Publications by Marta Andreia Da Silva Perez

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

Julien Racle, David Gfeller, Philippe Guillaume Coune, Florence Pojer, Marta Andreia Da Silva Perez, George Coukos, Kelvin Ka Ching Lau, Amédé Noredine Larabi, Alexandre Harari

CD4+T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward ...

CELL PRESS2023

The Structure of the Protonated Serine Octamer

Thomas Rizzo, Ursula Röthlisberger, Aurelien Stephen Arnaud Gregor, Marta Andreia Da Silva Perez, Valeriu Scutelnic, Stephan Warnke, Carsten Baldauf

The amino acid serine has long been known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretica ...

2018

A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein

Rudolf Hovius, Ursula Röthlisberger, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

The development of thermostable and solvent-tolerant metalloproteins is a long-sought goal for many applica- tions in synthetic biology and biotechnology. In this work, we were able to engineer a highly thermo- and organic solvent- stable metallo variant o ...

2018

Genetic-Algorithm-Based Optimization of a Peptidic Scaffold for Sequestration and Hydration of CO

Ursula Röthlisberger, Elizabeth Claire Brunk, Marta Andreia Da Silva Perez

Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profita ...

2016

Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling

Thomas Rizzo, Ursula Röthlisberger, Oleg Aseev, Marta Andreia Da Silva Perez

Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) seq ...

2015

Infrared Spectroscopy of Mobility-Selected H+-Gly-Pro-Gly-Gly (GPGG)

Thomas Rizzo, Ursula Röthlisberger, Antoine Louis Claude Masson, Michael Zachary Kamrath, Marta Andreia Da Silva Perez

We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational famili ...

2015

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Ursula Röthlisberger, Pablo Campomanes Ramos, Elizabeth Claire Brunk, Negar Ashari Astani, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

Through millions of years of evolution, Nature has accomplished the development of highly efficient and sustainable processes and the idea to understand and copy natural strategies is therefore very appealing. However, in spite of intense experimental and ...

2014

Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis

Marta Andreia Da Silva Perez

In this study, we present a detailed characterization of the full α/β interface in the farnesyltransferase (FTase) enzyme, an important target in drug design efforts. This characterization is presented in terms of hot spots, warm spots, and null spots and ...

2011