ILipo-PseAAC: Identification of Lipoylation Sites Using Statistical Moments and General PseAAC

Lysine Lipoylation is a protective and conserved Post Translational Modification(PTM)in proteomics research like prokaryotes and eukaryotes.It is connected with many biological processes and closely linked with many metabolic diseases.To develop a perfect and accurate classification model for identifying lipoylation sites at the protein level,the computational methods and several other factors play a key role in this purpose.Usually,most of the techniques and different traditional experimental models have a very high cost.They are time-consuming;so,it is required to construct a predictor model to extract lysine lipoylation sites.This study proposes a model that could predict lysine lipoylation sites with the help of a classification method known as Artificial Neural Network(ANN).The ANN algorithm deals with the noise problem and imbalance classification in lipoylation sites dataset samples.As the result shows in ten-fold cross-validation,a brilliant performance is achieved through the predictor model with an accuracy of 99.88%,and also achieved 0.9976 as the highest value of MCC.So,the predictor model is a very useful and helpful tool for lipoylation sites prediction.Some of the residues around lysine lipoylation sites play a vital part in prediction,as demonstrated during feature analysis.The wonderful results reported through the evaluation and prediction of this model can provide an informative and relative explanation for lipoylation and its molecular mechanisms.

A dual-function chemical probe for detecting erasers of lysine lipoylation

Lysine lipoylation plays vital roles in cell metabolism and redox processes.For example,removal of lipoylation will decrease pyruvate dehydrogenase activity and affect the citric acid cycle.Despite the important functions of lysine lipoylation,the mechanisms for the addition and removal of this modification remain largely unexplored.Very few useful chemical tools are available to study the interactions of lysine lipoylation with its regulatory delipoylation proteins.For example,immunoaffinity purification-mass spectrometry is one of such tools,which highly relies on antibody efficiency and purification techniques.Single-step activity based fluorogenic probes developed by our groups and others is also an efficient method to study the deacylation activity.Affinitybased labeling probe using photo-cross-linker is a powerful platform to study the transient and dynamic interactions of peptide ligands with the interacting proteins.Herein,we have designed and synthesized a dual-function probe KTLlip for studying enzymatic delipoylation(eraser)activity and interaction of lysine lipoylation with the eraser at the same time.We show that KTLlip can be used as a useful tool to detect delipoylation as demonstrated by its ability to fluorescently label the eraser activity of recombinant Sirt2.We envision that the probe will help delineate the roles of delipoylation enzyme in biology.

Catalytic domain of PDC-E2 contains epitopes recognized by antimitochondrial antibodies in primary biliary cirrhosis

AIM:To search for further immunodominant peptides of the pyruvate dehydrogenase complex E2-component (PDC-E2) recognized by antimitochondrial antibodies (AMA) in primary biliary cirrhosis (PBC). METHODS:Sera from 95 patients with PBC were tested by enzyme-linked immunosorbent assay against 33 synthetic overlapping peptides (25 amino acids; aa) covering the entire length of the E2-subunit of PDC-E2. Furthermore,the inner lipoyl peptide 167-184 was used in an unlip oylated and a lipoylated form as well as coupled to ovalbumin. Sera from 11 AMA negative/ANA posit ive PBC patients,63 patients with other liver disorders and 22 healthy blood donors served as controls.RESULTS:Of the 95 PBC-sera,74% reacted with the peptide 475-499 and 58% with the pept ide 407-431 located within the catalytic domain of PDC-E2. Patients with other disorders or healthy controls were positive in only up to 18%. Antibodies to the unlipoylatedand lip oylated pept ide 167-184 within the inner lipoyl domain were found in only 5% and 11% of the PBC sera,respectively; using ovalbumin-coupled peptides,the incidence increased up to 57% (unlipoylated form). CONCLUSION:Peptides within the catalytic site of PDC-E2 rather than the previously reported lipoyl binding peptide 167-184 may represent major immunodomin ant epitopes recognized by AMA in PBC.