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.
2019
Zapp C, Obarska-Kosinska A, Rennekamp B, Mercadante D, Barayeu U, Dick TP, Denysenkov V, Prisner T, Bennati M, Daday C, Kappl R, Gräter F (2019). Mechanoradicals in tensed tendon collagen as a new source of oxidative stress. Accepted on Nature Communications.
2018
Zosel F, Mercadante D, Nettels D, Schuler B. (2018). A Proline Switch Explains Kinetic Heterogeneity in a Coupled Folding and Binding Reaction. Nature Communications 9(1):332.
Irani AH, Mercadante D, Williams MAK. (2018). On the Electrophoretic Mobility of Partially Charged Oligosaccharides as a Function of Charge Patterning and Degree of Polymerization. Electrophoresis 39(12), 1497-1503.
Tan PS#, Aramburu IV#, Mercadante D#, Tiagi S, Chowdhury A, Spitz D, Shammas SL, Gräter F, Lemke EA. (2018). Two Differential Binding Mechanisms of FG-Nucleoporins and Nuclear Transport Receptors. Cell Reports, 22(13), 3660-3671.
2017
Sénéchal F, Habrylo O, Hocq L, Domon JM, Marcelo P, Lefebvre V, Pelloux J*, Mercadante D*. (2017). Journal of Biological Chemistry. 292(52), 21538-21547.
Mercadante D*, Wagner JA, Aramburu IV, Lemke EA, Gräter F. (2017). Sampling Long-versus Short-Range Interactions Defines the Ability of Force Fields to Reproduce the Dynamics of Intrinsically Disordered Proteins. Journal of Chemical Theory and Computation 13(9), 3964-3974.
2016
Irani AH, Owen JL, Mercadante D, Williams MAK. (2016). Molecular dynamics illuminate the role of counterion condensation in polyelectrolyte transport. (2017). Biophysical Journal 110(3), 592a.
Dugard CK, Mertz, RA, Rayon C, Mercadante D, Hart C, Benatti MR, Olek AT, San Miguel PJ, Cooper BR, Wolf-Dieter R, McCann MC, Carpita NC. (2016). The cell wall arabinose-deficient Arabidopsis thaliana mutant murus5 encodes defective allele of reversibly glycosylated polypeptide2. Plant Physiology 171(3), 1905-1920.
Tursch A, Mercadante D, Tennigkeit J, Gräter F, Özbek S. (2016). Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules. Scientific Reports 6; 25709.
Kent L, Loo TS, Melton LD, Mercadante D, Williams MAK, Jameson GB. (2016). Structure and properties of non-processive, salt-requiring, acidophilic pectin methylesterases from Aspergillus niger provide insights into the key determinants of processivity control. Journal of Biological Chemistry 291(3), 1289-1306.
2015
Beckmann A, Xiao S. Müller JP, Mercadante D, Nüchter T, Kröger N, Langhojer F, Petrich W, Holstein T, Benoit M, Gräter F, Özbek S. (2015) A fast recoiling silk-like elastomer facilitates nanoseconds nematocyst discharge. BMC Biology 13, 3.
Wagner J, Mercadante D, Nikič I, Lemke EA, Gräter F. (2015). Principles of bio-orthogonality in strain promoted click reactions. Chemistry: A European Journal 21(35), 12431-12435.
2014
2013
Cover Page Biophysical Journal 2013
2012
Cover Page Biophysical Journal 2012
#Equally shared first authorship. *Corresponding authorship**.
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.
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 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.
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.
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.
Group Leader
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?
PhD candidate
Education and training:
BSc Hons: The University of Auckland.
Hometown:
Suva, Fiji.
Favourite activity outside the lab:
Watching reality tv (especially kuwtk and rhobh)
Favourite food:
Anything Japanese
Hons Student
Education and training:
BSc: The University of Auckland.
Hometown:
Shanghai, China.
Favourite activity outside the lab:
Hanging out with friends and family
Favourite food:
Nachos and Sushi
Hons Student
Education and training:
BSc: 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
PhD Student
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
PhD Student
Education and training:
BSc/MSc: Masaryk University (Brno, Czech republic)
Hometown:
Ivaň, Czech republic
Favourite activity when not simulating:
Tramping, mountaineering (newbie), skiing and snowboarding!
Favourite food:
Steak, wine and coffee!
MSc Student
Education and training:
BSc: Shanghai Institute of Technology (Shanghai, China)
Hometown:
Hohot, Inner Mongolia, China
Favourite activity when not simulating:
Listening to (pop!) music
Favourite food:
Hotpot!
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!