BCH 380 1st Edition Lecture 9 Outline of Last Lecture I. Structures of proteinsA. Primary, Secondary, Tertiary, Quaternary II. Ramachandran PlotIII. The alpha helixOutline of Current Lecture IV. Beta Sheets B. Common motifsV.Cytochrome cVI. Proteins Current LectureB (Beta) Sheets- The side chains alternate from one side of the Beta strand to the other side- Both stands have a right-handed twist- Reverse turnso Type I Beta turn The structure is stabilized by a hydrogen bond between the carbonyl oxygen of the first N-terminal residue (Phe) and the amide hydrogen of the fourth residue (Gly) Note that the proline residue at position n+1 o Type II Beta turn This turn is also stabilized by a hydrogen bond between the carbonyl oxygen of the first N-terminal residue (Val) and the amide hydrogen of the fourth residue (Asn)Common motifs:- Arrows indicate the N- to C- terminal direction of the peptide bond- Helix-loop-helix- Coiled coil- Helix bundle- BaB unit (beta-alpha-beta)- Hairpin- Beta meander- Greek key- Beta-SandwichCytochrome c- Tuna cytochrome c bound to heme- Tuna cytochrome c polypeptide chain- Rice cytochrome c- Yeast cytochrome c- Bacterial cytochrome cSimilar amino acid sequences give similar 3D structures! - Enzymes with related functions often have similar structuresHuman serum albumin- Examples of tertiary structure in selected proteins- This protein has several domains consisting of layered alpha helices and helix bundles Jack bean concanavalin A- This carbohydrate-binding protein is a single-domain protein (lectin) made up of a large Beta-Sandwich foldJellyfish green fluorescent protein- This is a Beta-Barrel structure with a central alpha helix. The stands are anti-parallel. E. coli flavodoxin- The fold is a five-stranded parallel twisted sheet surrounded by alpha helicesCommon Domain folds:- Parallel twisted sheet- Beta Barrel- Alpha/Beta Barrel- Beta helix*Table 4.1 in textbookHomooligomers: made up of the same sub-unitsHeterooligomers: made up of different sub-unitsHIV-1 aspartic protease- Quaternary structure- This protein has two identical all-Beta subunits that bind symmetrically- Knowledge of the structure of the enzyme greatly accelerated development of therapeutic compounds Stretomyces potassium channel protein:- Quaternary structure- This membrane-bound protein has four identical subunitsBacterial flagellum- a protein machine composed of 21 core subunits found in all species- Two additional subunits are missing in Firmicutes and five others are sporadically distributed Consider a simple interaction between two proteins, P1 and P2:P1+P2   P1:P2The equilibrium constant for this reaction, which is an association is:Ka=