SCAN: Insights into the ATP-hydrolysis mechanism of an ABC transporter

SCAN Seminar

Title: Insights into the ATP-hydrolysis mechanism of an ABC transporter: Conformational changes in the NBD dimer of MJ0796

Speaker: Ana Sofia Oliveira, Protein Modelling Lab

Abstract:
Despite the rapid advances in the study of ABC transporters, many fundamental questions linked to ATP binding/hydrolysis and its relation to the transport cycle remain unanswered. In particular, it is still neither clear nor consensual how is the ATP energy used by the nucleotide binding domains (NBDs) to produce mechanical work and drive the substrate translocation. The major conformational changes in the NBDs induced by ATP hydrolysis during the transport cycle and the role played by the conserved family motifs in harnessing the energy associated with nucleotide hydrolysis are yet unknown. Additionally, the way energy is transmitted from the catalytic to the membrane domains, in order to drive substrate translocation, is also a fundamental question that remains unanswered. Due to the high structure similarities of the NBDs architecture throughout the whole ABC family it is likely that the mechanism of ATP binding, hydrolysis and communication with the transmembrane domains is similar in all family members, independently of the nature of the transported substrate. In this work we focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii. Several potential intermediate states of the ATP hydrolytic cycle are investigated, each consisting of different combinations of nucleotide bound forms. The results obtained allowed us to identify the conformational rearrangements induced by hydrolysis on the catalytic subunits, as well as the residues involved in this reorganization. The major changes are localized at specific regions of the protein, namely involving segments 11-19 and 93-124. Additionally, our results together with the knowledge of complete ABC transporters X-ray structures, suggest a possible NBD:TMD signal transmission interface.

Short CV:

2002 – Degree in Chemical Engineering by the Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa
2000 – Research student in the no Laboratório de Análises de Dopagem e Bioquímica do Centro de Medicina Desportiva - Instituto Nacional do
Desporto -, under the supervision of Dr. DeBower. Use of GC/MS (Gas Chromatography/Mass Spectrometry) Techniques.

2003/2006 – Research fellowship in the Protein Modelling group at Instituto de Tecnologia Química e Biológica of Universidade Nova de Lisboa, under the supervision of Prof. Cláudio Soares. The main goal of the work was to study the redox linked conformational changes in proteins existent in sulphate-reducing bacteria.
2006 to present day– PhD fellowship (SFRH / BD / 21433 / 2005) in the Protein Modelling group at Instituto de Tecnologia Química e Biológica of Universidade Nova de Lisboa, under the supervision of Prof. Cláudio Soares.