The prediction of the isoelectric point is currently performed using 21 methods (including four new ones), which can be grouped into two categories. The following changes have been introduced:Įach proteome is analysed by various methods. In this work, I present a major update of the original Proteome- pI database (Figure (Figure1) 1) ( 11). It should be stressed that experimental measurements of p K a values and isoelectric point are very limited (a few thousand records at most), but there are many computational methods that can be used to predict these features. Both p K a and isoelectric point estimates have been used in numerous techniques, such as two-dimensional gel electrophoresis (2D-PAGE) ( 3, 4), crystallization ( 5), capillary isoelectric focussing ( 6), and mass spectrometry (MS) ( 7, 8). Taken together, the p K a values of all charged groups can be used to calculate the overall charge of the molecule in any pH or to estimate the isoelectric point ( pI, IEP), that is, the pH at which there is an equilibrium of positive and negative charges and therefore the total net charge of the molecule is equal to zero ( 2). For proteins and peptides, the ionizable groups of seven charged amino acids should be considered: glutamate (γ-carboxyl group), cysteine (thiol group), aspartate (β-carboxyl group), tyrosine (phenol group), lysine (ε-ammonium group), histidine (imidazole side chains), and arginine (guanidinium group) ( 1). The charge of a protein is one of its key physicochemical characteristics and is related to the p K a dissociation constant (p K a is a quantitative measure of the strength of an acid in solution). In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides’ isoelectric point and molecular weights were calculated. The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. The Proteome- pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). Additionally, it can be obtained directly from the p K a values of individual charged residues of the protein. The isoelectric point-the pH at which a particular molecule carries no net electrical charge-is an important parameter for many analytical biochemistry and proteomics techniques. Proteome- pI 2.0 is an update of an online database containing predicted isoelectric points and p K a dissociation constants of proteins and peptides.
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