Structure analysis of protein
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The document discusses the importance of protein structure analysis and various methods to determine protein structures, including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. It highlights the role of structural proteomics in understanding protein function and evolutionary relationships, and the challenges in annotating orphan genes. Additionally, it mentions the applications of protein structural knowledge in biomedical informatics and drug design.
Structure analysis of protein
- 1. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 01 STRUCTURE ANALYSIS OF PROTEIN By KAUSHAL KUMAR SAHU Assistant Professor (Ad Hoc) Department of Biotechnology Govt. Digvijay Autonomous P. G. College Raj-Nandgaon ( C. G. )
- 2. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 02 SYNOPSIS INTRODUCTION STRUCTURAL PROTEOMICS WHAT IS THE IMPORTANCE OF STUDY OF PROTEIN METHODS FOR SOLVING PROTEIN STRUCTURE 1. X- RAY CRYSTALLOGRAPHY •INTRODUCTION •PROCEDURE •LIMITATIONS
- 3. Pacific Networks Pacific Networks STRUCTURE ANALYSIS OF PROTEIN -03 2.NUCLEAR MAGNETIC RESONANCE •PROTEIN STRUCTURE DETERMINATION 3. MASS SPECTROMETER •MALDI •ESI STRUCTURE MODELING APPLICATIONS CONCLUSION REFERENCES
- 4. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 04 INTRODUCTION Proteins are the most abundant biological macromolecules, occurring in all cells and all parts of cells. Proteins also occur in great variety; thousands of different kinds, ranging in size to large, may be found in a single cell. Proteins exhibit enormous diversity of biological function and are the most important. Proteins are the molecular instruments through which genetic information is expressed.
- 5. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 05 The principles of sequence analysis showed how, under certain circumstances, the function of a new gene could be assigned by comparison with genes with similar sequences whose functions have already been determined. Although not a foolproof method for functional annotation, this strategy has been successful in the functional classification of 30–40% of the genes discovered in the genome projects.
- 6. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 06 SACCHAROMYCES GENOME PROJECT 30% gene indentified by individual experiment. 30% gene indentified by sequence analysis. 30% gene were anonymous 10% are ORFs
- 7. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 07 STRUCTURAL PROTEOMICS The aim of structural proteomics is to express large numbers of genes and compare the three-dimensional structures of the resulting proteins revealing evolutionary relationships between orphan genes and those whose functions are known. This brings the determination of protein structure to the beginning of the investigative process.
- 8. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 08 SEQUECCE ANALYSIS Pairwise comparisons BLAST FASTA Really useful when there is >30% sequence hit between the query sequence and entries in the sequence databases.
- 9. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 09 SEQUENCE ANALYSIS ALONE IS NOT SUFFICIENT TO ANNOTATE ALL ORPHAN GENES
- 10. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 10 PROTEIN STRUCTURES ARE MORE HIGHLY CONSERVED THAN SEQUENCES Sequence comparison is a very powerful method for functional annotation, but even with sophisticated multiple alignment tools, fewer than 50% of newly discovered genes can be matched to previously identified genes with known functions. Structure is much more strongly conserved than sequence because of degeneracy, a concept that is most often applied to nucleotide sequences but is also relevant to protein structures
- 11. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 11 METHODS FOR SOLVING PROTEIN STRUCTURE Direct determination – X-ray crystallography Nuclear magnetic resonance (NMR) spectroscopy Mass spectroscopy Prediction method Comparative modeling -
- 12. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 12 X-ray crystallography is a method used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. X-RAY CRYSTALLOGRAPHY
- 13. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 13 PROCEDURE OF X –RAY DIFFRACTION
- 14. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEINS 14 Fig :The three-dimensional structure of penicillin EARLY ORGANIC AND SMALL BIOLOGICAL MOLECULES
- 15. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 15 Fig: Ribbon diagram of the structure of myoglobin showing coloured alpha helices
- 16. Pacific Networks Pacific Networksstructure analysis of protein 16 Two limiting cases of X-ray crystallography— "small-molecule“crystallography "macromolecular" crystallography Pure crystal LIMITATION OF X RAY CRYSTALLOGRAPHY
- 17. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 17 NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is a research technique that exploits the magnetic properties of certain atomic nuclei. It determines the physical and chemical properties of atoms or the molecules in which they are contained. Most frequently, NMR spectroscopy is used to investigate the properties of organic molecules, although it is applicable to any kind of sample that contains nuclei possessing spin.
- 18. Pacific Networks Pacific NetworksSTUCTURE ANALYSIS OF PROTEIN 18 PRINCIPLE In the presence of an external magnetic field (B0), two spin states exist, +1/2 and -1/2. The magnetic moment of the lower energy +1/2 state is aligned with the external field, but that of the higher energy -1/2 spin state is opposed to the external field.
- 19. Pacific Networks Pacific NetworksSTUCTURE ANALYSIS OF PROTEIN 19 PROCEDURE
- 20. Pacific Networks Pacific NetworksSTUCTURE ANALYSIS OF PROTEIN 20 NMR SPECTROSCOPY Can perform in solution. No need for crystallization Can only analyze proteins that are <300aa. Many proteins are much larger. Can’t analyze multi-subunit complexes Proteins must be stable.
- 21. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 21 Mass spectrometry works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios. Mass spectrometry is an important emerging method for the characterization and sequencing of proteins. The two primary methods for ionization of whole proteins are ESI and MALDI. MASS SPECTROMETR
- 22. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 22 PROCEDURE A sample (which may be solid, liquid, or gas) is ionized. The ions are separated according to their mass-to-charge ratio. This is the key step. The ions are dynamically detected by some mechanism capable of detecting energetic charged particles. The signal is processed into the spectra(singular spectrum) of the masses of the particles of that sample.
- 23. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 23 MATRIX ASSISTED LASER DESORPTION MASS SPECTROMETRY In one, proteins are placed in a light-absorbing matrix. With a short pulse of laser light, the proteins are ionized and then desorbed from the matrix into the vacuum system. This process, known as matrix-assisted laser desorption/ionization mass spectrometry, or MALDI MS, has been successfully used to measure the mass of a wide range of macromolecules.
- 24. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 24 ELECTROSPRAY IONIZATION MASS SPECTROMETRY
- 25. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 25 STRUCTURAL MODELING Comparative modeling Modeling the structure of a protein that has a high degree of sequence identity with a protein of known structure Must be >30% identity to have reliable structure. Threading/fold recognition Uses known fold structures to predict folds in primary sequence.
- 26. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 26 APPLICATION Biomedical informatics We focus on the development and application of computational methods to investigate the molecular basis of disease, and we explore new ways to apply the knowledge generated in improving disease prevention, diagnosis and therapy. Structural analysis of genetic variation
- 27. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 27 Biological process The three-dimensional structure and flexibility of proteins determine their function in biological processes. Knowledge about protein structure is used in structure-based drug design and optimization of biocatalysts. The goal of the recent years "structural genomics" projects is to map the fold space, to make it possible to generate a useful homology model of any protein of interest in the future.
- 28. Pacific Networks Pacific NetworksSTRUCTURE ANALYSIS OF PROTEIN 28 DIFFERENT STRUCTURES OF PROTEINS
- 29. Pacific Networks Pacific Networks STRUCTURE ANALYSIS OF PROTEIN 30 References PRINCIPLE OF GENE MANIPULATION AND GENOMICS BY : S.B. PRIMOSE AND R. M. TWYMAN – 7th EDITION LEHNINGER PRINCIPLE OF BIOCHEMISTRY BY :DAVID L. NELSON & MICHAEL M. COX - 4th EDITION BY INTERNETS