Structure of Proteins PDF

Structure of Proteins Department of Biochemistry Faculty of Pharmacy, Suez Canal University Protein Structure Proteins are composed of amino acids attached by peptide bonds =amide bond The string of amino acids folds and bends in certain ways Four hierarchies of pro...

Structure of Proteins Department of Biochemistry Faculty of Pharmacy, Suez Canal University Protein Structure Proteins are composed of amino acids attached by peptide bonds =amide bond The string of amino acids folds and bends in certain ways Four hierarchies of protein structure: primary, secondary, tertiary and quaternary  Primary Structure of Proteins Sequence of amino acids in protein: Asp – Glu – Cys – His – Lys – Met – Cys – Pro Many genetic diseases result from proteins with abnormal amino acid sequences Amino acids are covalently joined by peptide bonds Primary Structure of Proteins Peptide Bond Amide link between α- carboxyl group of one amino acid and α-amino group of another Is not broken by high heat or high urea concentrations Bond hydrolyzed non- enzymatically by prolonged exposure to strong acid or base or high temperature  Primary Structure of Proteins Naming the peptide A peptide is two or more amino acids attached via a peptide bond, or amide linkage The free amino end is the N-terminal The free carboxyl end is the C-terminal The N-terminal is written to the left and the C- terminal to the right Amino acid sequences are read from the N- to the C-terminal Each amino acid component of a peptide chain is called a residue (lost a water during formation of peptide bond)  Primary Structure of Proteins Characteristics of the peptide bond Partial double bond character: shorter than a single bond Rigid and planar: no free rotation around carbonyl carbon and amide nitrogen Trans-configuration: due to steric interference of the R-groups of amino acids  Primary Structure of Proteins Polarity of the peptide bond -C = O and –NH groups of amide linkage are uncharged and neither accept or release protons -C = O and –NH groups of amide linkage are polar and can be involved in hydrogen bonds The only charged groups on a polypeptide are: – N-terminal α- amino group – C- terminal α- carboxyl group – ionized groups in side chains of amino acids Secondary Structure of Proteins Polypeptide is a long chain of amino acids Polypeptide forms regular arrangements of amino acids located near each other Three examples of secondary structure: – α- helix – β-sheet – β-bend Secondary Structure of Proteins The α- helix Spiral structure Coiled polypeptide backbone Amino acid side chains extend outward from the central axis to avoid steric interference in the center Secondary Structure of Proteins The α- helix The α- helix is stabilized by hydrogen bonding between peptide-bond carbonyl oxygens and amide hydrogens Hydrogen bonds are parallel to the spiral Hydrogen bond extends from carbonyl oxygen of one peptide bond to the –NH group of the peptide bond 4 residues ahead All peptide bonds except the first and last are linked through hydrogen bonds between the c=o in the 1st amino acid and N-H in the 5th amino acid amino acids  Secondary Structure of Proteins The α- helix Each turn of the α-helix contains 3.6 amino acids Amino acid residues spaced 3 – 4 residues apart in the primary sequence are close together when folded in the α-helix Amino acids disrupting the α-helix: – Proline: secondary amino group not geometrically compatible with spiral of helix; it inserts a kink – Charged amino acids form ionic interactions or repel each other – Amino acids with bulky side chains (Trp) or those with branched side chains (Val, Ile) interfere with helical structure if present in large numbers Secondary Structure of Proteins The β-sheet All peptide bond components are involved in hydrogen bonding Surface is pleated Two or more polypeptide chains in almost fully extended form Hydrogen bonds form between carbonyl oxygen of and amide hydrogen of two adjacent polypeptides Secondary Structure of Proteins The β-sheet Parallel and antiparallel sheets: Antiparallel sheets: polypeptide chains arranged with N- and C-termini alternating Parallel sheets: polypeptide chains arranged with N-termini adjacent  Secondary Structure of Proteins The β-sheet A β-sheet can be formed from 2 or more different polypeptides, or from the same polypeptide: – Interchain bonds: hydrogen bonds formed between polypeptide backbonds of separate polypeptide chains – Intrachain bonds: hydrogen bonds formed between peptide bonds of the same polypeptide chain (common in parallel β-sheets)  Secondary Structure of Proteins Differences between α-helix and β-sheet β-sheets are composed or two or more polypeptides or polypeptide segments which are fully extended Hydrogen bonds are perpendicular to the polypeptide backbone  Secondary Structure of Proteins β-bends Also called reverse turns, β-turns Reverse direction of a polypeptide chain Allow polypeptide chains to form compact and globular shapes Found on surface of proteins, include charged residues Usually connect successive strands of parallel β-sheets  Secondary Structure of Proteins β-bends A β-bend consists of 4 amino acids: – Proline usually found (causes kink in polypeptide chain) – Glycine frequently found β-bends are stabilized by hydrogen and ionic bonds  Nonrepetitive Secondary Structures α-helices and β-sheets are repetitive structures Roughly half of proteins are organized into repetitive structures P-bend The remaining polypeptide chain has a loop or coil conformation called a “nonrepetitive secondary structure” Coils and loops are not random, but have less repetitive structure than helices and sheets  Supersecondary Structures Formed from the combination of different secondary structures e.g. α-helices, β-sheets and nonrepetitive sequences. beta bend Different secondary structures are connected by β-bends Also formed by packing side chains from adjacent secondary structures, α- helices and β-sheets adjacent in the amino acid sequence are usually adjacent in the final, folded protein Supersecondary Structures  3D Tertiary Structure of Proteins Refers to: – Folding of domains – Final arrangement of domains Globular proteins are compact with high density core Hydrophobic sidechains are buried in the interior of protein Hydrophilic groups are on the surface of the molecule  Tertiary Protein Structure Domains =100 amino acid Functional units of polypeptides Polypeptide chains greater than 200 amino acids in length consist of two or more domains A domain consists of different supersecondary structural elements (motifs) Folding of one domain is independent of other domains on the same polypeptide Each domain behaves as a globular protein structurally independent from other domains on the polypeptide chain  Tertiary Protein Structure Interactions stabilizing tertiary structure Interactions between amino acid side chains guide folding of polypeptides to form compact structures. Four types of interactions stabilize tertiary structure of globular proteins: covalent & ionic & physical 1. Disulfide bonds covalent 2. Hydrophobic interactions 3. Hydrogen bonds physical 4. Ionic interactions Tertiary Protein Structure Interactions stabilizing tertiary structure 1. Disulfide bonds: produced from oxidation of –SH group of two cysteine residues forming cystine Strong covelent bond, contributes to stability of 3-D shape of the protein Tertiary Protein Structure Interactions stabilizing tertiary structure 2. Hydrophobic interactions: Formed between amino acids with non-polar side chains Non-polar amino acids are located on the interior of the protein or polypeptide molecule (Amino acids with polar side chains are located on the surface of the protein, in contact with polar solvent) Tertiary Protein Structure Interactions stabilizing tertiary structure 3. Hydrogen bonds: Amino acid side chains with oxygen- or nitrogen- bound hydrogen form hydrogen bonds with electron-rich atoms e.g. NOF oxygen of carboxyl groups or carbonyl groups of peptide bonds Tertiary Protein Structure Interactions stabilizing tertiary structure 4. Ionic interactions: Negatively charged groups interact with positively charged groups -COO- of Asp or Glu can interact with the amino group (-NH3+) in the side chain of Lys  Tertiary Protein Structure Protein folding Interactions between side chains of amino acids determine how a polypeptide chain folds into a three-dimensional shape Proteins fold to attain a low-energy state: – Positive and negative side chains attract each other, similar charges are kept out of contact – Hydrophobic side chains aggregate on the inside of the protein, hydrophilic side chains are on the outside – Hydrogen bonds and disulfide bonds also affect folding Proteins begin to fold as the polypeptide chain is being synthesized in order to prevent misfolding  Tertiary Structure of Proteins Role of chaperones in protein folding Also called heat-shock proteins Chaperones are different types of proteins required for the correct folding of proteins Chaperones interact with the polypeptide at different stages during the folding process  Tertiary Structure of Proteins Role of chaperones in protein folding Functions of chaperones: 1. Keep protein unfolded until synthesis is finished 2. Act as catalysts, increase the rate of protein folding 3. Protect unfolded portions of protein as they fold (so that unfolded regions do not misfold) Quaternary Structure of Proteins Monomeric protein: consists of a single polypeptide folded into secondary and tertiary structure Quaternary structure: proteins with 2 or more monomeric protein polypeptides, called polypeptide subunits subunit  Quaternary Structure of Proteins Each polypeptide is called a subunit Arrangement of the subunits is called quaternary structure (N.B. proteins composed of a single polypeptide do not have quaternary structure) Subunits are held together by non-covalent interactions: hydrogen bonds, ionic bonds and hydrophobic interactions di sulfide bond Subunits may function cooperatively, or may be unrelated  Quaternary Structure of Proteins Isoforms: – Proteins that have the same function but are encoded by different genes and have different primary structure  Protein Denaturation Unfolding of protein secondary and tertiary structure without hydrolysis of peptide bonds Denaturing agents: – Heat – Organic solvents prolonged exposure to – Mechanical mixing acid bases heat – Detergents – Acids and bases – Heavy metals (lead, mercury) Denatured proteins usually do not return to their folded state and are permanently disordered Denatured proteins are insoluble and precipitate from solution  Protein Misfolding degradation Improperly folded proteins are usually degraded in the cell If not degraded, misfolded proteins accumulate and deposited in different body tissues causing disease Amyloidoses: a group of diseases occurring due to aggregation of amyloids Amyloids are aggregates of long fibrillar proteins (composed of β-sheets) that form due to misfolding Accumulation of amyloids is implicated in Alzheimer disease