F BICH 410 1st Edition Lecture 9 Outline of Last Lecture Secondary Structure o Globular Proteins o Fibrous Proteins Outline of Current Lecture Nonstandard amino acids in collagen formed after parent amino acid incorporated into collagen o Vitamin C ascorbace required for collagen o Deficiency scurvy Collagen triple helix much more extended then alpha helix 3 vs 3 6 residues turn o Creates sharp turns and every third residue faces center so it is typically Gly because it is small enough and permits turns Collagen unusual crosslinking triple helix stabilized by H bond between back bone amide of Gly and carbonyl of Pro o Fibrils strengthened by covalent crosslinking between Lys and His o Crosslinking increases with age o Carbohydrates can be found in the hole region of the helix o Gelatin is collagen extracted from bones connective tissue and intestines o Ehlers Danlos Syndrome Lysyl hydroxylase deficiency so no crosslinks and hyperextensibility ie rubberman o Osteogenesis imperfect brittle bone replace Gly with more bulkier amino acid disrupting the helix and causing bones to break easier Unit 2 Protein Structure Folding o Primary sequence contains info needed to adopt tertiary and quaternary or native structure o In Globular proteins native structure is only slightly more stable than unfolded protein 0 4kj mol which is approximately equal to the energy of a H bond o Weak noncovalent interactions along with covalent crosslink stabilize native structure o Denaturation loss of structure and loss of function only 1 native structure but many denatured Tend to be called random coil Proteins exhibit 2 state folding process folded or nonfolded These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute o o o o o o o o o o o o Does not disrupt 1o just 2 3 and 4o structures Disrupting weak noncovalent interactions Can be caused by Heat kinetic energy causing molecules to vibrate until atoms move apart pH change in H bonds detergents SDS interrupts hydrophobic interactions chaotropic agents urea guanidium chloride oxidation reduction disulfide crosslinks stabilize constrain structure but can be reduced with chemicals like DTT Christian Ansfinsin and Ribonuclease A Demonstrated that ribonuclease could be denatured and it could spontaneously renature slow folding intermediates had incorrect disulfide bonds but with an enzyme it properly refolded Discovered nothing is required but primary sequence for folding Liventhial paradox if peptide chain searched all possible conformations on its path to its native tertiary structure it would take longer than the apparent age of the universe And a protein can fold on millisecond timescale Protein folding typically secondary structure acquired first then hydrophobic collapse final steps involve formation of long range interactions between secondary structure Thermodynamics of protein folding Anfinses experiment determined that the folding of a protein is dependent on the amino acid sequence and the solvent and folds into the global minimum free energy Unfolded peptide high energy high entropy Native conformation single low entropy low energy For a favored structure internal interactions must be favored enthalpy less than 0 entropically favored too delta S greater than 0 Protein dynamics proteins not still they have local fluxations or breathings Peptide backbone area is stable secondary structure shows high flux Alpha helicies tend to fray at terminus but beta sheets are more stable Most stable areas of structure are sites of nucleation Peptide prolyl cis trans isomerase PPI help interconvery from cis to trans Protein folding in vivo in test tube redox environment can be different than in vitro Ie wrong di sulfide bonds can sometimes be fix to get global free energy minimum with protein disulfide isomerase Molecular Chaperones cell concentration of proteins can be high leading to aggregation of partially folded intermediates Chaperones then bind unfolded protein allowing favorable protein folding without competition HSP70 and chaperonins Protein folding diseases proteins aggregate Prion disease infectious agent consisting solely of proteins Prusiner collide prion proteinaceous infectious particle Protein causes other proteins to misfold