Computational design of peptide-based architectures for protein recognition

Sala 1.4.14, FCUL, Lisboa

Por Sara Fortuna (University of Trieste, Italy).

Abstract: An ideal binder should be capable of capturing with high affinity, sensitivity, and specificity a target molecule. Examples include antibodies and nanobodies optimised in vivo, DNAs and RNAs based aptamers evolved in vitro, and small peptides optimised in silico by exploiting advances in computer power together with the development of new and powerful algorithms for protein folding, docking, and structure prediction. A recent algorithm based on replica exchange Monte Carlo [1] can optimize simultaneously the sequence and conformation of small peptides in order to reach a high binding affinity to a target organic molecule. The algorithm was recently adapted for the generation of peptides for protein recognition. The sequences have been tested by surface plasmon resonance and electrospray ionisation mass spectrometry showing how the computer-generated peptides pinpoints the binding site they have been designed for with high affinity [2]. Further developments allow generating peptides with an even higher affinity towards their targets or even picking a surface exposed non-druggable binding site and design ex novo a binder capable of immobilizing a protein on a surface [3]. This has been shown by nuclear magnetic resonance, and atomic force microscopy. The same algorithm has been further implemented for the design of antibody fragments for biomarker recognition [4].

[1] R. P. Hong Enriquez, S.Pavan, F. Benedetti, A. Tossi, A. Savoini, F. Berti, and A. Laio, J. Chem. Theory Comput. 2012 8 (3), 1121-1128.
[2] A. Russo, P.L. Scognamiglio, R.P. Hong Enriquez, C. Santambrogio, R. Grandori, D. Marasco, A. Giordano, G. Scoles, and S. Fortuna, PLoS ONE, 2015, 10(8): e0133571.
[3] M.A. Soler, A. Rodriguez, A. Russo, A. Feyisara Adedeji, C.J. Dongmo Foumthuim, C. Cantarutti, E. Ambrosetti, L. Casalis, A. Corazza, G. Scoles, D. Marasco, A. Laio, and S. Fortuna, Phys. Chem. Chem. Phys., 2017, 19, 2740-2748.
[4] M.A. Soler,et al, in press.

Short bio: Sara Fortuna graduated in Chemistry in 2007 from the University of Trieste (Italy), has been awarded her PhD in Chemistry from Warwick University (UK) in 2010, and carried out postdoctoral activity in SISSA, Trieste (Italy). In 2013 she started her present activity first at the University of Udine (Italy), then Nova Gorica (Slovenia), and SISSA. Aim of her research is to provide novel theoretical solutions to problems of medical and biological interest through the multiscale modeling of molecular systems. In 2017 she moved to the University of Trieste (Italy) where she now coordinates a joint theoretical-experimental activity based on the computational design of antibody fragments for molecular recognition.

Departamento de Física
Logótipo da Unite!

Summer School no âmbito da Rede UNITE! (University Network for Innovation, Technology and Engineering), de que faz parte a ULisboa.

Cartaz do evento

Uma iniciativa com o objetivo de aproximar a ciência dos jovens de todas as idades, com desafios, palestras e muita diversão, num formato inteiramente online!

Primeira edição das Manhãs de Matemática na Aberta, dedicada à Geometria, com a participação de Carlos Florentino (Ciências ULisboa). 

Hi-Phi Seminar, por Lorenzo Baravalle (FCUL, CFCUL) e Maurizio Esposito (FCUL, CIUHCT).

Imagem ilustrativa da sessão

Sessão de homenagem no âmbito da 13.ª Reunião Anual da APG - Associação Portuguesa de Geólogos.

Colóquio de Matemática, por Teresa Monteiro Fernandes (Departamento de Matemática | Ciências ULisboa).

O curso visa apresentar uma série de perspetivas sobre o desenvolvimento conceitual da estatística e sobre o uso de inferências e modelos estatísticos nas ciências empíricas.

Mapa antigo

Workshop internacional associado ao projeto Medea-Chart.

Imagem ilustrativa do curso, acompanhada de várias informações úteis

Um curso dirigido ao público em geral e a estudantes de arte ou ciência (a partir dos 16 anos), com interesse em desenho de observação, ilustração e biologia, com ou sem experiência em desenho.

The objective of this course is to introduce participants to the details of communication and writing scientific publications.

Imagem ilustrativa do programa, acompanhada do respetivo título

Um programa de aceleração de ideias e negócios, promovido pela redeSaúde, com candidaturas até 30 de setembro de 2021.

The objective of this course is to introduce participants to the details of communicating science to non-specialized audiences, including, but not exclusive to, public and private stakeholders, students and teachers, and media professionals.

This course aims to evidence the importance of natural history collections for the study of biodiversity, to show new tools and approaches to extract and disseminate biodiversity data from natural history collections and to increase awareness of young researchers for the scientific and cultural value of Natural History Museums.

The course aims at providing an introduction to stable isotopes ratios as tools to understand global, ecosystem and community level bio/geo cycles; light isotopes: H, N, C, O and S isotopes, geo cycles and ecological significance; sampling and analytical methodologies in stable isotope analysis.

EvoS aims at turning evolutionary theory into a common language to areas that pertain to the natural world, including human affairs.

The course SoilEco aims at introducing attendants to an updated state of the art of diversity of the soil biota and the functional roles played by soil organisms in key ecological processes.

In this course, we promote a multidisciplinary approach presenting the most recent findings on the topic and challenging the traditional way of considering symbiotic associations as exceptions and not as the rule.

The goal of this course is to provide to the participants with current and practical knowledge on urban ecology, including ecological and social aspects.

This course aims to explore ways of communicating science to non-specialized audiences, such as policy makers, industry, general public (including students and teachers), through their engagement and participation in citizen science activities.

This course introduces the field of island biogeography, a discipline that has long influenced other research areas such as macroecology, community ecology, evolution and conservation biology.

Scientists, as the main actors in the production of scientific knowledge, have the responsibility of having an active voice in communicating this knowledge – and that can be achieved for example by a conscious use of the communication tools at their disposal and a better articulation with journalists, among other means.

This course aims at providing students with basic knowledge of R programming, allowing them to manipulate and visualize data with R.

This course aims at providing students with statistical knowledge and tools to manipulate, analyze and visualize biological data with R. It also includes an introduction to modeling, simulations and Bayesian statistics.

Under the general framework of Global Change Ecology, the goal of this course is to provide the participants with the most recent and practical knowledge on the use of Functional Diversity.

The course provides essential skills and knowledge that enable the participants to develop climate change adaptation strategies.