Survey
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Peptide synthesis wikipedia , lookup
Western blot wikipedia , lookup
Biochemistry wikipedia , lookup
Ribosomally synthesized and post-translationally modified peptides wikipedia , lookup
Metalloprotein wikipedia , lookup
Nuclear magnetic resonance spectroscopy of proteins wikipedia , lookup
Two-hybrid screening wikipedia , lookup
Interactome wikipedia , lookup
4. Protein Structure Dr. Dale Hancock [email protected] How does a protein hold its 3D shape? • Proteins are only biologically active when they have the right shape or 3D conformation. • It is no use having the correct amino acid sequence if the shape is wrong! Forces that maintain 3-D protein conformation • • • • • Hydrogen bonding Electrostatic or ionic interactions Van der Waal’s interactions Hydrophobic interactions Disulphide bridges 1 Weak Forces that maintain 3-D protein conformation • Hydrogen bonding – (12 -30 kJ/mol) • Electrostatic or ionic interactions – (20 kJ/mol) • Van der Waal’s interactions – (0.4 - 4 kJ/mol) • Hydrophobic interactions – (<40 kJ/mol) Covalent Bond Energies What are the bond energies of covalent bonds? Energy kJ/mol Bond H-H 436 C-H 414 C-C 343 C-O 351 Hydrogen Bonding • This results from the small dipole (uneven electron distribution) that exists in certain side chains and in the peptide bond itself. • (12 -30 kJ/mol) 2 Hydrogen Bonding: the peptide bond • The amide N of the peptide bond is an H bond donor while the carbonyl O (from another peptide bond) can act as an acceptor. • This interaction is largely sequence independent. Hydrogen Bonding δ-ve O H3N+ CH O δ+ve C CH3 N CH C H CH CH3 O- CH3 Hydrogen Bonding O -O C O CH N R H C O HN CH CH NH R R C N R δ-ve H CH C N O 3 Hydrogen Bonding: side chains • The polar non-ionic side chains can also participate in H bonding. Side chains with –OH (Ser, Thr, Tyr), -SH (Cys) and amide N-H (Asn, Gln) all act as H bond donors. Side chains with –C=O (Asn, Gln) and -OH can also act as acceptors. • Side chain interactions are sequence dependent. H Bonding Tyrosine O HN CH C CH2 δ-ve O H δ+ve H Bonding Cysteine Tyrosine O HN CH C O HN CH C CH2 CH2 SH O δ-ve H δ+ve 4 H Bonding Tyrosine Cysteine O Glutamine O HN CH O C HN CH C CH2 HN CH2 CH SH CH2 C δ-ve O δ+ve NH2 δ-ve O C CH2 H δ+ve H Bonding Tyrosine Cysteine O Glutamine O HN CH O C HN CH C CH2 HN CH2 CH SH CH2 C δ-ve O δ+ve NH2 δ-ve O C CH2 H δ+ve Donors H Bonding Tyrosine Cysteine O Glutamine O HN CH O C HN CH C CH2 CH2 Acceptor SH HN CH CH2 C O δ+ve NH2 δ-ve C CH2 δ-ve O Acceptor H Acceptor δ+ve Donors 5 Electrostatic interactions (20 kJ/mol) O HN • Side chains with a positive charge (His, Arg or Lys) can interact with those side chains with a negative charge (Asp or Glu) if they are close enough. CH C CH2 CH2 CH2 NH +NH2 C NH2 OO C CH2 C CH NH O Electrostatic interactions • Side chains with like charges will repel each other. HN O O CH H2C C -O C C CH HN O CH2 O CH2 C O- Electrostatic interactions • The strength of the interaction is also dependent on the local environment. The presence of high concentrations of salts (high ionic strength), particularly on the protein surface tend to weaken or dampen down the strength of this force. 6 Hydrophobic interactions (<40 kJ/mol) • Non-polar side chains will tend to cluster together rather than mix with polar solvents. • This is an entropic effect: polar solvent molecules (usually water) have more options when the non-polar groups are clustered than when they are scattered throughout the polar solvent. Non-polar solutes organise the water into a cage surrounding them Hydrophobic interactions • In order to minimize the loss of entropy the non-polar groups cluster together and bury themselves in the core of a water soluble protein. • It is this interaction which drives soluble proteins to fold. 7 Van der Waal’s interactions (0.4 - 4 kJ/mol) • occurs when a charged or polar group comes in close proximity with a non polar group. The charged group will induce a small dipole on the non-polar group. • A transient dipole can be induced just from fluctuations in the electron distribution in neighbouring atoms. Van der Waal’s interactions • While these interactions are quite weak singly, they make a major contribution in a macromolecule like a protein where many of these interactions occur. Disulfide bonds • In a reducing environment such as the cytosol of the cell, cysteine residues would exist in a reduced form i.e. as –SH. O HN CH C CH2 SH SH CH2 C CH NH O 8 Disulfide bonds • In a reducing environment such as the cytosol of the cell, cysteine residues would exist in a reduced form i.e. as –SH. O HN CH C CH2 SH SH CH2 C CH NH O Disulfide bonds • In an oxidising environment such as the cell surface or exported proteins, cysteine residues would exist as disulfide bonds O HN CH C CH2 S S CH2 C CH NH O Disulfide bonds • In an oxidising environment such as the cell surface or exported proteins, cysteine residues would exist as disulfide bonds O HN CH C CH2 S S CH2 C CH NH O 9 What 3D structures can proteins assume? What 3D structures can proteins assume? psi phi O +H3N CH O O H N C CH R1 H N C CH R2 C O- R3 What 3D structures can proteins assume? α carbon α carbon O +H3N CH R1 C α carbon O H N CH C O H N R2 Peptide bond, restricted rotation CH C O- R3 Free rotation A tripeptide at pH 7. 10 What 3D structures can proteins assume? α carbon α carbon O +H3N CH C O H N R1 CH C O These atoms are all in one plane C O- α carbon H N R2 Peptide bond, restricted rotation CH R3 Free rotation A tripeptide at pH 7. The angles phi and psi are shown here Figure 6.2 The amide or peptide bond planes are joined by the tetrahedral bonds of the -carbon. The rotation parameters are and . The conformation shown corresponds to = 180°and = 180°. Note that positive values of and correspond to clockwise rotation as viewed from C . Starting from 0°, a rotation of 180°in the clockwise direction (+180°) is equivalent to a rotation of 180°in the counterclockwise direction (-180°). (Illustration: Irving Geis. Rights owned by Howard Hughes Medical Institute. Not to be reproduced without permission.) Hierarchy of Protein Folding • Primary Amino acid sequence • Secondary Local structures Alpha helix & Beta sheet • Tertiary Overall 3D arrangement of a polypeptide chain • Quaternary Organisation of subunits 11 Alpha Helix Side chain Backbone Ribbon format Properties of alpha helices • All alpha helices found in naturally occurring proteins are right handed due to L-amino acids. • Rigid structure with a single polypeptide chain • Side chains all face outwards • All peptide C=O H-bond to an amide N Beta Sheets parallel Anti parallel 12 The Beta-Pleated Sheet Composed of beta strands • Also first postulated by Pauling and Corey, 1951 • Strands may be parallel or antiparallel • Backbone almost fully extended • Side chains orientate above and below the plane of the sheet. Figure 6.10 A “pleated sheet” of paper with an antiparallel β-sheet drawn on it. (Irving Geis) Figure 6.11 The arrangement of hydrogen bonds in (a) parallel and (b) antiparallel βpleated sheets. 13 Tertiary Structure Tertiary Structure • The backbone links between elements of secondary structure are usually short and direct • Proteins fold to make the most stable structures (make H bonds and minimize solvent contact) Quaternary Structure 14