Proteomics - 3rd Year Biotechnology PDF

Ecole Nationale Supérieure de Biotechnologie Biotechnology Departement « 3rd-year » Proteomics Dr. MADDI FERDJOUKH T t.maddi @ensbiotech.edu.dz  CHAPTER 3 Applied Proteomics Dr. MADDI 2023  Intro...

Ecole Nationale Supérieure de Biotechnologie Biotechnology Departement « 3rd-year » Proteomics Dr. MADDI FERDJOUKH T t.maddi @ensbiotech.edu.dz  CHAPTER 3 Applied Proteomics Dr. MADDI 2023  Introduction Proteomics is the large-scale study of proteins particularly their composition, structures, functions, and interactions of the proteins directing the activities of cell. Genomics can give a rough estimation of expression of a protein. Most of the proteins function in collaboration with other proteins, and the main goal of proteomics are to identify which proteins interact Applications of proteomics :  Pharmaceutical industry  Health Dr. MADDI 2023  Agriculture & food industry  Introduction After genomics, proteomics is often considered as the advanced step in the study of biological systems. It is much more complicated than genomics, mostly because while an organism’s genome is more or less constant, the total protein expression profile always changes with time, micro and macro environmental conditions Dr. MADDI 2023  Applications of proteomics Proteomics is widely used technique in biological fields, mainly applied in pharmaceutical industry, Bio- medicine, Oncology (Tumor biology), Agriculture and Food Microbiology. Dr. MADDI 2023  Pharmaceutical sector Protein Design Protein design is the process of creating new proteins with specific properties by manipulating the sequence of amino acids. It involves a combination of computational techniques, laboratory experiments, and interdisciplinary knowledge from fields such as biology, chemistry. Dr. MADDI 2023  Pharmaceutical sector Protein Design Protein design can also refers to the effort to create new protein molecules of a desired 3D structure and function. Dr. MADDI 2023  Pharmaceutical sector Protein Design It is a reverse procedure of protein structure prediction, and the solution of the problem therefore highly relies on the extent of our understanding on the principle of protein folding (Figure). Figure :Protein design is a reverse procedure of protein structure prediction Dr. MADDI 2023  Pharmaceutical sector Protein Design Medicine: We use design to develop therapeutics with high specificity and low toxicity. Example : Researchers have crafted proteins that selectively bind to cancer cells and others that inhibit viral infection, paving new paths for drug development. Dr. MADDI 2023  Pharmaceutical sector Protein Design Vaccines : Traditionally, antibodies are created in vivo by injecting the target protein into a lab animal. The animal’s immune system will produce antibodies against the disease, which are then harvested and purified Dr. MADDI 2023  Pharmaceutical sector Protein Design This method is great for producing antibodies for laboratory use, but because the antibodies originated in another species, they aren’t readily usable as treatments.The human body will perceive their foreign-looking amino acid sequences as a threat and try to interfere!!! Dr. MADDI 2023  Pharmaceutical sector Protein Design This problem can be overcome by adjusting the sequence to appear more human — or humanizing the antibody — but this may also change its structure. Dr. MADDI 2023  Secteur pharmaceutique Protein Design in silico design The aim of in silico design is to utilize bioinformatics and computational modeling to skip all of these steps — saving years in the process. Dr. MADDI 2023  Protein Design Drug design Proteomics is the systematic high- throughput separation and characterization of proteins within biological systems. Importantly, it is at the protein level that disease processes become manifest and at which most drugs act. Proteomics is consequently assuming a central place modern drug development with a wide spectrum of practical applications embracing diagnostic target discovery, target validation lead compound. Selection, investigation of drug modes of action, toxicology and chemical development Dr. MADDI 2023 Vishwakarma et al, 2010  Protein Design protein synthesis inhibitor A protein synthesis inhibitor is a substance that stops or slows the growth or proliferation of cells by disrupting the processes that lead directly to the generation of new proteins Dr. MADDI 2023  Protein Design protein synthesis inhibitor Example : Tyrosine kinase inhibitors (TKIs) are a kind of targeted therapy. Tyrosine kinases, TKs, are involved in signal transduction leading to cell growth and multiplication. It is generally a cascade of intracellular reactions comprising successive phosphorylations Dr. MADDI 2023  Protein Design protein synthesis inhibitor Example : Protein kinase inhibitors Certains cancers de la thyroïde Tumeurs gastro-intestinales cancer du rein In general, tyrosine kinase inhibitors slow cancer down and help people live longer. Polyarthrite rhumatoïde Dr. MADDI 2023 Protein Design Protein synthesis inhibitor Example 2 : Protease Inhibitors - VIH Dr. MADDI 2023  Health screening Protein identification Clinical proteomic studies aiming at biomarker discovery require a platform to identify sensitivity, accuracy, reproducibility and high sample throughput. Dr. MADDI Lopez, F. (2005). Protéomique et spectrométrie de masse: applications 2023 en clinique. Hépato-Gastro & Oncologie Digestive, 12(6), 427-435.  Health screening Protein identification The providing of extensive proteome coverage of complex samples is required to allow the detection of proteins whose concentration levels vary by several orders of magnitude. High- throughput MS-based profiling strategies, MALDITOF and SELDI for clinical samples such as tissue and bodily fluids present the rapid determination of molecular masses and the ability of screening with high-throughput small amounts of clinical samples for biomarker discovery (Figure ) Dr. MADDI Lopez, F. (2005). Protéomique et spectrométrie de masse: applications 2023 en clinique. Hépato-Gastro & Oncologie Digestive, 12(6), 427-435.  Protein identification Biomarkers Dr. MADDI Application of proteomics as a tool of new biomarker and drug 2023 discovery.  Protein identification Biomarkers One of the essential aspects in fundamental research and for subsequent current clinical applications is the discovery of protein markers specific to different pathologies (Bio-markers). Dr. MADDI 2023  Protein identification Biomarkers The term “biomarker”, a portmanteau of “biological marker”, refers to objective indications of medical state observed from outside the patient which can be measured accurately and reproducibly Or A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.” (National I of H) Strimbu et al (2011). What is biomarkers?. National library of medecine Dr. MADDI 2023 Protein identification Biomarkers The developed technology will enable the rapid diagnosis of viruses and disease protein markers. MS-based quantification of protein biomarkers is mainly performed by a bottom-up approach using peptide fragments obtained by enzymatic protein digestion with trypsin. Protein identification Biomarkers Qualitative biomarkers could be involved in a pathogenic process detection within an yes/no analysis, while quantitative biomarkers are involved in pathogenic process detection with a threshold effect. Purpose: Diagnose diseases or predict disease risks Masuda et al, 2021 Protein identification Biomarkers Proteomics is an indispensable methodology employed for identifying protein biomarkers Due to rapid and continuous developments, proteomics can now be used to comprehensively compare the expression of proteins in samples. Additionally, targeted proteomics with high sensitivity has been developed for protein quantification.  Protein identification Biomarkers The goal is to be able to establish a bio-signature from protein expression profiles, and if possible from biological fluids, allowing rapid, precise and reliable discrimination of different pathological states. Dr. MADDI 2023  Health screening To determine the presence of abnormal proteins in a patient's cells , proteomics makes it possible ! Indeed, many diseases lead to the expression of proteins that are not normally present in healthy cells... identifying these proteins enables early diagnosis of a disease, sometimes even before symptoms appear. By identifying these proteins or the interactions between them, we can develop treatments. Example: cancer screening and treatment Dr. MADDI 2023  Agriculture/food Agriculture The study of plant protein networks and plant traits mechanisms such as resistance to stresses help to sustain of agricultural crop production through protecting crops against biotic and abiotic stresses underlying the development and vitality of seeds. Dr. MADDI 2023  Agriculture/food Proteomics approaches have been a useful tool for determining the biological roles and functions of individual proteins and identifying the molecular mechanisms that govern seed germination, vigour and viability in response to ageing. 2D gel separation of seed proteins and the effect of ageing on seed protein abundance Dr. MADDI 2023 Nguyen et al, 2015  Agriculture/food Posttranslational modification (PTM) of proteins in dry seeds plays a central role in dormancy release, metabolism resumption, and ageing processes (Arc et al., 2011). These researchers also demonstrated that the accumulation of oxidized (carbonylated) proteins in dry seed is associated with ageing and might induce loss-of-function of proteins 2D gel separation of seed proteins and the effect of ageing on seed protein abundance and enzymes Nguyen et al, 2015 Dr. MADDI 2023  Agriculture/food Some factors including high temperature, salt and heavy metal stress, and pathogens cause serious problems for agricultural management and reduce grain yield and quality. The use of proteomics in agricultural is presented especially for analyzing the interaction between crops and bacteria Dr. MADDI 2023  biostimulant Currently, one of the objectives of the ecological transition in agriculture is to develop new natural products (biocontrol, biostimulant, etc.) in order to replace toxic pesticides. The most important biostimulant effects on crops Shahrajabian et al, 2021. Biostimulants Application: A Low Input Cropping Management Tool for Sustainable Farming of Vegetables  Agriculture/food Proteomics is used in food technology and food biotechnology for characterization and standardization of raw materials. It is used as a tool for the detection of possible bacterial contamination and microbial safety https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149639/ Dr. MADDI 2023  Agriculture/food Also it has been successfully applied to the study of food protein groups such as milk, meat, and Cereal proteins by many proteomic researches, and significant effort has gone into the characterization of their proteomes. Dr. MADDI 2023  Agriculture/food Proteomics approaches have been used to compare milk proteins from different species and other dairy products, deplete, fractionate, or remove some proteins of milk, and discover and characterize of bioactive milk components Dr. MADDI https://www.mdpi.com/1420-3049/25/15/3328 2023  Agriculture/food understanding the effects of environmental, nutritional, biological and industrial factors on fish meat quality were determined by using proteomic approaches Dr. MADDI 2023  Evolution Recent developments in new separation methods combined with considerable technological advances in mass spectrometers (precision, sensitivity, resolution, quantification) make proteomic analysis an essential methodology for obtaining very valuable protein information for understanding cellular mechanisms or for the identification of proteins involved.Proteomic analysis is becoming an increasingly sensitive and informative technique. Dr. MADDI 2023