A. Sofia F. Oliveira

Senior Research Associate @ University of Bristol

email: sofia.oliveira@bristol.ac.uk

ORCID: 0000-0001-8753-4950

Present Research interests

Currently, my research interests are centred on three membrane-protein families: nicotinic acetylcholine receptors (nAChRs), cytochrome c oxidases (CcOx) and ATP Binding Cassette (ABC) transporters.

Nicotine is the major biologically psychoactive agent in tobacco and it binds to the nAChRs. Currently, the FDA-approved anti-smoking compounds are only moderately effective in reducing the symptoms of nicotine withdrawal and may cause undesirable side effects. Currently, my work focus on the development of new agonists with improved nAChRs subtype specificity and in the identification of the molecular determinants that modulate ligand binding in each case.

CcOx are redox driven proton pumps that use the free energy of oxygen reduction for the creation of a proton gradient across the membranes. Until now and despite all the experimental data available for this family, the molecular mechanisms for reduction and proton pumping are mostly unknown. So, my main interest is to understand the proton pumping mechanisms at a molecular level. In particular, I am trying to identify the functionally relevant redox-induced conformational changes and understand how these rearrangements affect proton pumping.

ABC-transporters are proteins that transport actively substrates throughout membranes. Until this moment, it is still not clear which are the conformational changes induced by ATP-hydrolysis in the nucleotide binding domains, nor how these rearrangements are ‘‘transmitted’’ to the membrane domains. The identification of the conformational changes after ATP binding/hydrolysis and how the energy released from hydrolysis is harness and transferred to the membrane domains in order to achieve substrate unidirectional transport is my main interest.

Selected Research Highlights

2022

• “Structural and temporal basis for agonism in the α4β2 nicotinic acetylcholine receptor”, 2022, bioRxiv. DOI: 10.1101/2022.02.23.481608
• “Identification and Validation of Novel Microtubule Suppressors with an Imidazopyridine Scaffold through Structure Based Virtual Screening and Docking”, 2022, biRxiv. DOI:10.1101/2021.12.08.471724
• “Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2”, 2022, Nat Commun. DOI: 10.1038/s41467-021-27881-6
• “The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour”, 2022, Comput Struct Biotechnol J. DOI: 10.1016/j.csbj.2021.12.011

2021

• “#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol”, 2021, bioRxiv. DOI: 10.1101/2021.11.12.468428
• “A Functional Interaction Between the SARS-CoV-2 Spike Protein and the Human α7 Nicotinic Receptor”, 2021, ResearchSquare. DOI: 10.21203/rs.3.rs-938911/v1)
• “Molecular dynamic simulations support the hypothesis that the brGDGT paleothermometer is based on homeoviscous adaptation”, 2021, Geochim et Cosmochim Acta. DOI:10.1016/j.gca.2021.07.034
• “Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems”, 2021, Eur Phys J B. DOI: 10.1140/epjb/s10051-021-00157-0
• “ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK₂E importer”, 2021, Sci Rep. DOI:10.1038/s41598-021-89556-y
• “Allosteric communication in Class A β-lactamases occurs via Cooperative Coupling of Loop Dynamics”, 2021, eLife. DOI: 10.7554/eLife.66567
• “A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors”, 2021, Biophys J. DOI: 10.1016/j.bpj.2021.01.037

2020

• “F508del disturbs the dynamics of the nucleotide binding domains of CFTR before and after ATP hydrolysis”, 2020, Proteins. DOI: 10.1002/prot.25776
• “Precision design of single and multi-heme de novo proteins”, 2020, bioRxiv. DOI: 10.1101/2020.09.24.311514
• “A general mechanism for signal propagation in the nicotinic acetylcholine receptor family”, 2019, J. Am. Chem. Soc. DOI: 10.1021/jacs.9b09055
• “Exploration of the role of CHRNA5-A3-B4 genotype in smoking behaviours“, 2019, bioRxiv. DOI: 10.1101/818252
• “Rate-limiting transport of positive charges through the Sec-machinery is integral to the mechanism of protein transport”, 2019, bioRxiv. DOI: 10.1101/592543
• “Identification of the initial steps in signal transduction in the α4β2 nicotinic receptor: Insights from equilibrium and nonequilibrium simulations”, 2019, Structure. DOI: 10.1016/j.str.2019.04.008
• “Unlocking Nicotinic Selectivity via Direct C-H Functionalization of (-)-Cytisine”, 2018, Chem. DOI:10.1016/j.chempr.2018.05.007
• “Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus”, 2018, Redox Biology. DOI:10.1016/j.redox.2018.02.004
• “The key role of glutamate 172 in the mechanism of type II NADH:quinone oxidoreductase of Staphylococcus aureus”, 2017, BBA-Bioenergetics.  DOI: 10.1016/j.bbabio.2017.08.002
• “Molecular structure of FoxE, the putative iron oxidase of Rhodobacter ferrooxidans SW2″, 2017, BBA-Bioenergetics. DOI:10.1016/j.bbabio.2017.07.002
• “Structural and Functional insights into the catalytic mechanism of the Type II NADH:quinone oxidoreductase family”, 2017, Sci Rep. DOI:10.1038/srep42303.
• “Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study”, 2017, J. Chem. Inf. Model. DOI:10.1021/acs.jcim.6b00575
• “Coupling between protonation and conformation in cytochrome c oxidase: Insights from Constant-pH MD simulations”, 2016, BBA-Bioenergetics. DOI:10.1016/j.bbabio.2016.03.024
• “Exploring O2 Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site”, 2014, PLOS Comp. Biol. DOI:10.1371/journal.pcbi.1004010

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rch interests

Present Research interests