Why does β-secretase zymogen possess catalytic activity? Molecular modeling and molecular dynamics simulation studies

Comparative study on activation mechanism of carboxypeptidase A1, A2 and B: first insights from steered molecular dynamics simulations

Different forms of procarboxypeptidases (PCPs) zymogens are observed experimentally to show different rates and modes of activation: PCPA1 shows a slow, biphasic, activation pathway compared to PCPA2 and PCPB which have a faster, monotonic activation behavior. Detailed mechanisms involved in activating these zymogen forms to the active enzymes are not well understood yet. In this work, three PCP zymogens (subtypes A1, A2 and B) were in silico converted into the primary cleavage state of zymogens using available X-ray structures. Based on these cleaved forms of zymogen, we are able to investigate their spontaneous dissociation process of the prosegment from its associated enzyme domain using steered molecular dynamics simulation. The simulations revealed the highest rupture force in PCPB followed by PCPA2 and PCPA1. We also found that the cleavage substantially destabilizes most of the hydrogen bonds at the prosegment-enzyme interface in each zymogen structure. The mechanisms of the prosegment unbinding seem to be similar in both PCPA1 and PCPB but different in PCPA2: PCPA1 and PCPB show first rupture in the connecting segment followed by the globular domain, while PCPA2 conversely shows first rupture in the globular domain and then in the connecting segment. Our simulations have included the dynamic and long range conformational effects taking place after the first proteolytic cleavage in PCPs, providing first insights into the activation of carboxypeptidase A1, A2 and B.

The role of tyrosine 71 in modulating the flap conformations of BACE1

β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) is a potential target for treating Alzheimer's disease. BACE1's binding site is partially covered by a flexible loop on its N-terminal domain, known as the "flap," which has been found in several conformations in crystal structures of BACE1 and other aspartyl proteases. The side chain of the invariant residue Tyr71 on the flap adopts several rotameric orientations, leading to our hypothesis that the orientation of this residue dictates the movement and conformations available to the flap. We investigated this hypothesis by performing 220 ns of molecular dynamics simulations of bound and unbound wild-type BACE1 as well as the unbound Y71A mutant. Our findings indicate that the flap exhibits various degrees of mobility and adopts different conformations depending on the Tyr71 orientation. Surprisingly, the "self-inhibited" form is stable in our simulations, making it a reasonable target for drug design. The alanine mutant, lacking a large side chain at position 71, displays significant differences in flap dynamics from wild type, freely sampling very open and closed conformations. Our simulations show that Tyr71, in addition to its previously determined functions in catalysis and substrate binding, has the important role of modulating flap conformations in BACE1.