Protein Structure Lecture Slides PDF

Dr Stuart Knight Foundations of Medical Science Cell Biology and Signalling block Protein Structure Biochemistry Teaching Objectives Recognise the structures of the 20 common structural amino acids Identify the functional importance of amino ac...

Dr Stuart Knight Foundations of Medical Science Cell Biology and Signalling block Protein Structure Biochemistry Teaching Objectives Recognise the structures of the 20 common structural amino acids Identify the functional importance of amino acid side chains Describe the nature of the peptide bond between amino acids Show how the nitrogen and oxygen atoms of the peptide bond may form hydrogen bonds with other peptide units Describe the main structural features of an α-helix and role in typical globular, membrane-associated and fibrous proteins Describe the main structural features of the β-pleated sheet structure Describe the variety of side-chain interactions which are responsible for maintaining the tertiary structures of proteins, both non-covalent (hydrogen bonds, ionic, van der Waals and hydrophobic and covalent (disulphide bonds) Appreciate the importance of conformation in determining the biological functions of proteins and understand that conformation is uniquely determined by the primary sequence Appreciate the process of protein folding and understand why most folded proteins are only marginally stable, and readily denatured by heat, pH, detergents etc Understand that defects in amino acid metabolism and mis-folding may lead to disease  Some biological functions of proteins function example Structural collagen, keratin Movement actin, myosin Enzymes trypsin, DNA polymerase Transport haemoglobin, transferrin Membrane transport Na+/K+ pump Hormones insulin Receptors acetyl choline receptor Defence antibodies, clotting factors Gene regulation histones Chromosome separation tubulin 3 Structure of lysozyme  Polypeptides and direction First aa has NH3⁺ group – N-terminal end Last aa has COO⁻ group – C-terminal end 5  Post translational covalent modifications Disulphide (S-S) bridges between two cys – Joining subunits together e.g. insulin Glycosylation – O-linked -OH of thr and ser – N-linked -NH2 of asn 6  PROTEINS: structure 3D structure has 4 levels: - Primary – sequence of aa in peptide chain - Secondary – folding/coiling of peptide chain (usually into a α-helix or β-pleated sheet) - Tertiary – peptide chain folds upon itself - Quaternary – folded peptide chains join together 7 α-helix  α-helix in detail formed by H-bonds in same polypeptide chain (backbone not side chains) H-bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide regular right-handed helix 3.6 residues/turn stabilised by H-bonds R groups on the outside rigid cylinder shape, acts as ‘architectural’ support for protein 9 β-sheet  β-pleated sheets Linear peptide chains H-bonding between peptide chains holds strands together in a β-sheet Side chains in each strand alternately lie above and below the plane of the sheet 11 Types of β-sheet structures (A) = Antiparallel β sheet β–Hairpin bend: - widespread in globular proteins (B) = Parallel β sheet (arrows point to C terminus) 12  Collagen triple helix Three chains Found in collagen H-bonds between chains 3 residues/turn Left-handed helix - Gly - X - Y - Gly - X - Y - X= mainly proline Y= mainly hydroxy-proline Different proteins combine different amounts of a helix and b sheets Haemoglobin has 60% of its structure as α-helix 14  Proteins with high % of β sheet Fibrillar proteins – silk fibres (fibroin) properties of high tensile strength, but no elasticity 15  Tertiary structure How the whole polypeptide (subunit) is folded in 3D, it will consist of a number of different supersecondary structures (domains) Quaternary structure How the whole functional protein is formed in 3D, it may consists of a number of subunits e.g haemoglobin α2β2  Forces that stabilise the protein structure Covalent – Disulphide bridges (not all proteins have them) Non–covalent – Hydrogen bonds – Electrostatic interactions – Van der Waals forces – Hydrophobic effect  Hydrogen bonds 2 electro –ve atoms compete for same H atom H-Bond Donors (D): – O e.g. O-H (side chain of Ser, Thr, Tyr) – N e.g. N-H (peptide bond, Trp, His, Arg): NH3+ (Lys, Arg) H-Bond Acceptors (A): – O e.g. C=O carbonyl (peptide bond) – 3x covalent bonded N: =N- e.g. Trp, His) 18  The Hydrogen bond δ– δ+ δ– H δ– δ+ δ– C O H N O H O H 2.8 Å H/R (0.28 nm) DH  12 kJ mol-1  Electrostatic interactions Between charged side chains At physiological pH: Asp and Glu carboxyl groups are ionised – COO- Lys and Arg amino groups are ionised – NH3+  Van der Waals forces is the sum of the attractive or repulsive forces between molecules Excluding those due to – covalent bonds – hydrogen bonds – electrostatic interaction Dependent on dipole affect caused by the unequal distribution of electrons – Partial negative δ- and partial δ+ positive charge across a covalent bond  Distance for Van der Waals Forces Energy H H e.g. C H H C d H H 0 d = Van der Waals 2 radius of atom d + + d+ d- d+ d-  Hydrophobic effects Hydrophobic regions of a protein fold in such a way to minimise the contact with aqueous environment. Hydrophobic regions are unable to form hydrogen bonds  Protein structure and folding The amount of stablization energy in a protein is quite small Proteins are very sensitive to denaturation by – pH – Temperature – Ionic strength For any given protein there are thousands of possible structures only one of which is functional Amino acid sequence encodes the final structure but also the pathway that leads to that structure Case based discussion The relevance of proteins structure in human disease (details to be provided at the lecture and available via KEATS after the lecture) Make notes of the key observations as the case develops Dr Stuart Knight Summary [email protected] Key details of alpha helix and beta-pleated sheet 020 7848 6068 Tertiary and quaternary structure Henriette-Raphael House 1.17 Folding essential for function Why are they stable? Misfolding can cause disease