class V Restorations
The purpose of this study is to compare the clinical performance of three dental adhesive systems used to bond Class V cavity fillings in adult teeth.
High-Density Direct Current Brain Polarization
Background: - Direct current (DC) brain polarization is a technique in which very weak electricity is applied to the head. Doctors have used DC polarization for many years on pati...
Double Blind Trial of DC Polarization in FTD
This project is designed to test how direct current (DC) electrical polarization of the brain affects language and behavior in patients with frontotemporal dementia (FTD). FTD is the secon...
Direct Current Brain Polarization of the Frontal Lobes
This study will explore what effects, if any, direct current (DC) brain polarization may produce on mental processes, such as attention, reaction time, working memory, speed of information...
