Proteomics is the science that studies the structure and function of proteins as well as analyzes a complex network of protein-protein interactions in living cells. A cell reacts to environmental changes by proteome change (a set of proteins). In response, the synthesis of certain proteins increases, whereas others decrease. Therefore, proteome reflects information about the state of the organism under certain physiological conditions and at a particular period. It eventually influences the function of every cell. Proteomics has a long history, which can be divided into the following periods: protein sequencing (Sanger), crystallization, mass spectrometry and modern proteomic studies. Today, there are a number of researches in proteomics that play an important role in the scientific development and everyday life. The paper will discuss the history of proteomics, its methods, tasks as well as its modern researches.
History of Proteomics
One of the major events in the biological science was decoding information that was encoded in the human genome. The initiator of the project ‘Human Genome’, in which the international organization The Human Genome Organization was created, was Nobel laureate James Watson (Rédei, 2008). More than 10 years later, the first results of sequencing the human genome were published.
However, despite the significance of the project, data on the human genome and genomes of other organisms have caused new, more global problems. There were less human genes than it was expected. Their number was about 35 thousand while the number of proteins encoded in the genome amounted to about a million (Rédei, 2008). The variety of protein is explained by the presence of such processes as mRNA, post-translational modifications and processing of proteins. Inability to obtain detailed information on the composition of proteins of the body with the help of genomics was the main prerequisite for the development of post-genomic research and the emergence of a new science – proteomics.
The development of proteomics is explained by the use of high-tech methods to determine the amount of a particular protein in a sample, to identify the protein, its primary structure and post-translational modifications (Conrotto & Souchelnytskyi, 2008, p. 171). The beginning of the development of proteomics can be attributed to the experiments conducted by Frederick Sanger. In the 1940s-1950s, he studied the structure of insulin and defined its amino acid sequence and location of disulfide bonds (Kirch, 2008). Sanger proposed a method of sequencing proteins with the use of dinitrofluorobenzene.
Methods and Main Tasks of Proteomics
An important role in studying the structure of proteins is played by sequencing methods, i.e. methods that allow determining the sequence of amino acids in the protein (primary structure of the protein). NMR and X-ray analysis provide the most relevant and detailed information about tertiary structure of a protein and allow in depth studying the structure of proteins. The data on the tertiary structure of a protein provide important information about the functions that are performed by this protein while proteins with similar functions often have similar spatial structure (Rédei, 2008). The methods of ultracentrifugation and gel filtration allow studying the quaternary structure of a protein. Using a combination of described techniques allows defining the structure and properties of each individual protein and thus finding the answer to one of the basic questions of proteomics.
Another important problem of proteomics is characterizing the composition of all the proteins in a given cell. To solve this problem, the method of two-dimensional (2D) gel electrophoresis with mass spectrometry is used. 2D electrophoresis allows separating most of the proteins that make up cells. The method of mass spectrometry allows uniquely identifying each of the proteins. The purpose of such research is to compare protein expression in a normal condition and the operation of various factors in various pathological conditions. Determining the level of expression of a particular protein (protein markers) may be used in the diagnosis of cancer, neurodegenerative diseases and others.
In order to understand the processes that occur in the cell, it is not enough to know the nature and range of proteins that are expressed in different terms. A crucial issue is the study of what proteins interact with each other and how such interactions influence the structure and properties of protein partners. To analyze interactions between proteins, the method of co-immunoprecipitation (sorption of protein antigen and its partner proteins on immune sorbent) that is followed by mass spectrometry to identify protein partners, the two-hybrid method, phage display and many other methods are used. The determination of protein partners can disclose valuable information about the mechanism of functioning of the test protein. The determination of protein interactions allows describing different processes that occur within cells.
Researches on Proteomics
In 2001, an international organization for the study of the human proteome HUPO (Human Proteome Organization) was created (Srivastava, 2005). In 2008, the international research project ‘Human Proteome’ was approved (Marko-Varga, 2014). In doing this, the project involved research centers around the world. The aim of this initiative is to identify and catalogue all human proteins in normal and pathological conditions, construct a protein atlas of cells, organs and tissues, protein-protein interactions schemes and identify new markers of human diseases. It is necessary to emphasize an unprecedented scale and ambition of the project.
Medical aspects of implementation of the proteomics research are of particular interest. The effectiveness of treatment of many diseases (cancer, cardiovascular, pulmonary, neurodegenerative, endocrine, etc.) depends on timely and accurate diagnosis. Therefore, the efforts of scientists are aimed at finding proteins – markers of disease with diagnostic and therapeutic value and developing new diagnostic techniques and effective drugs (Rédei, 2008).
With a view to developing minimally invasive methods of diagnosis of certain diseases, it is convenient to use proteomic analysis of plasma/ serum of human blood. In addition to basic proteins present in a normal condition, blood plasma contains a dynamically changing set of proteins. Thus, each disease is characterized by its own set of protein biomarkers that can potentially be detected during a routine blood test. By controlling the content of protein markers in plasma, one can judge about the effectiveness of treatment and therapy and predict relapse of the disease before its clinical manifestations.
Modern scientific efforts are aimed at finding tumor markers that have high sensitivity and are specific for a particular type of tumor because most of the identified tumor markers do not meet these criteria. There is an interest in the development of methods to simultaneously detect a small sample of a few indicators (Rédei, 2008). A particular interest to clinical diagnostics is related to the development of proteomic microarray, which allows carrying out large-scale studies of biological samples for the presence of biomarkers of disease. Proteomic biochip is a matrix to which a molecule is chemically attached. They are capable of reacting only to specific marker proteins with the complete removal from all other sample substances. The detection of bound proteins is made by high-precision mass spectrometry. This approach improves the performance of diagnostic methods, reduces their cost and makes it possible to analyze a sample for the presence of multiple biomarkers in a short time.
Proteomic techniques are used in researches that are related to food and agriculture. They include identification of markers that are responsible for the quality of agricultural products (nutritional and taste characteristics of meat, milk), identification of diagnostic proteins that are responsible for resistance of plants and animals to pathogens, diagnosis of diseases of farm animals in the early stages (mastitis, gastrointestinal disease). Proteomic techniques of testing are used to monitor product freshness and determine the presence of pathogenic microorganisms, characterize wine, beer and cheese, detect the quality of raw material from which they are cooked, identify allergens in fruit, vegetables, food, etc. Proteomic studies are relevant to the selection process in agriculture, including identification and selection of certain animal breeds and plant varieties.
Assistance of proteomics in basic research, in particular in the analysis of intracellular signaling in animal and plant cells, is invaluable. Its results will be used in the development of methods for optimizing the processes of growing crops as well as for the creation of genetically modified plants with improved characteristics. Researches on biosecurity, which are conducted by means of analysis of proteomic status in order to identify possible changes in protein composition under the influence of the built and modified genes, present crucial importance. These surveys will form the basis for the development of proteomic diagnostics of economically useful signs of animal and plant breeding for efficient selection.
Proteomics is actively developing all over the world and, despite being relatively new field of studies, it has achieved impressive success. There is significant progress in proteomic diagnosis of several diseases, including the most common cancer (cancer of the ovary, stomach, prostate, etc.), diseases of the cardiovascular system (myocardial infarction, ischemic heart disease), and neurodegenerative disorders (schizophrenia, Alzheimer’s disease etc.).
Proteomics is the science that studies protein composition of biological objects as well as modifications, structural and functional properties of protein molecules. The multidimensional nature of the implementation of proteomic research in fundamental and applied areas indicates the scale of challenges that are faced by proteomics. Continuous improvement of proteomics methods, increasing sensitivity of analytical equipment and automation of research will undoubtedly enhance a deeper understanding of the molecular mechanisms of protein systems. This will give a possibility to manage these processes and assess the status of the organism and correct pathological conditions. Proteomics opens unlimited possibilities for medicine, agriculture, veterinary medicine, food industry, pharmaceutical industry and other related fields.