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Protein structure: details
Protein structure: details
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  1. 1.  Proteins are the most abundant organic molecules of the living system.  They constitute about 50% of the cellular dry weight.  They constitute the fundamental basis of structure and function of life.  In 1839, Dutch chemist G.J. Mulder was first to describe about proteins.  The term protein is derived from a Greek word proteios, meaning first place.  The proteins are nitrogenous macromolecules that are composed of many aminoacids.
  2. 2.  Amino acids are a group of organic compounds containing two functional groups – amino and carboxyl.  The amino group[ -NH2] is basic while the carboxyl group [- COOH] is acidic in nature.  There are about 300 aminocids occur in nature. Only 20 of them occur in proteins.
  3. 3.  Each amino acid has 4 different groups attatched to α- carbon ( which is C atom next to COOH).These 4 groups are : amino group, COOH group , Hydrogen atom and side chain(R).
  4. 4.  α- carboxyl group of one amino acid (with side chain R1) forms a covalent peptide bond with α- amino group of another amino acid (with side chain R2) by removal of a molecule of water.  The result is : Dipeptide.  The dipeptide can then form a second peptide bond with a third amino acid( with side chain R3) to give tripeptide.  Repetition of this process generates a polypeptide or protein of specific aminoacid sequence.  Has 40% double bond character, caused by resonance.
  5. 5.  Polypeptide backbone is the repeating sequence of the N-C- C-N-C-C… in the peptide bond.  The side chain or R group is not part of the backbone or the peptide bond.
  6. 6. • Configuration : geometric relationship between a given set of atoms. Ex: that distinguish L-amino acid from D-amino acid. • Conformation : spatial arrangement of atoms in a protein. • Thermodynamically the most stable conformations exist. • Stabilized largely by weak interactions.
  7. 7. • Stability - tendency to maintain a native conformation. • Native conformation stabilized by: Disulphide bonds Non covalent forces
  8. 8. Proteins have different levels of organisation  Primary Structure Secondary Structure Tertiary Structure Quaternary Structure
  9. 9. Primary structure - determined by covalent bonds Secondary, Tertiary, Quaternary structure - determined by weak forces
  10. 10. Primary Secondary Tertiary Quaternary Assembly Folding Packing Interaction
  11. 11.  The primary structure of protein refers to the sequence of amino acids present in the polypeptide chain.  Amino acids are covalently linked by peptide bonds or covalent bonds.  Each component amino acid in a polypeptide is called a "residue” or “moiety”.  By convention the primary structure of protein starts from the amino terminal (N) end and ends in the carboxyl terminal (C) end.
  12. 12.  It is a local, regularly occurring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms. Pauling & Corey studied the secondary structures and proposed 2 conformations o α helix o β sheets.
  13. 13.  Right handed spiral structure.  Side chain extend outwards.  Stabilized by H bonding that are arranged such that the peptide Carbonyl oxygen (nth residue) and amide hydrogen(n+4 th residue).  Amino acids per turn – 3.6  Pitch is 5.4 A°  Alpha helical segments, are found in many globular proteins like myoglobin,troponin C.  Length ~12 residues and ~3 helical turns.  phi = -60 degrees, psi = -45 degrees , falls within the fully allowed regions of the Ramachandran diagram.
  14. 14. α-helix Also called the 3.612 π-helix Very loosely coiled H- bonding pattern n + 5 Rarely found in nature. 310-helix Very tightly coiled H- bonding pattern n+3 rarely found in nature
  15. 15. o Formed when 2 or more polypeptides line up side by side. o Individual polypeptide – beta strand. o Each beta strand is fully extended. o They are stabilized by hydrogen bond between N- H and carbonyl groups of adjacent chains.
  16. 16. o Beta sheets come in two varieties Antiparallel beta sheet – neighboring hydrogen bonded polypeptide chains run in opposite direction. Parallel beta sheet - hydrogen bonded chains extend in the same direction. The connection between two antiparallel strands may be just a small loop but the link between tandem parallel strands must be a crossover connection that is out of the plane of the β sheet.
  17. 17. The two major sorts of connection between β strands:  a hairpin or same end connection  a crossover or opposite end connection.
  18. 18. It is the angle between two intersecting planes. It helps to maintain the protein structure.
  19. 19.  The backbone or main chain of a protein refers to the atoms that participate in peptide bonds, ignoring the side chains of the aminoacid residues.  The only reasonable free movements are rotations around the Cα – N bond(measured as Φ) and the Cα –C bond ( measured as Ψ).  These angles are both defined as 180° when the polypeptide chain is in full conformation.  The conformation of the backbone can therefore be described by the torsion angles ( also called dihedral angles or rotational angles).
  20. 20.  Ramachandran plot – to visualize the backbone of aminoacid residues.  The aminoacids with larger side chains will show less number of allowed region within the ramachandran plot.
  21. 21.  A Ramachandran plot is a way to visualize backbone dihedral angles ψ against φ of amino acid residues in protein structure.  A Ramachandran plot can be used to show which values, or conformations, of the ψ and φ angles are possible for an amino- acid residue in a protein and to show the empirical distribution of datapoints observed in a single structure.  The darkest areas correspond to the "core" regions representing the most favorable combinations of phi-psi values.
  22. 22. o Glycine and proline has no preffered Ramachandran Plot. o Glycine is formally nonpolar, its very small side chain makes no real contribution to hydrophobic interactions. o Proline has an aliphatic side chain with a distinctive cyclic structure. The secondary amino group of proline residues is held in a rigid conformation that reduces the structural flexibility of polypeptide residues containing proline.
  23. 23.  The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions.  Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape.  Protein folding occurs in the cytosol.
  24. 24. 2 regular folding patterns have been identified – formed between the bonds of the peptide backbone.  -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns).  -sheet – protein folds back on itself as in a ribbon – globular protein.
  25. 25.  Loops and Turns  In addition to α helices and β strands, a folded polypeptide chain contains two other types of secondary structure called loops and turns.  Loops and turns connect α helices and β strands.  The most common types cause a change in direction of the polypeptide chain allowing it to fold back on itself to create a more compact structure.  Loops have hydrophilic residues and they are found on the surface of the protein.  Loops that have only 4 or 5 amino acid residues are called turns when they have internal hydrogen bonds.  Reverse turns are a form of tight turn where the polypeptide chain makes a 180° change in direction.  Reverse turns are also called β turns because they usually connect adjacent β strands in a β sheet.
  26. 26.  Also known as beta bends or tight turns.  In a beta turn, a tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain. This hydrogen bond stabilizes the beta bend structure.  Proline and Glycine are frequently found in beta turns, proline because its cyclic structure is ideally suited for the beta turn, and glycine because, with the smallest side chain of all the amino acids, it is the most sterically flexible.  A beta turn is a means by which the protein can reverse the direction of its peptide chain.  Beta turns often promote the formation of antiparallel beta sheets.
  27. 27.  The tertiary structure defines the specific overall 3-D shape of the protein.  Tertiary structure is based on various types of interactions between the side-chains of the peptide chain
  28. 28. In globular proteins  Tertiary interactions are frequently stabilized by sequestration of hydrophobic amino acid residues in the protein core.  Consequent enrichment of charged or hydrophilic residues on the protein's water-exposed surface. In secreted proteins  disulfide bonds between cysteine residue helps to maintain the protein's tertiary structure
  29. 29. Interactions stabilizing tertiary structure : 1. Disulfide bonds 2. Hydrophobic interactions 3. Hydrogen bonds 4. Ionic interactions 5. Vander Waals force
  30. 30. Covalent bond between sulfur atoms on two cysteine amino acids.
  31. 31.  H bonds are weak which allows to be broken and reformed easily.  Allows structural change and produces ‘functional’molecules
  32. 32. • Ions on R groups form salt bridges through ionic bonds. • NH3 + and COO- areas of the protein attract and form ionic bonds.
  33. 33.  Close attraction of non-polar R groups through dispersion forces.  They are non attractive interactions, but results from the inability of water to form hydrogen bonds with certain side chains.  Very weak but collective interactions over large area stabilize structure.  Repel polar and charged molecules/particles.
  34. 34.  Globular proteins fold up into compact, spherical shapes.  Their functions include biosynthesis, transport and metabolism.  For example, myoglobin is a globular protein that stores oxygen in the muscles. - myoglobin is a single peptide chain that is mostly -helix - the O2 binding pocket is formed by a heme group and specific amino acid side-chains that are brought into position by the tertiary structure
  35. 35.  Fibrous proteins consist of long fibers and are mainly structural proteins.  For example, -keratins are fibrous proteins that make hair, fur, nails and skin. - hair is made of twined fibrils, which are braids of three -helices (similar to the triple helix structure of collagen) - the -helices are held together by disulfide bonds -keratins are fibrous proteins found in feathers and scales that are made up mostly of -pleated sheets
  36. 36. Association of secondary structures.  1. beta sheet super secondary structure  2.alpha helix super secondary structure  3. mixed super secondary structure
  37. 37.  A domain is a basic structural unit of a protein structure distinct from those that make up the conformations.  Part of protein that can fold into a stable structure independently.  Different domains can impart different functions to proteins.  Proteins can have one to many domains depending on protein size.
  38. 38.  Myoglobin is a small, monomeric protein which serves as an intracellular oxygen storage site.  It is found in abundance in the skeletal muscle of vertebrates, and is responsible for the characteristic red color of muscle tissue.  Myoglobin is closely related to hemoglobin, which consists of four myoglobin-like subunits that form a tetramer and are responsible for carrying oxygen in blood.
  39. 39.  The quaternary protein structure involves the clustering of several individual peptide or protein chains into a final specific shape.  A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains into a particular geometry.  Two kinds of quaternary structures: both are multi- subunit proteins. Homodimer : association between identical polypeptide chains. Heterodimer : interactions between subunits of very different structures.  The interactions within multi subunits are the same as that found in tertiary and secondary structures
  40. 40.  Quaternary structure adds stability by decreasing the surface/volume ratio of smaller subunit  Simplifies the construction of large complexes – viral capsids and proteosomes
  41. 41. Proteins cannot have inversion or mirror symmetry because bringing the protomeres into coincidence would require converting chiral L residues to D residues. Thus , proteins can have only rotational symmetry. CYCLIC SYMMETRY Protomeres are related by a single axis of rotation. Objects with 2, 3, or n fold rotational axis are said to have c2 c3 c4 symmetry respectively.
  42. 42.  2. Dihedral symmetry  Dihedral symmetry, a more complicated type of rotational symmetry, is generated when an n-fold rotation axis and a 2-fold rotation axis intersect at right angles.  D2 symmetry is, by far, the most common type of dihedral symmetry in proteins.
  43. 43. o Haemoglobin is a globular protein with 4 polypeptide chains bonded together. It therefore has a quartenary structure. o There are 4 haem groups each contain iron. o Each haem group can carry one molecule of oxygen. o The four polypeptide chain consists of two alpha and two beta chains.
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