ABSTRACT
This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.
Subject(s)
Magnetic Resonance Spectroscopy/methods , Proteomics/methods , Algorithms , Data Interpretation, Statistical , Models, Molecular , Proteins/chemistryABSTRACT
The labelling of metabolites with the NMR active nucleus 13C allows not only metabolite enrichments to be monitored, but also the relative fluxes through competing pathways to be delineated. [2-13C, 15N]alanine was used as a metabolic probe to investigate compartmentation in superfused cerebral slices. Perchloric acid extracts of the tissue were investigated using 13C NMR spectroscopy. The spectra were obtained using a CryoProbe optimised for 13C detection (dual CryoProbe [13C, 1H]) in which the receiver and transmitter coils are cooled to approximately 20K to reduce contributions to noise in the signal obtained. Compared with conventional inverse geometry probe, the signal-to-noise ratio (S/N) was increased by approximately 17-fold using this device. A large proportion of alanine was initially metabolised over the first 20 min by glial cells, as indicated by the relative importance of the glial, only enzyme pyruvate carboxylase to the labelling pattern of glutamate, with the ratio of pyruvate carboxylase to pyruvate dehydrogenase derived glutamate being 0.25, and exported [2-13C, 15N]aspartate. Using the increased sensitivity of the CryoProbe, [2-13C, 15N]aspartate was also detected in the extracts of cerebral tissue. This metabolite could only have been derived via the pyruvate carboxylase pathway, and given the large export of the metabolite into the superfusion buffer suggests the occurrence of a "metabolon" arrangement of enzymes within glial cells.
Subject(s)
Alanine/metabolism , Carbon Isotopes/analysis , Cell Compartmentation , Neuroglia/metabolism , Nuclear Magnetic Resonance, Biomolecular , Alanine/chemistry , Animals , Aspartic Acid/biosynthesis , Citric Acid Cycle , Electronics , Glutamic Acid/biosynthesis , Glutamine/metabolism , Guinea Pigs , In Vitro Techniques , Male , Nerve Tissue Proteins/metabolism , Neuroglia/ultrastructure , Nuclear Magnetic Resonance, Biomolecular/instrumentation , Pyruvate Carboxylase/metabolism , Sensitivity and SpecificityABSTRACT
The observation of nuclear Overhauser effects (NOEs) between bound water and biological macromolecules such as proteins and nucleic acids can be improved by inverting the water resonance selectively while compensating for radiation damping effects. The efficiency of inversion, the offset profiles, and the appearance of 2D NOE-NOESY spectra can be improved in comparison with earlier methods.
Subject(s)
Nuclear Magnetic Resonance, Biomolecular/methods , Proteins/chemistry , Water/chemistry , Protein Binding , Proteins/metabolism , Solutions , Solvents/chemistry , Water/metabolismABSTRACT
The pKa values of eight glutamic acid residues in the homotrimeric coiled coil domain of chicken matrilin-1 have been determined from 2D H(CA)CO NMR spectra recorded as a function of the solution pH. The pKa values span a range between 4.0 and 4.7, close to or above those for glutamic acid residues in unstructured polypeptides. These results suggest only small favorable contributions to the stability of the coiled coil from the ionization of its acidic residues.
Subject(s)
Extracellular Matrix Proteins/chemistry , Glycoproteins/chemistry , Protein Conformation , Animals , Escherichia coli , Matrilin ProteinsABSTRACT
The structure of the headpiece of the TraM protein was investigated in different solvents. The very first 22 amino acids which alternate in their hydrophilic and hydrophobic character formed a helical structure in the presence of a membrane mimetic. In water alone the structure was flexible with a small amount of helicity according to circular dichroism measurements, whereas a loop structure was observed in dimethyl sulphoxide.
