Notes on Detection of rare Partially folded molecules in equilibrium with the native conformation of RNaseH
RNase H*: E. coli ribonuclease H with all three free cysteines replaced by alanines
- · Three-dimensional structure of ribonuclease H from E. coli: http://www.nature.com/nature/journal/v347/n6290/abs/347306a0.html
The enzyme RNase H is a non-specific endonuclease and catalyzes the cleavage of RNA via a hydrolytic mechanism. Members of the RNase H family can be found in nearly all organisms, from archaea and prokaryota and eukaryota.
RNase H’s ribonuclease activity cleaves the 3’-O-P bond of RNA in a DNA/RNA duplex to produce 3’-hydroxyl and 5‘-phosphate terminated products. In DNA replication, RNase H is responsible for removing the RNA primer, allowing completion of the newly synthesized DNA.
The term molten globule (MG) was first coined by A. Wada and M Ohgushi in 1983. It was first found in cytochrome c, which conserves a native-like secondary structure content but without the tightly packed protein interior, under low pH and high salt concentration. For cytochrome c and some other proteins, it has been shown that the molten globule state is a "thermodynamic state" clearly different both from the native and the denatured state, demonstrating for the first time the existence of a third equilibirum (i.e., intermediate)state.
Challenge of characterizing partially folded molecules
Examination of amide hydrogen exchange
Hypothesis developed by Englander: kinetic folding pathways of proteins can be deduced by determining the structure and stability of partially folded conformations under native conditions.
- Behavior of how a protein folds can be inferred from the conformations of intermediate structures of the protein
Folding kinetics of RNaseH are known
Measurements for 53 amide protons, at 12 different denaturant concentrations
Exchanged measured as a function of time ranging from hours to months
Slower exchange than in unfolded polypeptide
Addition of guanidine (denaturant) decreases protein stability, open form increases
- Hydrogen exchange rates give info about structural transitions allowing that H exchange
Local fluctuations allow exchange without denaturant sensitivity m=0
Opening events dominating hydrogen exchange depend on denaturant conc. and amide proton being considered
RNase H unfolds in 3 regions
Blue=more stable 10kcal/mol avg, green region=8.7kcal/mol,
Therefore, the alpha helix of proteins and the double helix of nucleic acids have CD spectral signatures representative of their structures. The capacity of CD to give a representative structural signature makes it a powerful tool in modern biochemistry with applications that can be found in virtually every field of study.
Measuring exchange rates as function of denaturant reveals information pertaining to partial unfolding events or local flunctuations present at equilibrium
Helices are very stable interactions
Mutually stabilizing helices contribute more to stability than do beta sheets
Identify minima in energy landscape
Structure of one intermediate resembles molten globule occurring at low pH
- Molten globules can model intermediates in folding pathways
Residues responsible for stability are also responsible for folding dynamics