Protein structure

1. Protein structure

2. BIOMEDICAL IMPORTANCE • Protein function • Catalyze metabolic reactions • Power cellular motion • Provide structural integrity • Defect in protein maturation • Genetic or nutritional • Creutzfeldt- Jakobdisease, scrapie, Alzheimer’s disease, and bovine spongiform encephalopathy (mad cow disease). • Scurvy

3. BIOMEDICAL IMPORTANCE • Defect in primary structure • Sickle cell • the structure of a protein provides insight into how it fulfills its functions.

4. Configuration • the geometric relationship between a given set of atoms • configurational alternatives requires breaking covalent bonds • Conformation • the spatial relationship of every atom in a molecule.

5. Classification of proteins • Solubility, shape, or the presence of nonprotein groups. • Solubility • Soluble • At physiologic pH and ionic strength • Integral membrane proteins • Shape • Globular proteins • Most enzymes • Fibrous proteins • Many structural proteins

6. Classification of proteins • Nonprotein groups • Lipoproteins • Glycoproteins • Hemoproteins • Myoglobin, hemoglobin, cytochromes • Metalloproteins • Classification based on homology • Sequence & structure.

8. THE FOUR ORDERS OFPROTEIN STRUCTURE • Primary structure • the sequence of the amino acids in a polypeptide chain • Secondary structure • The folding of short (3- to 30-residue),contiguous segments of polypeptide into geometrically ordered units

9. Tertiary structure • the three-dimensional assembly of secondary structural units • Quaternary structure • the number and types of polypeptide units of oligomeric proteins

10. Secondary structure • the two most common types, • α-helix • β-sheet • The Alpha Helix • The R groups, face outward • right-handed • Represent as cylinders

11. The stability • Hydrogen bonds • proline disrupts the conformation of the helix

13. Hydrogen bonds

14. The Beta Sheet • Zigzag or pleated pattern • Highly extended • Stability from hydrogen bonds • Between segments, or strands, of the sheet • Parallel β sheet • in the same direction amino to carboxyl • Antiparallel sheet • Represents β sheets as arrows • amino to carboxyl

16. Antiparallel β sheet parallel β sheet

17. Loops & Bends • Turns and bends • Short segments of amino acids that join two units of secondary structure • Proline and glycine often are present in β turns. • Loops • Much Longer than turn & bends • serve key biologic roles • Participate in catalysis

18. A β-turn that links two segments of antiparallel β sheet

19. Loops & Bends • Helix-loop-helix motifs • binding portion of DNA binding proteins • repressors & transcription factors • many loops and bends reside on the surface of proteins • Epitopes • lack apparent structural regularity • Stabilized through • hydrogen bonding, salt bridges, and hydrophobic interactions

20. Disordered regions • Disordered regions • at the extreme amino or carboxyl terminal • High onformational flexibility • ligand-controlled switches

21. Tertiary Structure • the entire three dimensional conformation of a polypeptide • Domains • Assembly of secondary structures • Helices, sheets, bends, turns, and loops • a section of protein structure sufficient to perform a particular chemical or physical task • Binding to ligand • Single/multiple domains

22. Examples of tertiary structure of proteins A single -domain structure

23. Two-domain structure

24. Quaternary structure • assembled from more than one polypeptide, or protomer • Monomeric • Dimeric • Homodimers • Heterodimer • Greek letters (α, β, γ etc) are used • α2β2γ (five subunits of three different types)

25. FACTORS STABILIZE TERTIARY & QUATERNARY STRUCTURE • Noncovalent interactions • hydrophobic interactions • Interior of the protein • Hydrogen bonds and salt bridges • Individually weak • Covalent • disulfide (S-S) bonds • Intrapolypeptide • Interpolypeptide

27. Techniques • Study of higher orders of protein structure • X-ray crystallography, NMR spectroscopy, • THREE-DIMENSIONAL STRUCTURE • analytical ultracentrifugation • Gel filtration • Gel electrophoresis

30. Techniques • Mass spectrometry • A tool for determining primary structure and for the identification of posttranslational modifications. • DNA cloning • Genomics • Increases the speed and efficiency for determination of primary structures of proteins.

31. Proteome • to determine the primary sequence and functional role of every protein expressed in a living cell

32. PROTEIN FOLDING • Occurs via a stepwise process • Short segments fold into secondary structural units that provide local regions of organized structure

34. Denatured (Unfolded) • treatment with acid or base, chaotropic agents, or detergents • Aggregates • disordered complexes of unfolded or partially folded polypeptides held together by hydrophobic interactions • Auxiliary Proteins Assist Folding • Chaperones • Hsp70 • Prevent aggregation

35. Operate in • Folding • Unfolding • Protein Disulfide Isomerase • Catalyzing disulfide exchange • Rupture & reformation • Proline-cis,trans-Isomerase • Particularly common in β-turns

36. SEVERAL DISEASES RESULT FROM ALTERED PROTEIN CONFORMATION • NEUROLOGIC DISEASES • Prion diseases • Creutzfeldt-Jakob disease, scrapie • α-helical structure to the β-sheet structure • Alzheimer’s Disease • Diseases of collagen maturation • Ehlers-Danlos syndrome • Scurvy

38. Summary • Proteins may be classified on the basis of • the solubility, • Shape, • Function, • the presence of a prosthetic group • Such as heme • Proteins perform complex physical and catalytic functions

39. Primary structure • The gene-encoded sequence of amino acids. • Stabilized by covalent peptide bonds • Secondary structure results from • folding of polypeptides into hydrogen-bonded motifs such as the α helix, the β-pleated sheet, β bends, and loops. • Supersecondary motifs • Combinations of these motifs

40. Tertiary structure • the relationships between secondary structural domains. • Quaternary structure • Proteins with two or more polypeptides (oligomeric proteins)