Catalytic Mechanism of Interfacial Water in the Cycloaddition of Quadricyclane and Diethyl Azodicarboxylate

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone

BACKGROUND

The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentration of hydrophobic residues in the center (hydrophobic core). Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core.

RESULTS

The current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID-6PSI)-the client molecule. The availability of WT form of the folding protein-alkaline phosphatase (PDB ID-1EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone.

CONCLUSIONS

The FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.

The Origin of Anion-π Autocatalysis

The autocatalysis of epoxide-opening ether cyclizations on the aromatic surface of anion-π catalysts stands out as a leading example of emergent properties expected from the integration of unorthodox interactions into catalysis. A working hypothesis was proposed early on, but the mechanism of anion-π autocatalysis has never been elucidated. Here, we show that anion-π autocatalysis is almost independent of peripheral crowding in substrate and product. Inaccessible asymmetric anion-π autocatalysis and sometimes erratic reproducibility further support that the origin of anion-π autocatalysis is more complex than originally assumed. The apparent long-distance communication without physical contact calls for the inclusion of water between substrate and product on the catalytic aromatic surface. Efficient anion-π autocatalysis around equimolar amounts but poor activity in dry solvents and with excess water indicate that this inclusion of water requires high precision. Computational models suggest that two water molecules transmit dual substrate activation by the product and serve as proton shuttles along antiparallel but decoupled hydrogen-bonded chains to delocalize and stabilize evolving charge density in the transition state by "anion-π double bonds". This new transition-state model of anion-π autocatalysis provides a plausible mechanism that explains experimental results and brings anion-π catalysis to an unprecedented level of sophistication.