A molecular dynamics analysis of “ligand imprinting”

ITQB PhD Seminars

Title: A molecular dynamics analysis of “ligand imprinting”

Speaker: Diana Lousa

Laboratory: Protein Modelling

Abstract:

Enzymatic catalysis in nonaqueous solvents has attracted the attention of biotechnologists and biochemists for more than two decades. Despite the great progresses that have been made in this area, many of the molecular determinants of enzyme behavior in organic solvents remain unclear. In the Protein Modeling Laboratory we have been developing and using simulation methodologies to study enzymes in organic solvents.
One of our recent studies focused on the structural determinants of the phenomenon known as “ligand imprinting”. This phenomenon was first reported in 1988, when Russell and Klibanov observed that lyophilizing subtilisin in the presence of competitive inhibitors could significantly enhance its activity in an anhydrous solvent. They further observed that this enhancement did not occur when the same assays were carried out in water. We have used a molecular dynamics simulation approach to analyze this behavior. To simulate the effect of placing an enzyme in the presence of a ligand before its lyophilization, an inhibitor was docked in the active site of subtilisin and 20 ns MD simulations in water were performed. The ligand was then removed and the resulting structure was used for subsequent MD runs using hexane and water as solvents. As a control, the same simulation setup was applied the structure of subtilisin in the absence of the inhibitor. We observed that the ligand maintains the S1 pocket in an open conformation and this configuration is retained after the removal of the ligand when the simulations are carried out in hexane. In agreement with experimental findings, the structural configuration induced by the ligand is lost when the simulations take place in water. Our r.m.s. fluctuation analysis indicates that this behavior is a result of the decreased flexibility displayed by enzymes in anhydrous solvents, relatively to the aqueous situation. In the absence of water the enzyme is rigid, and thus it gets kinetically trapped in the conformation induced by the inhibitor:
the enzyme behaves as if it has a “memory”. In water, the protein becomes more flexible and rapidly deviates from the ligand imprinted state.

Short-CV

2007 to present - PhD student in the Protein Modeling Laboratory at ITQB/UNL, under the supervision of Professor Cláudio M. Soares and Dr.
António M. Baptista

2006 - Grant holder (BI) in the Protein Modeling Laboratory, under the supervision of Professor Cláudio M. Soares

2004-2005 - Pos-graduation in Bioinformatics at IGC and FCUL

1999-2004 – Degree in Applied Chemistry (Biotechnology branch) at FCT/UNL