Biophysics I Mar 2th – June 16th, 2016 Korea University Kyung Hyun Kim, Ph.D. Department of Biotechnology & Bioinformatics BK21+ Infectious Disease Research Unit KOREA UNIVERSITY [email protected] Crystal Concept • In 1611 Kepler suggested that snowflakes derived from a regular arrangement of minute brick-like units. -The essential idea of a crystal. X-rays • Discovered by Rontgen 1895 • Cause of tremendous scientific excitement. • 1,500 scientific communications within first twelve months. • US scientists repeated experiments within four weeks. The Nobel Prize in Chemistry 1907 "for his biochemical researches and his discovery of cell-free fermentation" Eduard Buchner Germany Landwirtschaftliche Hochschule (Agricultural College) Berlin, Germany b. 1860, d. 1917. Theory of Diffraction • 1910 von Laue derived theory of diffraction from a lattice. Bragg’s Law of diffraction 1912 • Diffraction observed if X-rays scattering from a plane add in phase. • Path difference D = 2d sin q. - d is the spaceing between planes & q is the angle of incidence. • Scatter in phase if path difference is nl - n is an integer & l is the X-ray wavelength. 2d sin q = n l • First structure (NaCl) in 1912. W. H. Bragg & W. L. Bragg Urease crystals ( X 728) Sumner, J. B. (1926) “ The isolation and crystallization of the enzyme urease” J. Biol. Chem. 69:435-441. The Nobel Prize in Chemistry 1946 “ for his "for their preparation of enzymes and discovery that virus proteins in a pure form" enzymes can be crystallized" James Batcheller John Howard Northrop Wendell Meredith Sumner Stanley 1/2 of the prize 1/4 of the prize 1/4 of the prize Cornell University Rockefeller Institute for Rockefeller Institute for Ithaca, NY, USA Medical Research Medical Research Princeton, NJ, USA Princeton, NJ, USA 1887-1955 1891-1987 1904-1971 1953: Double helix structure of DNA • Crick & Watson used X-ray diffraction to work out the way genes are encoded. Diffraction pattern • Crystals & diffraction pattern recorded by Rosalind Franklin. • Revealed the symmetry of the helix & pitch of helix. First Protein Structure • Myoglobin. • Protein purified from whale blood. • John Kendrew 1958. • Showed a 75% a-helical fold. • 155 amino acids, ~ 17 kDa. First Protein Complex • Hemoglobin. • Two copies each of a & b chains of myoglobin in a complex. • Solved by Max Perutz. Structure of Nucleic Acid & Protein complex • Nobel prize to Aaron Klug in 1982. • Also contribution to electron microscopy. Not all enzymes are proteins: Some RNA molecules (ribozymes) were found to be catalytic (Sidney Altman and Thomas Cech, 1981). Ribozymes are found to promote RNA processing. Sidney Altman visiting PKU Photosynthetic Reaction Centre Structure • First membrane protein structure in 1985. • Nobel prize to Michel, Deisenhofer & Huber 1988. • Showed the technique of detergent solubilised membrane protein crystallisation. Structure of F1-ATPase • Revealed the details of the rotational mechanism of ATP- synthase. • Nobel prize in Chemistry 1997 to John Walker Structure of the K+ channels • Revealed the structural basis for ion transport across a membrane. • Deep physiological relevance. • Nobel prize in Chemistry 2003 to Roderic MacKinnon. Ribosome • 50 S and 70 S ribosome structures in 2000. • Massive RNA:Protein complexes. • Revealed details of how proteins synthesyzed by RNA. • Nobel prize in Chemistry 2009 to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath Protein functions • Catalytic proteins (Enzymes) • Contractile/Motile proteins • Structural proteins • Transport proteins • Defense proteins • Nutrient/Storage proteins • Regulatory proteins Enzymes: biological catalysts Almost all reactions in cell catalyzed by enzymes Examples: Protein kinase RNase Chymotrypsin Reverse transcriptase DNA topoisomerase Reverse transcriptase (HIV) • Catalyze almost every reaction in the cell • Operate under mild conditions (in cells) • Increase reaction rate 106-1012-fold • Structurally diverse (»functionally diverse) 1000-4000 enzymes in an animal cell DNA topoisomerase II (yeast) Active site • Recognizes and binds substrate (reactant) • Performs reaction catalysis Structural proteins Support or strengthen biological structures Examples: • Collagen–tendon, cartilage, leather • Keratin–hair, fingernails, horns, feathers • Fibroin–silk, spider web Transport proteins Bind and carry specific molecules or ions Examples: Hemoglobin–O2 Defense proteins Protect organism from other organisms or injury Examples: Antibodies (immunoglobulins) Antibiotics Snake venom Nutrient and storage proteins Source of amino acids for growth and development Examples: Ovalbumin–egg white Casein–milk Contractile and motile proteins Allow cells or organisms to move Examples: Actin and myosin–muscle Regulatory proteins Modulate biological activity Examples: Hormones Insulin–regulates sugar metabolism DNA-binding proteins Transcription factors–Lac repressor, Antp Membrane proteins • Integral: embedded in phospholipid bilayer • Lipid-linked: covalently attached to lipid • Peripheral: weakly bound to membrane CFTR Function • CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) is a chloride transporter found in the membrane of epithelial cells • In normal cells, the protein allows the release of Cl from the cell. The protein’s physiological role A normal lung Chloride into airway; sodium out - keeps mucus moist and thin Normal CFTR regulates the sodium channel (inactivates it) A CF Lung Chloride does not get into airway; more sodium leaves; More salt in cell - water comes in. This makes the mucus thick The CF gene • Due to the deletion of Codon 508, the amino acid phenylalanine is not present on the chain, which changes the protein’s structure. Sickle-cell anemia • Even a slight change in primary structure can affect a protein’s conformation and ability to function. • In individuals with sickle cell disease, abnormal hemoglobins, oxygen-carrying proteins, develop because of a single amino acid substitution. – These abnormal hemoglobins crystallize, deforming the red blood cells and leading to clogs in tiny blood vessels..