10-10-2012, 08:11 PM
(This post was last modified: 10-10-2012, 08:33 PM by Administrator.)
In the last decade, there has been vast development in the field of science and biomedicine. The whole sequencing of the human genome is certainly a milestone in the development and progress of science. This has helped in the rapid development in the field of medicine by providing knowledge about gene therapy, individual-based treatment for various diseases, different modes of treatment for genetic diseases, etc. Proteome can be defined as the set of various proteins expressed by a particular genome. The study of the different proteins, their dynamics and their interplay and interactions constitute the study of proteomics.
Although, both Proteomics and Protein chemistry involve the identification of various proteins expressed within the body, they are totally unrelated to each other. The protein chemistry is a part of the structural biology, dealing with physical biochemistry of the various proteins from a mechanistic point of view and relates mainly to the structure and function modelling studies and the effect of one on the other. Proteomics, on the other hand, involves systems biology, dealing with multiprotein systems and characterizing the behaviour of the whole system.
Measurement of gene expression is possible using various techniques; however, study of proteomics plays an important role considering the instability of the mRNAs preventing the formation of proteins as well as the regulatory functions of the different proteins in the biological and molecular mechanisms within the body. The gene expression can be measured by the use of cDNA as well as microarray system. Analysis of proteome is a complex task owing to the presence of posttranslational modification in proteins and also the fact that protein recognition is not based on sequence unlike oligonucleotides. Hence, special tools have been developed for proteomics such as
i)databases of protein, EST and genome sequence Mass spectrometry (MS),
ii)Mass Spectrometry (MS)
iii)collection of software that is capable of comparing the MS data with the protein sequence database, and
iv)protein separation technology
Analytical proteomics has become an emerging field in science. The identification of different proteins within the cell and their characterization is gaining importance even in medical field. The analysis of the whole protein is somewhat difficult. Hence, the tools for proteomics utilize different approaches for proper protein analysis. The protein is firstly converted to peptides and the sequence of the peptides is analysed. The sequence of the peptides is then matched with the sequence in the database to identify the proteins. The main problem in proteomics is the presence of a protein mixture in the biological sample. The protein analysis with the use of mixture is difficult; hence, the separation of the proteins is essential. The separation techniques involve the use of SDS-PAGE, which may be one-dimensional (1D) or two-dimensional (2D), High Performance Liquid Chromatography (HPLC). Proteins have also been analysed by digesting them and then carrying out separation using capillary electrophoresis or Isoelectric focusing (IEF). However, the protein separation by 2D SDS-PAGE followed by digestion into peptide fragments has emerged to be the better approach in analytical proteomics, due to numerous advantages offered by 2D SDS-PAGE. The proteins are digested using various proteases, which cleave at specific amino acids, thereby helping in the analysis with MS. Two types of instruments have been used for proteomics study: the MALDI-TOF and the ESI-tandem MS. Although, both the instruments work on completely different principles, they provide complementary information, hence both serve definite unique purpose. Peptide mass fingerprinting is a protein identification method used in high throughput proteomic study. In this method, the proteins are digested using trypsin and mass is analysed using MALDI-TOF. However, the difficulty in differentiation of homologous proteins and the similar proteins from different species limit the use of the method.
The main four applications of proteomics are:- Mining, protein expression profiling, protein network mapping and mapping of protein modifications. Mining refers to the identification of the proteins in a given sample i.e. the composition of the proteome is identified from the gene expression data from microarrays. Protein expression profiling is the identification of protein composition specific for a particular state of an organism or as a function to the effect of a drug or any other stimulus. Protein network mapping refers to the study of the interactions of various proteins in the functional network within the body and gives detailed information about the proteins in any signal transduction pathway. Mapping of protein modifications involves the study and identification of the nature and specificity of the posttranslational modification in a given protein. The development of protein arrays is under progress and if found successful, will create a great impact in the field of proteomics.
Although, both Proteomics and Protein chemistry involve the identification of various proteins expressed within the body, they are totally unrelated to each other. The protein chemistry is a part of the structural biology, dealing with physical biochemistry of the various proteins from a mechanistic point of view and relates mainly to the structure and function modelling studies and the effect of one on the other. Proteomics, on the other hand, involves systems biology, dealing with multiprotein systems and characterizing the behaviour of the whole system.
Measurement of gene expression is possible using various techniques; however, study of proteomics plays an important role considering the instability of the mRNAs preventing the formation of proteins as well as the regulatory functions of the different proteins in the biological and molecular mechanisms within the body. The gene expression can be measured by the use of cDNA as well as microarray system. Analysis of proteome is a complex task owing to the presence of posttranslational modification in proteins and also the fact that protein recognition is not based on sequence unlike oligonucleotides. Hence, special tools have been developed for proteomics such as
i)databases of protein, EST and genome sequence Mass spectrometry (MS),
ii)Mass Spectrometry (MS)
iii)collection of software that is capable of comparing the MS data with the protein sequence database, and
iv)protein separation technology
Analytical proteomics has become an emerging field in science. The identification of different proteins within the cell and their characterization is gaining importance even in medical field. The analysis of the whole protein is somewhat difficult. Hence, the tools for proteomics utilize different approaches for proper protein analysis. The protein is firstly converted to peptides and the sequence of the peptides is analysed. The sequence of the peptides is then matched with the sequence in the database to identify the proteins. The main problem in proteomics is the presence of a protein mixture in the biological sample. The protein analysis with the use of mixture is difficult; hence, the separation of the proteins is essential. The separation techniques involve the use of SDS-PAGE, which may be one-dimensional (1D) or two-dimensional (2D), High Performance Liquid Chromatography (HPLC). Proteins have also been analysed by digesting them and then carrying out separation using capillary electrophoresis or Isoelectric focusing (IEF). However, the protein separation by 2D SDS-PAGE followed by digestion into peptide fragments has emerged to be the better approach in analytical proteomics, due to numerous advantages offered by 2D SDS-PAGE. The proteins are digested using various proteases, which cleave at specific amino acids, thereby helping in the analysis with MS. Two types of instruments have been used for proteomics study: the MALDI-TOF and the ESI-tandem MS. Although, both the instruments work on completely different principles, they provide complementary information, hence both serve definite unique purpose. Peptide mass fingerprinting is a protein identification method used in high throughput proteomic study. In this method, the proteins are digested using trypsin and mass is analysed using MALDI-TOF. However, the difficulty in differentiation of homologous proteins and the similar proteins from different species limit the use of the method.
The main four applications of proteomics are:- Mining, protein expression profiling, protein network mapping and mapping of protein modifications. Mining refers to the identification of the proteins in a given sample i.e. the composition of the proteome is identified from the gene expression data from microarrays. Protein expression profiling is the identification of protein composition specific for a particular state of an organism or as a function to the effect of a drug or any other stimulus. Protein network mapping refers to the study of the interactions of various proteins in the functional network within the body and gives detailed information about the proteins in any signal transduction pathway. Mapping of protein modifications involves the study and identification of the nature and specificity of the posttranslational modification in a given protein. The development of protein arrays is under progress and if found successful, will create a great impact in the field of proteomics.
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