BioMolEng Lab

Biomolecular Engineering Lab

mimiclab

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  

Alfonso Gautieri, PhD

Assistant Professor
Molecular Dynamics

Tel.: +39-02-2399-3515
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Simone Vesentini, PhD

Associate Professor
Molecular Dynamics

Tel.: +39-02-2399-3375
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Monica Soncini, PhD

Associate Professor
Molecular Dynamics

Tel.: +39-02-2399-3336
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Postdocs  

Federica Rigoldi, PhD

Research Fellow
Molecular Dynamics

Tel.: +39-02-2399-3327
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PhD Students  

Francesca Donnaloja, MSc

PhD Candidate
Molecular Mechanotransduction

Tel.: +39-02-2399-4729
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Lorenzo Sori, MSc

PhD Candidate
Amyloidogenic Peptides

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

  1. 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.

  2.  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).

  3.  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.

  4.  F. Rigoldi, P. Metrangolo, A. Redaelli, A. Gautieri. 2017. Nanostructure and stability of calcitonin amyloids. Journal of Biological Chemistry 292, 7348-7357.

  5.  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.

  6.  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.

  7.  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.

  8.  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.

  9. 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).

  10.  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

  11.  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.

  12.  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.

  13.  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.

  14.  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.

  15.  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


 

Massachusetts Institute of Technology, USA

Collaborations on: Multi-scale modeling of collagen

Contacts | Prof. MJ Buehler


 

Yokohama National University, Japan

Collaborations on: Synthesis and characterization of peptidic Self-Assembled Monolayers

Contacts | Prof. J Fukuda


 

Weizmann Institute of Science, Israel

Collaborations on: In silico protein design

Contacts | Prof. SJ Fleishman


   

ETH Zurich, Switzerland

Collaborations on: Effect of age-induced glycation on collagen mechanics

Contacts | Prof. J Snedeker


   

Italian Institute of Technology, Italy

Collaborations on: Crystallography and enzyme experimental characterization

Contacts | Prof. E Parisini 


Università Bicocca, Italy

Collaborations on:Synthesis and characterization of brush-like mechanoresponsive molecules

Contacts | Prof. L Cipolla 


http://www.biomech.polimi.it/images/CB-lab/Logos/lumc_01.png

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.


http://www.biomech.polimi.it/images/CB-lab/Logos/lumc_01.png

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.


 

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)

  

Open positions

........ coming soon!

 

Contacts and Location

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Building 21 – Via Golgi 39 – Phone: +39-02-2399-3515

 
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