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Welcome to the Mercadante Group Page

We study molecular dynamics and link it to molecular function

About The Mercadante Lab

Our group

reconstructs dynamics of molecules by using a diverse set of computational strategies and ultimately comparing our findings with the ones coming from experiments in a highly multidisciplinary environment. Our microscope is the computer, which allow us to obtain a lot of information at once.
By simulating the dynamics of a molecule, we can:
Understand molecular function and how interactions between molecules function.
Predict molecular properties in different micro-environmental conditions.
Design strong binders for known macromolecules.
Design new molecules with enhanced function.
Molecualr simulations greatly increase the resolution range of experiments, help formulating new hypothesis by predicting molecular behaviour and have a crucial role for formulating new strategies to tackle scientific problems.

Publications

2022

2021

2020

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2014

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2012

#Equally shared first authorship. *Corresponding authorship.

Featured Research

We are interested in a broad set of questions that target the understanding and the design of molecular systems. Our approaches are based on the use of the so-called computational microscope. ### As a microscope is powered by light and a lens, our microscope is fuelled by the laws of physics, the potential energy functions and parameters that make up force fields. Thanks to this we can investigate how the dynamics of molecules is linked to their function at a high level of resolution.

  • Study of Intrinsic disorder in the context of genetic transcription

    Intrinsically disordered proteins (IDPs) do not naturally fold into 3D structures but they are key in a myriad of cellular processes. Disordered proteins perform ensemble-mediated rather than structure-mediated functions and their lack of structure gives them unconventional properties, like the ability to function at the centre of signalling hubs binding a moltitude of molecular partners (molecular promiscuity). They are centerpieces of genetic transcription and we study how disorder enables the formation of complexes that ultimately regualate gene-reading. To do so, we use a combination of computational approaches, encompassing molecular modelling and molecular dynamics simulations, heavily interfacing our results with single-moleucule experiments, which we outsource from collaborations.

  • How do post-translational modifications regulate protein affinity?

    One of the main strategies to regulate proteins activitiy is to modify them after they have been expressed in cells. Since they occur after protein expression, these modification as called post-translational. Post-translational modifications (PTMs) consist in the addition/removal of chemical groups to/from amino acid sidechains in key positions along the protein sequence. Knowing how the occurrence of post-translational modification impacts the function of proteins is key to understand how dynamics regulates function. In the long term, this understanding might reveal opportunities to desire protein-like polymers with highly tunable properties for a set of applications.

  • Protein design to co-evolutionary approaches

    Protein structure and dynamics has been shaped by evolution and the fitness of protein sequences is optimised by the set of functions a protein must fulfil and within the micro-environment it operates. Recently, models that can predict the fitness of a protein sequence have become more and more efficient. Such predictions are often coupled to the analysis of protein homologous sequences and can be used to even generate sequences with a higher fitness. Those sequences are candidates for applications outside cells, like industrial applications where their usage needs to be coupled to higher temperatures or pressure. With our research, we will exactly this need: aiming to discover protein sequences with a higher fitness through co-evolutionary based design.

  • Study of molecular motors "without fuel".

    Molecular motors are able to convert chemical energy into mechanical energy or vice-versa. Other molecular motors are powered by an ion gradient, such as the rotary motor that synthesises ATP. Still other motors are powered by the free energy released when a nucleotide triphosphate is hydrolysed. The more processive a motor is the more unidirectional is the motion gleaned from the chemical free-energy released. In these motors, the free energy released constitutes a Brownian ratchet, preventing the reverse process. Remarkably, a class of enzymes called pectin methylesterase (PME) is involved in the processing of polysaccharide chains in plants, behaving as molecular motors that do not use high-energy exogenous co-substrates for their action, but carry the free energy for the Brownian ratchet endogenously. Understanding how PMEs achieve this, will lay the basis for the design of PME isoforms with enhanced or reduced processivity. Ultimately enhancing industrial processes and targeting events with serious economic downturns, such as plant parasitism and crop infection, in which PMEs play a big role.

  • What defines pH-dependent specificity for substrates in proteins?

    The sequence-to-structure relationship in proteins define their ability to work in a specific microenvironment. A particular class of enzymes that modifies carbohydrates into the plant cell wall is particularly redundant in plant genomes. Plants express a large number of different isoforms for the same protein, which by a series of sequence variations can act specifically at different pH values. We investigate the molecular determinants of this specificity by relating molecular dynamics, position and protonation of protonatable residues.

We are always looking for motivated students and postdocs to join the lab!
If you are interested, please send an email to Davide directly and enquire about potential opportunities

Davide Mercadante

Group Leader

Contact Davide by e-mail

Education and training:
BSc/MSc: Naples, Italy., PhD: Auckland, Postdocs: Heidelberg, Zurich

Hometown:
Naples, Italy.

Favourite (and only!) football team:
SSC Napoli

Favourite food:
Pasta and Pizza..what else?

Vanessa Ung

PhD Student

Contact Vanessa by e-mail

Education and training:
BSc Hons: The University of Auckland.

Hometown:
Auckland, New Zealand.

Favourite musical:
Hamilton

Favourite activity outside the lab:
Hiking/Swimming on a sunny day or a good book on a rainy day

Jordan McIvor

PhD Student

Contact Jordan by e-mail

Education and training:
BSc Hons: The University of Canterbury.

Hometown:
Christchurch, New Zealand.

Favourite activity when not simulating:
Running and Skiing!

Favourite food:
Coffee and Chocolate

Nadia Snegirev

Hons Student

Contact Nadia by e-mail

Education and training:
BSc: The University of Auckland.

Hometown:
Tauranga, New Zealand.

Favourite activity when not simulating:
Going sailing and making sourdough!

Favourite boardgame:
Wingspan.

News

JANUARY 2022

  • Our latest work on how nucleosomes can be remodelled thanks to competitive substitution of intrinsically disodered chaperones has finally been published in Nature Chemistry! The article has been overall well-received in the community and beyond! It hopes to provide insights how, thanks to disordered proteins, tight molecular interactions can be regulated within timescales acceptable for life..happy reading! The article can be accessed here

DECEMBER 2021

  • Davide has become the director of the Scholars Programmes at The University of Auckland. He's looking forward to bring his contribution to the growth and constant improvements of these flagship programmes of the university.

     

  • Congratulations to Davide for being awarded a Riddet Institute PhD Scholarship! The project will oversee the computational design of new proteins with appeal for the Food industry. The PhD position will be advertised soon!

SEPTEMBER 2021

  • Congratulations to Junqi Bai for completing her MSc in Chemistry in our group! Junqi looked at the conformational ensembles of peptides obtained from milk proteins upon tripsin digests! We wish Junqi all the best for her upcoming PhD!

MARCH 2021

  • We are delighted to announce that Summer Wong has joined the group for her Hons projects! Summer, in collaboration with the Selenko group at the Weizmann Institute of Science will study the behaviour of αSynuclein: a protein involved in the onset of Parkinson's disease. Welcome Summer!

JANUARY 2021

  • Because of her excellent performance in her Hons degree and project, Vanessa Ung has been awarded a MSc scholarship from the University of Auckland! Vanessa is now a MSc student in the Mercadante group! Congratulation Vanessa, well-deserved!

DECEMBER 2021

  • Congratulations to Lynne Sun and Vanessa Ung for succesfully completing their Hons degrees! We are now looking forward to your graduation day during the southern emisphere winter! It will be a sunny day no matter if it rains! Congrats!

OCTOBER 2020

  • Congratulations to Davide for being appointed review editor of Structural Biology, within the specialty section of Frontiers in Molecular Bioscience, Cell and Developmental Biology. Davide is looking forward to contribute to the publication of excellent work contributing to our understanding of molecular behaviour...

JULY 2020

  • We are very happy to announce that Veronika Laskova is a new PhD student in the lab! She comes all the way from the Czech Republic but has fallen in love with NZ and decided to stay for longer! She will study some interesting molecular motors belonging to the 'carbohydrate world'..Welcome to the group Veronika!

JUNE 2020

  • Exciting news for the group, Jordan McIvor previously a student at the University of Canterbury joins us a PhD student. She will study, using a combination of computational methods, the effects of post-translational modifications on the dynamics and function of chromatin-binding proteins. Welcome Jordan! We all hope you'll enjoy the much warmer Auckland weather!
  • After few weeks of isolation and caution, moving across few emergency levels NZ has been declared Covid19-free and we are "back in business"! Looking forward to the start of few more projects in the upcoming weeks!

APRIL 2020

  • We have all moved into our "bubbles" to stop the spread of Covid-19 in New Zealand. However, we are all working remotely to cope as best as we can with the current situation still having fun with Science!

MARCH 2020

  • Vanessa Ung joins the lab! She will complete her Hons investigating the behavior of some intrinsically disordered proteins in very peculiar microenvironments!! Welcome Vanessa!
  • Welcome to Lynne Sun, which joins the lab for her Hons! Lynne will design and test the stability of new sequences 'evolved' from natural proteins via co-evolutionary approaches. Welcome to the lab!