Research: Towards a novel docking algorithm: development of new computational methods for the investigation of the molecular mechanisms underlying the interaction among proteins
PHD THESIS:
Title: Towards a novel docking algorithm: development of new computational methods for the investigation of the molecular mechanisms underlying the interaction among proteins
This project focuses on the development of new computational methods to understand the molecular mechanisms underlying protein interactions, which is fundamental for the prediction of binding regions, and consequently for drug-ability and design.
Binding regions are known to display a combination of geometrical and chemical matches, which allow distant proteins to recognize themselves in the crowded cellular environment. Some of these characteristics (e.g., their preferentially hydrophobic composition and their shape complementarity) are well established. Other features are still being investigated to improve the characterization of the binding. However, this also results in higher computational costs.Thus, the final objective is addressing these two important challenges in computational biology: identifying the interfaces in reasonable computational times and determining the most efficient parameters to predict protein-protein interaction. With this aim, we want to develop a computational method to predict protein interactions by quickly verifying the complementarity of as many features as possible by means of the Zernike polynomials expansion.
Thematic area: Structural biology
SSD: FIS/07
EDUCATION:
- PhD student in Life Science. University La Sapienza, in collaboration with the Center for Life Nanoscience & Neuro-Science, Fondazione Istituto Italiano di Tecnologia Viale Regina Elena 291, 00161 Rome, Italy (Rome, starting from November 2021).
- Master degree (English courses) in Applied Physics. University of Bologna, 110/110 cum laude (Bologna, September 2021).
Master degree thesis: A novel computational strategy for defining the minimal protein molecular surface representation.
Advisors: Prof. G.Ruocco, Prof. A.Bazzani. Co-advisors: Dr. E.Milanetti.
(Bologna University, Center for Life Nano-science & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy).
- Bachelor’s degree in Physics. University of Trieste, 104/110 (Trieste, September 2019).
Bachelor’s degree thesis: Causalità di Wiener-Granger applicata a serie temporali estratte da C. elegans.
Supervisors: Prof. E.Milotti, Prof. L.Rigon and Dr. V.Folli.
(Trieste University, Center for Life Nano-science & Neuro-Science, Fondazione Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy).
PUBLISHED PAPERS:
- D’Antoni C, Mautone L, Sanchini C, Tondo L, Grassmann G, Bezzi P, Cordella F, Di Angelantonio S. Unlocking Neural Function with 3D In Vitro Models: A Technical Review of Self-Assembled, Guided, and Bioprinted Brain Organoids and Their Applications in the Study of Neurodevelopmental and Neurodegenerative Disorders. International Journal of Molecular Sciences. 2023 May. https://doi.org/10.3390/ijms241310762
- Grassmann G, Miotto M, Di Rienzo L, Gosti G, Leonetti M, Ruocco G, Milanetti E. Electrostatic complementarity at the interface drives transient protein-protein interactions. Scientific reports. 2023 June. https://doi.org/10.1038/s41598-023-37130-z
- Miotto M, Di Rienzo L, Grassmann G, Desantis F, Gosti G, Leonetti M, Ruocco G, Milanetti E. Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex. Frontiers in Molecular Biosciences. 2023 June. https://doi.org/10.3389/fmolb.2023.1205919
- Di Rienzo L, Miotto M, Desantis F, Grassmann G, Ruocco G, Milanetti E. Dynamical Changes of SARS-Cov-2 Spike Variants in the Highly Immunogenic Regions Impact the Viral Antibodies Escaping. Proteins: Structure, Function, and Bioinformatics. 2023 April. https://doi.org/10.1002/prot.26497
- Grassmann G, Miotto M, Di Rienzo L, Gosti G, Ruocco G, Milanetti E. A novel computational strategy for defining the minimal protein molecular surface representation. Plos ONE. 2022 April. https://doi.org/10.1371/journal.pone.0266004
- Grassmann G, Miotto M, Di Rienzo L, Salaris F, Silvestri B, Zacco E, Rosa A, Tartaglia GG, Ruocco G, Milanetti E. A Computational Approach to Investigate TDP-43 RNA-Recognition Motif 2 C-Terminal Fragments Aggregation in Amyotrophic Lateral Sclerosis. Biomolecules. 2021 Dec 19;11(12):1905. doi: 10.3390/biom11121905. PMID: 34944548; PMCID: PMC8699346.
- Grassmann G. Letter to the editor of Heliyon re: "New considerations on the validity of the Wiener-Granger causality test." Heliyon. 2020; 6(10): e05208
- Grassmann G. New considerations on the validity of the Wiener-Granger causality test. Heliyon, Volume 6, Issue 10 (2020).
https://doi.org/10.1016/j.heliyon.2020.e05208
SUBMITTED PAPERS:
- Grassmann G, Miotto M, Di Rienzo L, Gosti G, Desantis F, Ruocco G, Milanetti E. Computational approaches to predict molecular interactions in crowded cellular environments. Chemical Reviews. 2023 January.
FOUNDED RESEARCH PROJECT:
- Progetti per Avvio alla Ricerca - Tipo 1 (1000.00 €)
Towards a novel docking algorithm.
Grassmann G (PI) (University La Sapienza of Rome, November 2023)
- PRIN: progetti di ricerca di rilevante interesse nazionale (190000.00 €)
Coexistence between Ordered and DIsordered Regions in proteins: a multiscale overview on the mechanisms regulating
aggregate-associated diseases (CODIR).
Milanetti E (PI), Parisi V, Giansanti A, Grassmann G, Montemiglio L.C., Mattarelli M, Fioretto D, Passeri AA (March 2023)
- Progetti di Ricerca (Piccoli, Medi) - Progetti Piccoli (3000.00 €)
The role of the electrostatic contribution to the interface of protein complexes: a Zernike polynomial based method.
Milanetti E (PI), Grassmann G (University La Sapienza of Rome, December 2022)
TALK:
- Third MaSBiC Symposium Advances in Protein Science: Exploring Structure, Function, and Beyond: Electrostatic complementarity drives transient protein-protein interactions (Ancona, September 2023).
- Workshop on New Frontiers in Molecular Crowding: A computational approach to investigate TDP-43 RNA-Recognition Motif 2 C-Terminal fragments aggregation in Amyotrophic Lateral Sclerosis (ESRF Grenoble, June 2022)
POSTERS:
- XVI International Workshop on Complex Systems: Electrostatic complementarity evaluation at the protein interfaces: prediction of transient protein-protein interactions (Andalo, March 2023)
- Second DiSVA-MaSBiC Annual Symposium - Protein Structure and Function in Biology, Medicine and Nanotechnology: A computational approach for biomolecular binding characterization: TDP-43 C-terminal fragment aggregation in ALS (Ancona, October 2022)
- Workshop on New Frontiers in Molecular Crowding: A computational approach for biomolecular binding characterization: TDP-43 C-terminal fragment aggregation in ALS (ESRF Grenoble, June 2022)
- The I MASBIC-DISVA annual symposium: A computational approach to investigate TDP-43 C-terminal fragments aggregation in Amyotrophic Lateral Sclerosis (ALS). (Ancona, September 2021).
ATTENDED SEMINARS/MEETINGS:
- Emerging role for m6A RNA modification in cancer: learning from leukemia (online, March 2022).
- Functional and Pathological Interactions of α synuclein (online, March 2022).
- Amino acid metabolism: involvement in tumor progression and new therapeutic approaches (online, March 2022).
- Neurodegenerative Diseases: The Role of TDP-43 in mRNA transport and Localization (online, April 2022).
- Mechanism of a cell wall transporter involved in lipoteichoic acid synthesis and bacterial adaptation (online, April 2022).
- Evolution of Klebsiella pneumoniae high-risk clones to pan-resistance (online, April 2022).
- Architecture of the human erythrocyte ankyrin-1 complex (online, April 2022).
- Metabolic control of T cell immunity (online, April 2022).
- RNA-based therapeutic approaches for neurodegenerative tauopathies (online, May 2022).
- NADPH Oxidase: Structure, Enzymology and Drug Design (online, May 2022).
- When viral RNA met the cell: a story of protein-RNA interactions (online, May 2022).
- Protective / Preventive Role Of Natural Compounds In Human Health: Biochemical Approaches To Target Ageing And Neurodegeneration (online, June 2022).
- New frontiers for molecular crowding (ESRF Grenoble, June 2022).
- Physics of biomolecules: structure, dynamics and function (Bressanone, September 2022).
- Structures and functions of proteins in biology, medicine and nanotechnologies (Ancona, October 2022).
- Engineering Proteins To Boost LTP And Memory (Rome, March 2023).
- Application of deep learning to the protein structure prediction: the tale of a “gigantic leap” (Rome, March 2023).
- Deciphering self-renewal traits in epidermal stem cells (Rome, March 2023).
- Insulin Signaling in Alzheimer’s Disease Brain and Models Thereof (Rome, March 2023).
- Educating tutor-associate macrophages under metabolic stress (Rome, March 2023).
- XVI International Workshop on COMPLEX SYSTEMS (Andalo, March 2023).
- Synthetic Biology: what, why and how (Rome, April 2023).
- Protecting our genome: mechanisms to maintain DNA repeats stability in human cells (Rome, April 2023).
- Regulation of enzymatic activity mediated by liquid-liquid phase separation (Rome, April 2023).
- The chaperonin GroEL nano-machine: allostery and function (Rome, May 2023).
- The axonal transport machinery and its dysfunctions in neurodegenerative diseases (online, May 2023).
- Riboregulation from bacteria to eukaryotes: mechanisms and challenges (Rome, June 2023).
- Third MaSBiC Symposium Advances in Protein Science: Exploring Structure, Function, and Beyond (Ancona, September 2023).
ATTENDED COURSES:
- Fundamentals of Enzyme kinetics (online, February 2022).
- Science Stories: boost your communication techniques by talking and going social (Rome, June 2022).
- Introduction to ML/DL and to Pytorch (online, November 2023).
- From Linear Regression to Deep Models using Neural Networks (online, December 2023).
- Advanced Deep Learning (online, December 2023).
- La Terza Missione dell’Università e il Public Engagement (online, December 2023).
- Etica e Scienza (online, December 2023).
- Fare start-up in Sapienza, istruzioni per l’uso (online, December 2023).
- Catalogo delle pubblicazioni IRIS: finalità e modalità di utilizzo (online, December 2023).
- Valorizzare i risultati della Ricerca: la tutela brevettuale in ambito accademico (online, December 2023).
- Comunicazione e divulgazione scientifica (online, December 2023).
PROGRAMMING SKILLS:
- Matlab
- Python
- C++
LANGUAGES:
- English: IELTS certificate: overall band score: 8.0. CEFR level: C1. (Bologna, December 2020).
- German: basic.