圆二色极化光谱仪).ppt

Protein Structures Primary structure Amino acid sequence Edman degradation, MS, deduce from DNA Secondary structure Recurring structural pattern Circular dichroism (CD, 圓二色極化光譜儀) Tertiary structure 3D folding of a polypeptide chain X-ray crystallography, NMR Quaternary structure Subunits arrangement within a protein The 3-D structure of proteins Protein stability Unfolded (denatured) High degree of conformational entropy H-bond of polypeptide with solvent (H2O) Folded (native) Lowest free energy Stabilized by disulfide bond (covalent) and weak (non-covalent) interactions: Weak interactions Van der Waals interaction H-bond Hydrophobic Ionic Peptide bond OC-NH is shorter Coplanar peptide group Trans configuration (O vs. H) Electrons resonance (partial sharing) between the carbonyl O and the amide N. (electric dipole) OC-NH can not rotate Limited rotation for Ca-C (?, psi) and N-Ca (?, phi) Protein secondary structure Local conformation, regular backbone pattern Restricted ? and ? in 2o structures Determined by primary structure a-helix (e.g. a-keratin in hair) b-sheet (e.g. silk fibroin – layers of b-sheets) b-turn a-helix A right-handed a-helix: 3.6 a.a. per turn 5.4 ? (1 ? = 0.1 nm) per turn R groups extended outward perpendicular to the helical axis H-bonding between adjacent turns H-bond between the -CO of residue (i) and the -NH of residue (i+3). 2 H-bonds per residue 3 or 4 H-bonds per turn Provide stability a-helix constraints Electrostatic interactions of Ri and Ri+1 Size of the R group Interactions between Ri and Ri+3 or Ri+4 Pro and Gly End residues (electric dipole) Electric dipole of an a-helix Peptide bond dipole Helix dipole End residues and helix stability b-conformation Zigzag, extended protein chain, with the R groups alternating above and below the backbone. Side by side b-conformation ? b-sheet H-bonds between adjacent peptide chain (backbone). Parallel or antiparallel orientations Silk fibroin – layers of b-sheets b-turn A 180o turn involving