Structural and functional insights into the anti-BACE1 Fab fragment that recognizes the BACE1 exosite

Abstract

A molecular modeling study giving structural, functional, and mutagenesis insights into the anti-BACE1 Fab fragment that recognizes the BACE1 exosite is reported. Our results allow extending experimental data resulting from X-ray diffraction experiments in order to examine unknown aspects for the Fab-BACE1 recognition and its binding mode. Thus, the study performed here allows extending the inherently static nature of crystallographic structures in order to gain a deeper understanding of the structural and dynamical basis at the atomic level. The characteristics and strength of the interatomic interactions involved in the immune complex formation are exhaustively analyzed. The results might explain how the anti-BACE1 Fab fragment and other BACE1 exosite binders are capable to produce an allosteric modulation of the BACE1 activity. Our site-directed mutagenesis study indicated that the functional anti-BACE1 paratope, residues Tyr32 (H1), Trp50 (H2), Arg98 (H3), Phe101 (H3), Trp104 (H3) and Tyr94 (L3), strongly dominates the binding energetics with the BACE1 exosite. The mutational studies described in this work might accelerate the development of new BACE1 exosite binders with interesting pharmacological activity.

Keywords:

• BACE1
• Alzheimer
• immune complex
• molecular dynamics simulation
• allosteric control

Acknowledgments

This work was supported by Universidad Nacional de San Luis (UNSL) and CONICET grants 2-0312 and PIP00474, respectively. R.D.E. and H.A.B. are staff members of the National Research Council of Argentina (CONICET, Argentina). L.J.G. gratefully acknowledges financial support from CONICET with a fellowship. We sincerely thank the anonymous reviewers for helpful comments and suggestions on the manuscript.