Analysis of the Human Casein Phosphoproteome by 2-D Electrophoresis and MALDI-TOF/TOF MS Reveals New Phosphoforms

Reproducible microwave-assisted acid hydrolysis of proteins using a household microwave oven and its combination with LC-ESI MS/MS for mapping protein sequences and modifications

A new set-up for microwave-assisted acid hydrolysis (MAAH) with high efficiency and reproducibility to degrade proteins into peptides for mass spectrometry analysis is described. It is based on the use of an inexpensive domestic microwave oven and can be used for low volume protein solution digestion. This set-up has been combined with liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry (LC-ESI QTOF MS) for mapping protein sequences and characterizing phosphoproteins. It is demonstrated that for bovine serum albumin (BSA), with a molecular mass of about 67,000 Da, 1292 peptides (669 unique sequences) can be detected from a 2 microg hydrolysate generated by trifluoroacetic acid (TFA) MAAH. These peptides cover the entire protein sequence, allowing the identification of an amino acid substitution in a natural variant of BSA. It is shown that for a simple phosphoprotein containing one phosphoform, beta-casein, direct analysis of the hydrolysate generates a comprehensive peptide map that can be used to identify all five known phosphorylation sites. For characterizing a complex phosphoprotein consisting of different phosphoforms with varying numbers of phosphate groups and/or phosphorylation sites, such as bovine alpha(S1)-casein, immobilized metal-ion affinity chromatography (IMAC) is used to enrich the phosphopeptides from the hydrolysate, followed by LC-ESI MS analysis. The MS/MS data generated from the initial hydrolysate and the phosphopeptide-enriched fraction, in combination with MS analysis of the intact protein sample, allow us to reveal the presence of three different phosphoforms of bovine alpha(S1)-casein and assign the phosphorylation sites to each phosphoform with high confidence.

Proteomic quantification of disulfide-linked polymers in raw and heated bovine milk

Disulfide bond formation between milk protein molecules was quantified in raw and heated bovine milk using reducing and nonreducing two-dimensional electrophoresis. Analysis of protein profiles in raw milk indicated that 18% of alpha(S2)-casein, 25% of beta-lactoglobulin, and 46% of kappa-casein molecules were involved in disulfide-linked complexes (calculated through differences in spot volumes on two-dimensional electrophoretograms under reducing and nonreducing conditions), whereas levels of alpha(S1)- and beta-caseins were similar under both conditions. Following heat treatment at 90 degrees C for 30 min, spot volumes of serum albumin, beta-lactoglobulin, and kappa-casein decreased by 85%, 75%, and 75%, respectively, with the formation of several spots on nonreducing gels corresponding to polymers. Homopolymers and heteropolymers of kappa-casein and alpha(S2)-casein were identified by mass spectrometry in raw milk samples; polymers involving only alpha(S2)-casein or only kappa-casein accounted for 43% and 12% of the total polymers present, respectively. In addition, 45% of polymers in raw milk involved alpha(S2)-casein in association with other proteins as heteropolymers, indicating the key role of this protein in intermolecular disulfide bridging between proteins in raw milk. The intensity of monomeric kappa-casein spots decreased progressively with heating time at 90 degrees C, with greatest changes in spots with acidic isoelectric points. Interactions and association of milk proteins via disulfide bridges are discussed in relation to the proteins involved and their potential protective function against formation of fibril aggregates.

Highlights on the capacities of "Gel-based" proteomics

Gel-based proteomic is the most popular and versatile method of global protein separation and quantification. This is a mature approach to screen the protein expression at the large scale, and a cheaper approach as compared with gel-free proteomics. Based on two independent biochemical characteristics of proteins, two-dimensional electrophoresis combines isoelectric focusing, which separates proteins according to their isoelectric point, and SDS-PAGE, which separates them further according to their molecular mass. The next typical steps of the flow of gel-based proteomics are spots visualization and evaluation, expression analysis and finally protein identification by mass spectrometry. For the study of differentially expressed proteins, two-dimensional electrophoresis allows simultaneously to detect, quantify and compare up to thousand protein spots isoforms, including post-translational modifications, in the same gel and in a wide range of biological systems. In this review article, the limits, benefits, and perspectives of gel-based proteomic approaches are discussed using concrete examples.

An E. coli over-expression system for multiply-phosphorylated proteins and its use in a study of calcium phosphate sequestration by novel recombinant phosphopeptides

Phosphoproteins and phosphopeptides were expressed by E. coli to give yields of 30-200mg of purified protein per litre with an average degree of phosphorylation at multiple sites of 61-83%. The method employed two compatible cohabiting plasmids having low and high copy number, expressing a protein kinase and, more abundantly, the substrate (poly)peptide, respectively. It was used to phosphorylate recombinant beta-casein or osteopontin at multiple casein kinase-2 sites. Two constructs were designed to produce shorter peptides containing one or more clusters of phosphorylation sites resembling the phosphate centres of caseins. In the first, a 53-residue 6-His tagged phosphopeptide was expressed at a 5-fold higher molar yield. The second had multiple tandem repeats of a tryptic phosphopeptide sequence to give a similar increase in efficiency. Each recombinant phosphopeptide was purified (30-100mg) and small-angle X-ray scattering measurements showed that they, like certain casein and osteopontin phosphopeptides, sequester amorphous calcium phosphate to form calcium phosphate nanoclusters. In principle, the method can provide novel phosphopeptides for the control of biocalcification or be adapted for use with other kinases and cognate proteins or peptides to study the effect of specific phosphorylations on protein structure. Moreover, the insertion of a phosphate centre sequence, possibly with a linker peptide, may allow thermodynamically stable, biocompatible nanoparticles to be made from virtually any sequence.