Reductive denaturation in addition to oxidative renaturation of RNase A Plausible mechanism

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Reductive denaturation in addition to oxidative renaturation of RNase A Plausible mechanism

Cohen, Sanford, Host has reference to this Academic Journal, PHwiki organized this Journal Reductive denaturation in addition to oxidative renaturation of RNase A Plausible mechanism as long as the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein protein disulfide isomerase Primary structure of porcine proinsulin C-chain needed to direct proper disulfide bond as long as mation

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Determinants of Protein Folding A. helices/sheets predominate in proteins because they fill space efficiently B. protein folding is directed mainly by internal residues (protein folding is driven by hydrophobic as long as ces) C. protein structures are organized hierarchically Hierarchical organization of globular proteins (subdomains) Determinants of Protein Folding (cont.) D. protein structures are highly adaptable E. secondary structure can be context-dependent

NMR structure of protein GB1 “chameleon” sequence: AWTVEKAFKTF (unfolded free in solution) Determinants of Protein Folding (cont.) F. dependence of protein fold on primary sequence X-ray structure of Rop protein, a homodimer of aa motifs that associate to as long as m a 4-helix bundle created by changing 50% of the 56 residues in GB1 not all residues have equally important roles in specifying a specific fold

The Levinthal Paradox 2n backbone torsions, n-residue protein: ~10n structures time to explore all structures: t = 10n/1013 s-1 as long as a 100-residue protein: t = 1087 s Conclusion: proteins fold via an ordered pathway or set of pathways Experimental Methods to Monitor Protein Folding A stopped-flow device: 40 ms dead-times (UV/ VIS/ fluorescence /CD) cold denatured proteins / T-jump

UV absorbance spectra of the three aromatic amino acids, phenylalanine, tryptophan, in addition to tyrosine molar extinction coefficient Circular dichroism (CD) spectra of polypeptides eL in addition to eR differ (circularly polarized light); measure e Pulsed H/D Exchange X-H + D2O X-D + HOD Used to follow the time course of protein folding by 2D NMR a. Denatured protein in D2O b. Dilute with H2O in addition to allow to fold as long as time tf c. Increase pH to initiate D-H exchange (10-40 ms) d. Lower pH; allow to completely fold e. Determine which amide protons are protonated in addition to deuterated

L in addition to scape Theory of Protein Folding Polypeptides fold via a series of con as long as mational adjustments that reduce their free energy in addition to entropy until the native state is reached. There is no single pathway or closely related set of pathways that a polypeptide must follow in folding to its native state. The sequence in as long as mation specifying a particular fold is both distributed throughout the polypeptide chain in addition to highly overdetermined. Folding funnels: An idealized funnel l in addition to scape Folding funnels: The Levinthal “golf course” l in addition to scape

Folding funnels: Classic folding l in addition to scape Folding funnels: Rugged energy surface Closer mimic of an actual folding pathway Polypeptide backbone in addition to disulfide bonds of native BPTI (58 residues, three disulfide bonds) Folds via an ordered pathway: involves well defined intermediates

Renaturation of BPTI: protein primary structures evolved to specify efficient folding pathways as well as stable native con as long as mations Folding accessory proteins A. Protein disulfide isomerases (PDI) B. Peptidyl prolyl cis-trans isomerases C. Molecular chaperones Reactions catalyzed by protein disulfide isomerase (PDI). (a) Reduced PDI catalyzes the rearrangement of the non-native disulfide bonds. A folding accessory protein

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Reactions catalyzed by protein disulfide isomerase (PDI). (b) The oxidized PDI-dependent synthesis of disulfide bonds in proteins. NMR structure of the a domain of human protein disulfide isomerase (PDI-a) in its oxidized as long as m. (a) The polypeptide backbone is shown in ribbon as long as m. homodimer; eukaryotic; each subunit consists of four domains Cys 36 in addition to 39 exposed NMR structure of the a domain of human protein disulfide isomerase (PDI-a) in its oxidized as long as m. (b) The molecular structure as viewed from the bottom. Cys 36 is located in a hydrophobic patch Oxidized PDI-a is less stable than reduced PDI-a

Peptidyl Prolyl Cis-Trans Isomerases (PPIs) Xaa-Pro peptide bonds: ~10% cis PPIs catalyze the otherwise slow interconversion of Xaa-Pro peptide bonds between their cis in addition to trans con as long as mations; accelerate the folding of Pro-containing polypeptides. Two families: cyclophilins in addition to FKBP12 (based on known inhibitors) Unfolded proteins in vivo have a great tendency to as long as m intramolecular in addition to intermolecular aggregates. Molecular chaperones prevent/reverse improper associations, especially in multidomain in addition to multisubunit proteins. Function by binding solvent-exposed hydrophobic surfaces reversibly to promote proper folding Many chaperones are ATPases. Classes of Chaperones A. Heat shock proteins 70: 70 kD monomeric proteins B. Chaperonins: as long as m large multisubunit cage-like assemblies C. Hsp90: involved in signal transduction; very abundant in eukaryotes D. Nucleoplasmins: acidic nuclear proteins involved in nucleosome assembly

Figure 9-37 Primary structures of some representative c-type cytochromes. Figure 9-38 Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37. Figure 9-39 The two-structurally similar domains of rhodanese.

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