LEVELS OF PROTEIN STRUCTURE, DOMAINS, MOTIFS, AND FOLDS IN PROTEIN STRUCTURE

LEVELS OF PROTEIN STRUCTURE, DOMAINS, MOTIFS, AND FOLDS IN PROTEIN STRUCTURE

1. MPL 203T P resented by, Rojamani N M.Pharm II st Sem PRINCIPLES OF DRUG DISCOVERY Department of Pharmacology MSRUAS LEVELS OF PROTEIN STRUCTURE, DOMAINS, MOTIFS, AND FOLDS IN PROTEIN STRUCTURE

2. CONTENTS Introduction levels of protein structure 1. Primary levels 2. Secondary levels 3. Tertiary levels 4. Quaternary levels Folds Motifs Domains in protein structure

3. Introduction Protein an important class of biological macromolecules which are the polymers of amino acids • Biochemists have distinguished several levels of structural organization of proteins They are: – Primary structure Secondary structure Tertiary structure Quaternary structure

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6. Amino acid letter code

7. Protein Structure is Hierarchical Primary ( sequence ) Secondary ( local folding ) Tertiary ( long-range folding ) Quaternary ( multimeric organization )

8. Primary Structure of Proteins

9. Importance of Protein structure To predict secondary & tertiary structures from sequence homologies with related proteins S tructure prediction Many genetic diseases result from abnormal amino acid sequences To understand the molecular mechanism of action of proteins Methods of amino acid sequence determination:- End group analysis – Edman degradation Gene sequencing method

10. Protein fold Compact, globular folding arrangement of the polypeptide chain Chain folds to optimize packing of the hydrophobic residues in the interior core of the protein Rossman Fold

11. Folds in Proteins

12. Common folds

13. TIM Barrel The eight-stranded a /b barrel (TIM barrel) The most common tertiary fold observed in high-resolution protein crystal structures 10% of all known enzymes have this domain

14. Secondary structures The primary structure of a protein — its amino acid sequence — drives the folding and intramolecular bonding of the linear amino acid chain, which ultimately determines the protein's unique three-dimensional shape Hydrogen bonding between amino groups and carboxyl groups in neighboring regions of the protein chain sometimes causes certain patterns of folding to occur

15. Linus Pauling proposed some essential features of peptide units and polypeptide backbone They are: – The amide group is rigid and planar as a result of resonance. So rotation about the C-N bond is not feasible Rotation can take place only about N- Cα and Cα – C bonds Trans-configuration is more stable than cis- for R groups at Cα From these conclusions, Pauling postulated 2 ordered structures : α helix and β sheet These stable folding patterns make up the secondary structure of a protein

16. Alpha helix Spiral structure Tightly packed, coiled polypeptide backbone core Side chain extends outwards Stabilized by H bonding b/w carbonyl oxygen and amide hydrogen Amino acids per turn – 3.6 Pitch is 5.4 A Alpha helical segments are found in many globular proteins like myoglobin, troponin- C etc

17.  -60º  -40º First -NH and last C=O groups at the ends of helices do not participate in H-bond H- bond between C=O of i th residue & -NH of (i+4) th residue Ends of helices are polar, and almost always at surfaces of proteins Always right-handed

18. Helical wheel Residues i , i+4, and i+7 occur on one face of helices and hence show a definite pattern of hydrophobicity/ hydrophilicity

19. Beta pleated sheet • Formed when 2 or more polypeptides line up side by side • Individual polypeptide - β strand • Each β strand is fully extended •They are stabilized by H bond b/w N-H and carbonyl groups of adjacent chains

20. Secondary structures

21. Rotational constraints emerge from interactions with bulky groups ( i.e side chains) Phi & Psi angles define the secondary structure adopted by a protein The dihedral angles at the C atom of every residue provide polypeptides requisite conformational diversity, whereby the polypeptide chain can fold into a globular shape

22. A graphical representation in which the dihedral angle of rotation about the alpha-carbon to carbonyl-carbon bond in polypeptides is plotted against the dihedral angle of rotation about the alpha-carbon to nitrogen bond

23. Tertiary structures

24. Tertiary structure examples: All- a Alamethicin t he lone helix Rop helix-turn-helix

25. Tertiary structure examples: All- b b sandwich b barrel

26. Tertiary structure examples: a/b triose phosphate isomerase a/b barrel placental ribonuclease inhibitor a/b horseshoe

27. 24 amino acid peptides with a hydrophobic surface Assembles into 4 helix bundle through hydrophobic regions Maintains solubility of membrane proteins Four helix bundle

28. Quaternary structures

29. Quaternary structure proteins The quaternary structure of a protein is the association of several protein chains or subunits into a closely packed arrangement Each of the subunits has its own Primary , Secondary, and Tertiary structure The subunits are held together by hydrogen bonds and van der Waals forces between nonpolar side chains The subunits in a quaternary structure must be specifically arranged for the entire protein to function properly Any alteration in the structure of the subunits or how they are associated causes marked changes in biological activity

30. Quaternary structure of multidomain proteins

31. Leucine Zipper Helix Turn Helix Motif

32. Motifs (super secondary structures) A motif is a recognizable folding pattern involving two or more elements of secondary structure and the connection(s) between them Or “The connectivity between secondary structure elements and the type of secondary structure elements involved define the level of structural organization called structural motifs” A motif is is simply a folding pattern Motifs do not allow us to predict the biological functions: they are found in proteins and enzymes with dissimilar functions In proteins, a structural motif describes the connectivity between secondary structural elements

33. A motif can be very simple, such as two elements of secondary structure folded against each other, and represent only a small part of a protein An example is a β-α-β loop A motif can also be a very complex structure involving scores of protein segments folded together, such as the β barrel

34. Motif mediated protein-protein interactions as drug targets

35. Common motifs Supersecondary structure: Crossovers in b - a - b -motifs

36. EF Hand Consists of two perpendicular 10 to 12 residue alpha helices with a 12-residue loop region between Form a single calcium-binding site (helix-loop-helix) Calcium ions interact with residues contained within the loop region Each of the 12 residues in the loop region is important for calcium coordination In most EF-hand proteins the residue at position 12 is a glutamate. The glutamate contributes both its side-chain oxygens for calcium coordination Found in Calcium-binding proteins such as Calmodulin Calmodulin, recoverin: Regulatory proteins Calbindin, parvalbumin: Structural proteins EF Fold

37. Helix Turn Helix Motif Consists of two a helices and a short extended amino acid chain between them  Carboxyl-terminal helix fits into the major groove of DNA This motif is found in DNA-binding proteins, including l repressor, tryptophan repressor, catabolite activator protein (CAP)

38. Leucine Zipper

39. A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn 2+ ) in order to stabilize the fold Zinc Finger Motif

40. Transmembrane motif Beta-barrel Anti-parallel sheets rolled into cylinder Outer membrane of Gram-negative bacteria Helix bundles Long stretches of a polar amino acids Fold into transmembrane alpha-helices “Positive-inside rule ”

41. Domains A protein domain is a conserved part of a given protein sequence and (tertiary) structure that can evolve , function, and exist independently of the rest of the protein chain Each domain forms a compact three-dimensional structure and often can be independently stable and folded A domain usually contains between 40 and 350 amino acids, and it is the modular unit from which many larger proteins are constructed The different domains of a protein are often associated with different functions. E.g the Src protein kinase, which functions in signaling pathways inside vertebrate cells This protein has four domains: the SH2 and SH3 domains have regulatory roles, while the two remaining domains are responsible for the kinase catalytic activity The central core of a domain can be constructed from α helices, from β sheets, or from various combinations of these two fundamental folding elements. Each different combination is known as a protein fold

42. Domains are independently folding structural units. Domain swapping: Parts of a peptide chain can reach into neighboring structural elements: helices/strands in other domains or whole domains in other subunits Domain-swapped diphtheria toxin:

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