Transcript Slide 1
LEARNING OBJECTIVES •STRUCTURE OF PROTEINS •HOW ARE PROTEINS DENATURED? •CLINICAL APPLICATIONS Different proteins can be formed from 20 a.a in diff sequences determined by the genetic code Native conformation of a protein( unique 3D structure) is determined by the sequence Binding sites are formed after folding, dictating function of the protein Clinical consequences Changes in protein structure Conformational changes in proteins that affect solubility and degradability E.g. Amyloidosis- IgG chains form an insoluble protein aggregate called amyloid in organs and tissues Prion diseases result from misfolding and aggregation of normal cellular protein SCA, point mutation in Hb affects the 4° structure and its solubility, not ability to bind oxygen Roles that proteins play: Catalytic Structural Regulatory Cell differentiation Cell communication Muscle contraction Transport Storage Proteins rock! Description of Protein Structure? Levels of Structure Primary structure - linear sequence of amino acids - peptide bonds Secondary structure - local folding( Regular arrangements of amino acids) - H-bonding within the backbone Tertiary structure - over all folding and 3D conformation - mainly R group interactions within one chain Quaternary structure - multi-chain interactions - mainly R group interactions among polypeptide chains Peptide Bond Formation a. Lack of rotation around the bond: partial double bond rigid and planar bond between -C and -amino or –CO group is Non rotatable b. Trans configuration: (steric interference in cis position) c. Uncharged but polar: like all –CONH2 links, peptide bonds do not protonate between pH 2-12 only side chains and N- and C- terminals can ionize peptide bond is polar (charged) and can be involved in H-bonding. Proteins Polypeptides and Proteins Proteins are polyamides. When formed by amino acids, each amide group is called a peptide bond. Peptides are formed by condensation of the -COOH group of one amino acid and the NH group of another amino acid. The acid forming the peptide bond is named first. Example: if a dipeptide is formed from alanine and glycine so that the COOH group of glycine reacts with the NH group of alanine, then the dipeptide is called glycylalanine. Not broken when proteins are denatured Prolonged exposure to acid or base at high temps is necessary to break bonds. 1. Naming the peptide a. order of amino acids in a peptide Left (N-terminal a.a.) is written first, C-terminal next b. Naming of polypeptides component a.a. in peptides called moieties or residues. Except C-terminal, all moieties called –yl instead of –ine –ate, or -ic E.g. valylglycylleucine Characteristics of the peptide bond 3. Trans configuration • minimizes steric hindrance Characteristics of the peptide bond - summary • partial double bond character • rigid and planar • trans configuration • uncharged but polar trans config amide plane O H C H3N R1 C R2 N H O C C H O This results in the formation of a series of planes as indicated by the dotted lines In this structure there is no rotation about the bond: Primary structure gives the kind, number and sequence of amino acids in the linear polypeptide chain. basis for abnormality in genetic diseases starts with the N-terminus and ends with the C-terminus amino acids ends are joined together by peptide bonds in a polypeptide chain Determining a protein’s primary structure by DNA sequencing Secondary structures locally folded structure/regular arrangements in regions of the polypeptide mainly formed through hydrogen bonds between backbone atoms Types: stable secondary structures (interior and surface) alpha helices beta-sheets unstable secondary structures (surface) bends, random coils, loops, turns Formed between the –CO group of one peptide bond and the –NH group of an adjacent peptide bond Helps to stabilize secondary structures -if the H-bonds form between peptide bonds in the same chain helical structure (α-Helix) or turns (β-Turns) develops -if the H-bonds form between peptide bonds in different chain , extended structures are formed e.g.: βPleated sheets -helix right -handed helix H-bonding almost parallel to main axis of helix (weak bonds) Each –CO is Hydrogen bonded to –NH of a peptide bond that is 4 residue away from it allows extensibility PRO and GLY disrupt alpha Helix Left-hand helix Right-hand helix Intrachain Hydrogen Bonding is important in maintaining secondary protein structure. Here (in the α helix) the carbonyl oxygen from one amino acid is H-bonded to an alpha nitrogen of the 4th distant amino acid in the polymer. Hydrogen bond b Sheet • “pleated” • all peptide bond components involved in H-bonding • strands visualized as broad arrows N terminal C terminal • may be parallel or antiparallel • Have a right handed curl , twisted sheets form core of globular proteins b Sheet b-bends Reverse the direction of a polypeptide chain, helping it form a compact, globular shape Often found on the surface of protein molecules Generally composed of four amino acids with Proline and glycine as common Components Stabilized by Hydrogen and Ionic Bonds SUPER Secondary structures combinations of secondary structures also called motifs Tertiary structure describes the packing of alpha-helices, beta-sheets and random coils with respect to each other on the level of one whole polypeptide chain due to R group or side chain interactions or between R groups at a distance and backbone associated with domains Tertiary structure Side chain interactions (R groups) which stabilize the tertiary structure H-bonds – O or N bound H atoms of Ser, Thr with COO- or carbonyl grp.↑ solubility Disulfide bonds – Cysteine →Cystine e.g. in Igs secreted by cells Ionic Bonds – btw acidic n basic side chains (salt bridges) Hydrophobic interactions – non-polar side chains on the interior and vice-versa Domains Fundamental functional and 3-D structural units of polypeptides >200 amino acids 2 or more domains folding within domain independent of folding within other domains each domain has characteristics of small, compact, globular protein Quaternary structure only exists if there is more than one polypeptide chain present in a complex protein describes the spatial organization of the chains associated with subunits assembled usually via electrostatic, H-bonding or hydrophobic interactions(Non- Covalent interactions) 1) In the cell folding is achieved by: Protein Disulfide Isomerase Catalyzes the formation of proper disulfide bond. 2) Chaperones Chaperones (“heat shock” proteins) Specialized group of proteins •assists protein folding •Catalyzes the proper folding of protein by inhibiting improper folding and interactions with other peptides prevent protein aggregation and misfolding by limiting the number of unproductive folding pathways Why do proteins fold? •To achieve a stable 3D Conformation •Flexible •Able to function in the correct site of the cell •Capable of being degraded by cellular enzymes Protein Denaturation •Unfolding and disorganization of the protein’s secondary, tertiary and quaternary structures. •Peptide bonds are not hydrolyzed. (Primary structure) •Denaturing agents: heat, organic solvents, mechanical mixing, strong acids or bases, detergents and heavy metal ions lead and mercury •Ideally, protein denaturation is reversible. Folded Protein Unfolded Protein Protein Misfolding Diseases When we boil or fry an egg, the proteins in the white unfold. But when the egg cools, the proteins do not return to their original shapes. Instead, they form a solid, insoluble (but tasty) mass. This is misfolding ! When Proteins Go Unwell • Mutation in the DNA so that the amino acid sequence differs from normal. • Lack of an enzyme or chaperone needed to fold a protein. • Correctly folded protein becoming misfolded by accumulated damage due to oxidation or other chemical reaction. • Interaction with other misfolded proteins. Amyloidosis • a group of protein misfolding diseases characterized by the accumulation of insoluble fibrillar protein that leads to cell death and tissue degeneration •The dominant component in amyloid plaque that accumulates in Alzheimer's is Aβ •The amyloid precursor protein is a single trans membrane protein. In Alzheimer's there will be accumulation of neurofibrillary tangles in the brain, which contains a key an abnormal form of the tau protein, which in its healthy form helps in assemble of microtubular structure. Amyloidoses -antitrypsin Ig light chain Apolipoprotein Cystatin C Procalcitonin Amylin Bri-L keratoepithelin b-2-microglobulin Ab peptide -synuclein Huntingtin emphysema myeloma hereditary aortic disorder cerebral hemorrhage thyroid medullary cancer diabetes type 2 familial British dementia dystrophy of the cornea dialysis related amyloidosis Alzheimer Disease Parkinsonism Huntington Disease Mad cow and other mad species are infectious diseases transmitted by prions A proteinaceous infectious particle, or prion is an infectious agent composed primarily of protein known as TSE transmissible spongiform encephalopathies - creutzfeldt-jakob disease CJD, Scrapie and BSE bovine spongiform encephalopathy transmitted by inoculation, cannibalism, genetic inheritance PrP Non-infectious PrPSc Infectious FIBRILS Prions propagate by transmitting a mis-folded protein state: so as with viruses the protein cannot replicate by itself. Instead, when a prion enters a healthy organism the prion form of a protein induces pre-existing normal forms of the protein to convert into the rogue form. Since the new prions can then go on to convert more proteins themselves, this triggers a chain reaction that produces large amounts of the prion form. All known prions induce the formation of an amyloid fold, in which the protein polymerizes into an aggregate consisting of tightly packed beta sheets. Amyloid aggregates are fibrils, growing at their ends, and replicating when breakage causes two growing ends to become four growing ends.