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Download Introduction to Protein Structure and Its Prediction
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Introduction to Protein Structure Rui Kuang Why do we study protein structure • Protein – Derived from Greek word proteios meaning “of the first rank” in 1838 by Jöns J. Berzelius. • Crucial in all biological processes, such as Enzymatic catalysis, transport and storage, immune protection…… • Functions depend on structures --- structure can help us to understand function Building blocks • Amino acid Hydrophobic: AVLIFPM Charged residues: DEKR Polar: STCNQHYW Special : G • Polypeptide chain Extend from its amino terminus to its carboxy terminus Special Amino Acids • Glycine Side chain is –H, very flexible • Proline has two covalent bonds with backbone • Cysteine can form disfulfide bridge to stabilize structure How to Describe Protein Structure • • • • Primary: amino acid sequence Secondary structure: alpha helix, beta sheet and loops Tertiary: Phi-Psi angle Quaternary: arrangement of several polypeptide chains Secondary Structure : Alpha Helix hydrogen bonds between n and n+i (i=3,4,5) Secondary Structure : Beta Sheet Antiparallel Beta Sheet Parallel Beta Sheet We can also have mix. Secondary Structure : Loop Regions Less conserved structure – Insertions and deletions are more often – Conformations are flexile Tertiary Structure Phi – N -C bond Psi – C-C’ bond Protein Domains • A polypeptide chain or a part of a polypeptide chain that can fold independently into a stable tertiary structure. • Built from different combinations of secondary structure elements and motifs Three Main Classes of Domain Structures • During the evolution, the structural core tends to be conserved • Alpha domains : The core is build up exclusively from alpha helices • Beta domains : The core comprises antiparallel beta sheets packed against each other • Alpha/Beta domains : a predominantly parallel Beta sheet surrounded by alpha helices Alpha-Domain Structures • It’s coiled coil structure • The most common one is four-helix bundle but we can have large and complex ones. Alpha-Domain Structures • Knobs in holes • Ridges in grooves Beta-Domain Structures • The cores built up by four or five to ten beta strands • Beta strands are predominantly antiparallel • The three most frequently groups: up-and-down barrels, Greek keys, and jelly roll barrels • Parallel Beta-helix is an exeception Beta-Domain Structures Up-and-down barrels Greek key Jelly roll Beta-Domain Structures • • • • The most frequent domain structures Barrel :beta-core surrounded by alpha-helix Open twist :parallel or mixed beta with alpha on both sides Horseshoe :Parrallel beta curve with alpha outside Determination of Protein Structures • X-ray crystallography The interaction of x-rays with electrons arranged in a crystal can produce electron-density map, which can be interpreted to an atomic model. Crystal is very hard to grow. • Nuclear magnetic resonance (NMR) Some atomic nuclei have a magnetic spin. Probed the molecule by radio frequency and get the distances between atoms. Only applicable to small molecules.
