José Arcadio Farías Rico

Systems Biology and Synthetic Biology Laboratory Researcher

Assistant Professor

Academic history

https://www.fariaslab.org/

Research

Protein evolution and the effect of the ribosome on the proteome

The ribosome is the cellular factory that synthesizes all proteins, the functional agents of life. To become functional, proteins fold into unique three-dimensional shapes and they do so within the ribosomal exit tunnel. The explosion of ribosomal structural information has challenged the classical view that the ribosomal exit tunnel is only a passive channel that secretes proteins. The tunnel is emerging as an active zone that provides a specific microenvironment for proteins to fold and evolve. Yet, we still lack basic knowledge on the evolutionary and biophysical forces acting in the exit tunnel. Therefore, I propose to study the interplay between the ribosome and the proteome to uncover how different sequence and structural motifs impact the process of cotranslational folding and evolution of the protein structures. This basic knowledge can be applied in a wide range of synthetic biology experiments, from protein engineering to the discovery of novel antibiotics. In our studies we combine bioinformatics and experimental approaches. The questions we try to answer are:

Is it possible to detect folding intermediates in natural and designed protein structures?

Is it possible to engineer the ribosome based on evolutionary information to modulate the folding of proteins?

Can we establish specie-specific structural determinants within the exit tunnel that
improve the expression of target proteins?

Biography

Jose Arcadio finished a bachelor in Biology (Sciences Faculty) and a Master’s in Biochemistry (Dr. Lorenzo Segovia, Biotechnology Institute) both at the National Autonomous University of Mexico. Later on he moved to Germany for his doctoral work on protein design and evolution under the supervision of Prof. Birte Höcker in the Max Planck Institute (campus Tübingen). During his PhD training he became experienced in structural biology and bioinformatics. After Germany, he moved to Stockholm Sweden for his post doctoral work to study the folding of proteins in the ribosome under the supervision of Prof. Gunnar von Heijne. During his post-doctoral training he acquired experience to study the folding of proteins in vivo and became experienced on synthetic biology techniques. Currently he is a member of the national system of researchers (SNI, candidate “c”) and on November 2019 he started a position as a Associate Professor in the Systems and Synthetic Biology Laboratory from the Center for genome Sciences (UNAM).

Links

http://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=A0852225
https://www.nature.com/articles/nchembio.1579
https://phys.org/news/2014-07-protein-evolution-modular-principle.html
https://www.pnas.org/content/115/40/E9280.long
Google Scholar

Selected publications

Nat Chem Biol. 2014
Evolutionary relationship of two ancient protein superfolds.
Farías-Rico JA, Schmidt S, Höcker B.

Proc Natl Acad Sci U S A. 2018
Effects of protein size, thermodynamic stability, and net charge on cotranslational folding on the ribosome.
Farías-Rico JA, Ruud Selin F, Myronidi I, Frühauf M, von Heijne G.

Telephone: (777) 3291686
Email: jafarias@ccg.unam.mx

Publications

YearPublicationPMID
2020Ferruz N, Lobos F, Lemm D, Toledo-Patino S, Farías-Rico JA, Schmidt S, Höcker B. (2020). "Identification and Analysis of Natural Building Blocks for Evolution-Guided Fragment-Based Protein Design.". Journal Of Molecular Biology. 432(13):3898-3914. [doi:10.1016/j.jmb.2020.04.013]32330481