Proteome

PROTEOME

HARIS & ARUNMSC BIOTECHNOLOGYMAC & AL-AZHARERNAKULAM

Introduction• A genome is defined as a sequence of

nucleotides..• While a proteome cannot be defined as only

the sequence of proteins present in it.• It is required to know about the structure of

protein in proteome.• The functional interaction between the

protiens..

• Proteome is defined as the full complement of proteins produced by a particular genome.

• The word proteome was coined from 2 words protein and genome.

• In 1994 by Marc Wilkins.Proteomics • is the large- scale study of proteins• How they are modified• When and where are they expressed• How they are involved in metabolic pathways• How they interact with one another

• A proteome is larger than the genome, especially in eukaryotes, in the sense that there are more proteins genes.

• This is due to the alternative splicing or genes and post-transcriptional modifications.

PROTEOMICS

• It is the study of proteome, done by separation of proteins by two dimensional gel electrophoresis.

• In 1st dimension, the proteins are separated by iso electric focusing, which resolves proteins on basis of charge.

• In 2nd dimension, by molecular weight by SDS PAGE.(coomassie blue)

• Mass spectrophotometer has also been used in proteomics.

MS driven techniques• MS identification of proteins after quantitative analysis by 2DE– Peptide mass fingerprinting (Maldi MS)– Sequence based identification (MS/MS)

Generation of peptides for MS analysis

• Proteins digestion– Typically by trypsin; cleaves on the C-side of Argand Lys i.e. generates peptides having R or K atthe C-terminus– Also other cleaving enzymes e.g. clostripain,endopeptidase Lys-C• Peptide analysis– Total mass of a peptide– Peptide fragmentation (mass of single amino

acids

Tryptic peptides co-crystallized with matrix compound on sample stage•Irradiation with UV-laser•Matrix compound vaporized and included peptide ions moved to gas phase•Protonated peptide ions

APPLICATIONSApplication of Proteomics in the Study of Tumor Metastasis.•Tumor metastasis is the dominant cause of death in cancer patients.•The identification of protein molecules with their expressions correlated to the metastatic process would help to understand the metastatic mechanisms and thus facilitate the development of strategies for the therapeutic interventions and clinical management of cancer.

Application of proteomics in renal disease diagnosis.•In the diagnosis and treatment of kidney disease, a major priority is the identification of disease-associated biomarkers•two-dimensional gel electrophoresis with more sophisticated techniques, such as MS.The Application of Proteomics in Neurology•In neurology and neuroscience, many applications of proteomics have involved neurotoxicology and neurometabolism.

•The rapid spread of proteomics technology, which principally consists of twodimensional gel electrophoresis (2-DE) with in-gel protein digestion of protein spots and identification by massspectrometry, has provided an explosive amount of results

Application of proteomics to diabetes research.•qualitative and quantitative evidence of altered protein expression.

New drugs for treatment of disease•Most promising development that has come from the proteomics, is the identification of potential new drugs for treatment of diseases•For example, if a certain protein is implicated in a disease, its 3D structure provides the information to design drugs to interfere with the action of protein.•A molecule that fits the active site of an enzyme, cannot be released by enzyme, will inactivate.•This is the basis of new drug discovery tools which aim to find new drugs to inactvate the protien in disease

Role of Proteomics in Nutrition Research•There are about 100,000 proteins in humans with various physiological functions. The complement of proteins in the organism as well as their interactions is defined as the proteome. Its analysis (proteomics) by highly specific, sensitive, and accurate MS has been made possible with matrix-assisted laser.

•characteristics of dietary and body proteins; digestion, absorption, and metabolism of nutrients; functions of nutrients and other dietary factors in growth, reproduction, and health; biomarkers of the nutritional status and disease; and individualized requirements of nutrients. •The proteome analysis is expected to play an important role in solving major nutrition-associated problems in humans and animals, such as obesity, diabetes, cardiovascular disease, cancer, aging, and intrauterine fetal retardation.

Conclusions•2-DE is a powerful technique to separate of complex protein mixtures and analyze proteomes.•Mass Spectrometry microsequencing can identify proteins from 2-DE gels and other samples.•There are multiple databases and computer programs available to analyze MS data for protein Identification•Proteomics approach can be used to identify all proteins in particular sample, elucidate additional components of biochemical pathway(s), or analyze post-translational modifications at a small or large scale.

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