BioMolEng Lab
Biomolecular Engineering Lab
The Biomolecular Engineering Lab focuses on the investigation and engineering of biomolecules and biomaterials by using molecular modeling simulations.
Molecular modelling provides a virtual microscope, which allows us to investigate the properties of biomolecules in a way which is not possible in laboratory experiments. We use computational simulations to study the structure and properties of proteins and other relevant biomolecules in order to predict their structure when inaccessible with experiments, to investigate key biophysical properties, or to understand the molecular mechanisms of diseases.
Molecular modelling allows us also to rationally design new or improved biomolecules. We develop bioinformatics tools to guide atomistic design of new biomolecular structures and functions, limiting the cost- and time-consuming laboratory trial-and-error procedures. By using computer algorithms we engineer biomolecules to achieve novel or improved feature such as peptides that self-assemble in organized structures or enzymes with improved thermal stability. Experiments in collaborating laboratories are used to validate our designs and computational methods and to highlight areas for improvement in the computational methods.
Research interests
Current research activities include:
- Investigation and engineering of extracellular matrix proteins
- Characterization and design of enzymes
- Investigation of the molecular mechanisms of diseases
- Design of biomaterials for nanobiotechnological applications
Team
Faculties | |
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Assistant Professor Tel.: +39-02-2399-3515 |
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Associate Professor Tel.: +39-02-2399-3375 |
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Associate Professor Tel.: +39-02-2399-3336 |
Postdocs | |
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Research Fellow Tel.: +39-02-2399-3327
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PhD Students | |
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Francesca Donnaloja, MSc PhD Candidate Tel.: +39-02-2399-4729
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Lorenzo Sori, MSc PhD Candidate Tel.: ---
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Master Students | |
Cedric Bourdarias, BSc | |
Alumni | |
2018 Archimede Torretta, Msc Davide Ripamonti, Msc Sara Palladino, Msc Cecilia Brambilla Pisoni, Msc 2017 Irene Cristiani, Msc 2016 Flavia Bonalumi, Msc Francesca Marchese, Msc Ludovica Spero, Msc 2015 Massimo Bagnani, Msc 2014 Alejandro Pando, Msc Vincenzo Colangelo, Msc |
Publications
Selected Publications
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F. Rigoldi, S. Donini, F. Giacomina, F. Sorana, A. Redaelli, T. Bandiera, E. Parisini, A. Gautieri. 2018. Thermal stabilization of the deglycating enzyme Amadoriase I by rational design. Scientific Reports 8, article number 3042.
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F. Rigoldi, S. Donini, A. Redaelli, E. Parisini, A. Gautieri. 2018. Engineering of Thermostable Enzymes for Industrial applications. APL Bioengineering 2, article number 011501 (cover paper).
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E. Bianchi, M. Piergiovanni, C. Arrigoni, J. Fukuda, A. Gautieri, M. Moretti, G. Dubini. 2017. Herringbone-like hydrodynamic structures in microchannels: A CFD model to evaluate the enhancement of surface binding. Medical Engineering and Physics 48, 62-67.
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F. Rigoldi, P. Metrangolo, A. Redaelli, A. Gautieri. 2017. Nanostructure and stability of calcitonin amyloids. Journal of Biological Chemistry 292, 7348-7357.
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J. Enomoto, T. Kageyama, T. Osaki, F. Bonalumi, F. Marchese, A. Gautieri, E. Bianchi, G. Dubini, C. Arrigoni, M. Moretti, J. Fukuda. 2017. Catch-and-Release of Target Cells Using Aptamer-Conjugated Electroactive Zwitterionic Oligopeptide SAM. 2017. Scientific Reports 7:43375.
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A. Gautieri, F. Passini, M. Guizar-Sicairos, G. Carimati, P. Volpi, M. Moretti, A. Redaelli, M. Berli, J.G. Snedeker. 2016. Advanced glycation end-products: mechanics of aged collagen from molecule to tissue. Matrix Biology 59, 95-108.
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A. Apicella, M. Marascio, V. Colangelo, M. Soncini, A. Gautieri, C.J.G. Plummer. 2016. Molecular Dynamics Simulations of the Intrinsically Disordered Protein Amelogenin. Journal of Biomolecular Structure and Dynamics 35, 1813-1823.
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F. Rigoldi, L. Spero, A. Dalle Vedove, A. Redaelli, E. Parisini, A. Gautieri. 2016. Molecular dynamics simulations provide insights into substrate specificity of FAOX family members. Molecular Biosystems 12, 2622-2633.
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F. Rigoldi, A. Gautieri, A. Dalle Vedove, A. Luccarelli, S. Vesentini, E. Parisini. 2016. Crystal Structure of the Deglycating Enzyme Amadoriase I in its Free Form and Substrate-bound Complex. Proteins: Structure, Function and Bioinformatics 84, 744-758 (cover paper).
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JG Snedeker, A. Gautieri. 2014. The role of collagen crosslinks in ageing and diabetes - the good, the bad, and the ugly. Muscles, Ligaments and Tendons Journal 4, 303-308
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L. Russo, A. Sgambato, P. Giannoni, R. Quarto, S. Vesentini, A. Gautieri, A., L. Cipolla. 2014. Response of osteoblast-like MG63 on neoglycosylated collagen matrices. Medchemcomm 5, 1208-1212.
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A.K Nair, A. Gautieri, M.J. Buehler. 2014. Role of Intrafibrillar Collagen Mineralization in Defining the Compressive Properties of Nascent Bone. Biomacromolecules 15, 2494-2500.
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L. Russo, A. Gautieri, M. Raspanti, F. Taraballi, F. Nicotra, S. Vesentini, L. Cipolla. 2014. Carbohydrate-functionalized collagen matrices: design and characterization of a novel neoglycosylated biomaterial. Carbohydrate Research 389, 12-17.
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G. S. Ugolini, A. Gautieri, A. Redaelli, M. Soncini. 2013. Structural analysis and ion translocation mechanisms of the muscle-type acetylcholine receptor channel. Journal of applied biomaterials & functional materials 11, 53-60.
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A. Gautieri, A. Redaelli, M.J. Buehler, S. Vesentini. 2014. Age- and diabetes-related nonenzymatic crosslinks in collagen fibrils: Candidate amino acids involved in Advanced Glycation End-products. Matrix Biology 34, 89-95.
Prizes and Honors
Journal Awards
Cover Paper on APL Bioengineering: F. Rigoldi, S. Donini, A. Redaelli, E. Parisini, A. Gautieri. 2018. Engineering of Thermostable Enzymes for Industrial applications. APL Bioengineering 2, article number 011501.
Cover Paper on Proteins: Structure, Function and Bioinformatics: F. Rigoldi, A. Gautieri, A. Dalle Vedove, A. Luccarelli, S. Vesentini, E. Parisini. 2016. Crystal Structure of the Deglycating Enzyme Amadoriase I in its Free Form and Substrate-bound Complex. Proteins: Structure, Function and Bioinformatics 84, 744-758.
Collaborations
Collaborations
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Massachusetts Institute of Technology, USA Collaborations on: Multi-scale modeling of collagen Contacts | Prof. MJ Buehler |
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Yokohama National University, Japan Collaborations on: Synthesis and characterization of peptidic Self-Assembled Monolayers Contacts | Prof. J Fukuda |
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Weizmann Institute of Science, Israel Collaborations on: In silico protein design Contacts | Prof. SJ Fleishman |
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ETH Zurich, Switzerland Collaborations on: Effect of age-induced glycation on collagen mechanics Contacts | Prof. J Snedeker |
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Italian Institute of Technology, Italy Collaborations on: Crystallography and enzyme experimental characterization Contacts | Prof. E Parisini |
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Università Bicocca, Italy Collaborations on:Synthesis and characterization of brush-like mechanoresponsive molecules Contacts | Prof. L Cipolla |
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Politecnico di Milano Collaborations on: Characterization of amyloid fibrils and halogenated biomolecules Contacts | Prof. P MetrangoloThis email address is being protected from spambots. You need JavaScript enabled to view it. |
Università dell'Insubria Collaborations on: Enzyme characterization Contacts | • Prof. L PollegioniThis email address is being protected from spambots. You need JavaScript enabled to view it. |
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Equipment and available technologies
Equipment
The Biomolecular Engineering Lab is equipped with several local workstations with Nvidia GPUs for modelling and visualization. The Lab has access to the Z3 cluster equipped with state-of-the-heart linux nodes for supercomputing activities (63 nodes for a total of 884 cores, 3056 GB RAM, 2 Nvidia K40, 2 Nvidia K80)
Available software for molecular modelling include Materials Studio, Gromacs, Namd, ACEMD, Rosetta.
Funding
BioMolEng Lab is grateful to the following funders and partners that have supported our research:
Cariplo Foundation
“CollAGEing: understanding and preventing age-related glycation in connective tissues (grant nr. 2016-0481)” - (2017-2020)