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You are on the personal home page of Adrien Melquiond.

I'm a postdoc with Dr. Alexandre Bonvin. I'm studying the specificity of protein-protein interactions by molecular modeling approaches.

Have a look on my scientific CV (last updated april 2012, PDF format)

Current Research

Ubiquitin enzymes are key regulating units for many fundamental processes required for cell viability. Our main objective is to develop reliable bioinformatic and computational approaches to predict, model and dissect biomolecular interactions at an atomic level. For this, bioinformatic data such as sequence conservation and structural information will be combined with available proteomic data to drive the modelling process. This will be used as an input for our information-driven docking program HADDOCK (High Ambiguity Driven protein-protein DOCKing) to predict and unravel the specificity of E2-E3 interactions. By the homology modelling effort, we aim to offer a new web resource (SMURF) to complement the lack of structural knowledge on human E2/E3 enzymes.

Want to know more? have a look at the HADDOCK website

PhD thesis

I defended my PhD thesis on September 18, 2007 on the aggregation of amyloid peptides by computer simulations. You can download the manuscript in french (PDf format). The publications associated to this work are listed in the text.

Abstract

More than twenty human diseases, including Alzheimer's disease and dialysis-related amyloidosis, are associated with the pathological self-assembly of soluble proteins into transient cytotoxic oligomers and amyloid fibrils. Because this process is very complex, the detailed aggregation paths and structural characterization of the intermediate species remain to be determined. In this work, we first review our current understanding of the dynamics and free energy surface of the assembly of small amyloid-forming peptides (KFFE and IAPP22-27) using coarse-grained protein force field (OPEP) coupled to the activation-relaxation technique (ART) and molecular dynamics (MD). Next, we present replica exchange MD simulations (REMD) on the dimers of Alzheimer's peptides A&beta1-40 and A&beta1-42 and discuss the role of amino acids 23-28 in fibril formation. Finally, we probe the first steps of A&beta16-22 oligomer dissociation in the presence of N-methylated inhibitors by MD-OPEP simulations.

Keywords :

amyloid fibril formation, soluble oligomers, aggregation, coarse-grained force field, activation-relaxation technique, molecular dynamics, replica exchange method

contact

Dr. Adrien Melquiond

Computational Structural Biology

Bijvoet Center for Biomolecular Research

Utrecht University

Padualaan 8, 3584 CH Utrecht - The Netherlands -

Phone: +31.(0)30.2533641 Fax: +31.(0)30.2537623

E-mail: a.s.j.melquiond_AT_uu.nl

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