Dynamics of biological processes

Dynamics of biological processes

Gustavo Fuertes Vives

Gustavo Fuertes Vives — Project head

The Institute of Biotechnology of the Czech Academy of Sciences

About us

The aim of this Project is to understand how light controls the structure, dynamics and activity of photosensitive proteins.

Mission and vision

The aim of this Project is to understand how light controls the structure, dynamics and activity of photosensitive proteins. We focus on transcription factors that interact with specific sequences of DNA in a light-dependent manner (EL222, CarH, CooA). Photon absorption by the embedded chromophores triggers conformational changes in the protein chain that ultimately alter protein-protein and protein-DNA interaction networks in the cell. Our plan is to unveil the molecular details of photoswitching between “dark” and “light” states on time scales ranging from femtoseconds to hours. The acquired knowledge will allow us to create novel photoreceptors for use in areas like synthetic biology, photopharmacology and optogenetics.

Methods

We employ an integrative 4D structural biology approach combining methods with distinct spatial and temporal resolution:

  • Molecular biology:
    • Molecular cloning, protein production & engineering. 
    • Site-specific isotopic labeling (SSIL).
    • Genetic code expansion (GCE) technology to incorporate non-canonical amino acids.
  • Steady-state and time-resolved biophysical methods:
    • Femtosecond-stimulated Raman spectroscopy (FSRS).
    • 1D and 2D-infrared spectroscopy (2D-IR).
    • Fluorescence spectroscopy (FRET, FCS and FA).
    • Small-angle neutron (SANS) and X-ray scattering (SAXS).
  • Computational methods:
    • Density functional theory (DFT).
    • Quantum mechanics / molecular mechanics (QM / MM).
    • Molecular dynamics (MD).

Objectives

  • Molecular basis of photocontrolled protein-protein and protein-DNA interactions.
  • Development of GCE technology for the site-specific labeling of proteins.
  • Analysis of photoinduced processes in biomolecules using advanced computational tools.
  • Elucidation of vibrational energy transfer pathways in biomolecules.

News

Publications

2023

Liu, Y.; Chaudhari, A.S.; Chatterjee, A.; Andrikopoulos, P.C.; Picchiotti, A.; Rebarz, M.; Kloz, M.; Lorenz-Fonfria, V.A.; Schneider, B.; Fuertes, G. Sub-Millisecond Photoinduced Dynamics of Free and EL222-Bound FMN by Stimulated Raman and Visible Absorption Spectroscopies. Biomolecules 2023, 13, 161. https://doi.org/10.3390/biom13010161

Chaudhari, A.S.; Chatterjee, A.; Domingos, C.A.O.: Andrikopoulos, P. C.; Liu, Y.; Andersson, I.; Schneider, B.; Lórenz-Fonfría, V.A.; Fuertes, G. Genetically Encoded Non-canonical Amino Acids Reveal Asynchronous Dark Reversion of Chromophore, Backbone and Side-chains in EL222. Protein Science. 2023 https://doi.org/10.1002/pro.4590

Pham, P.N.; Zahradnik, J.; Kolarova, L.; Schneider, B.; Fuertes, G. Regulation Of IL-24/IL-20R2 Complex Formation Using Photocaged Tyrosines and UV Light. Front. Mol. Biosci. 2023, 10. https://doi.org/10.3389/fmolb.2023.1214235

 

Fuertes, G.; Sakamoto, K.; Budisa, N. Editorial: Exploring and expanding the protein universe with non-canonical amino acids. Front. Mol. Biosci. 2023, 10. https://doi.org/10.3389/fmolb.2023.1303286

2022

Chaudhari, A.S.; Chatterjee, A.; Domingos, C.A.O.: Andrikopoulos, P. C.; Liu, Y.; Andersson, I.; Schneider, B.; Lórenz-Fonfría, V.A.; Fuertes, G. Genetically Encoded Non-canonical Amino Acids Reveal Asynchronous Dark Reversion of Chromophore, Backbone and Side-chains in EL222. bioRxiv 2022. https://doi.org/10.1101/2022.09.16.506679

2021

Andrikopoulos, P. C.; Chaudhari, A.S.; Liu, Y.; Konold, P.E.; Kennis, J.T.M.; Schneider, B.; Fuertes, G. QM Calculations Predict the Energetics and Infrared Spectra of Transient Glutamine Isomers in LOV Photoreceptors. Phys. Chem. Chem. Phys. PCCP 2021. https://doi.org/10.1039/d1cp00447f.

Pham, P. N.; Huličiak, M.; Biedermannová, L.; Černý, J.; Charnavets, T.; Fuertes, G.; Herynek, Š.; Kolářová, L.; Kolenko, P.; Pavlíček, J.; Zahradník, J.; Mikulecky, P.; Schneider, B. Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. Viruses 2021, 13 (2). https://doi.org/10.3390/v13020190.

 
2020

Andrikopoulos P. C.; Liu Y.; Picchiotti A.; Lenngren N.; Kloz M.; Chaudhari A. S.; Precek M.; Rebarz M.; Andreasson J.; Hajdu J.; Schneider B.; Fuertes G.; Femtosecond-to-Nanosecond Dynamics of Flavin Mononucleotide Monitored by Stimulated Raman Spectroscopy and Simulations, PCCP 2020, https://doi.org/10.1039/C9CP04918E

2019

Fuertes, G., Nevola, L., and Esteban-Martin, S. (2019). Perspectives on drug discovery strategies based on IDPs in Intrinsically Disordered Proteins: Dynamics, Binding, and Function, Academic Press, pp. 275-327. https://doi.org/10.1016/B978-0-12-816348-1.00009-0

2018

Fuertes, G., Banterle, N., Ruff, K.M., Chowdhury, A., Pappu, R.V., Svergun, D.I., and Lemke,E.A (2018). Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.” Science 361 (6405). https://doi.org/10.1126/science.aau8230

2017

Fuertes, G., Banterle, N., Ruff, K.M., Chowdhury, A., Mercadante, D., Koehler, C., et al. (2017). Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc. Natl. Acad. Sci. 114, E6342–E6351. https://doi.org/10.1073/pnas.1704692114

Team

Gustavo Fuertes Vives Gustavo Fuertes Vives

Gustavo Fuertes Vives

Junior Researcher and Head of Program “Dynamics of Biological Processes”

gustavo.fuertes@ibt.cas.cz
+420325873741
prof. Ing. Bohdan Schneider, CSc., DSc prof. Ing. Bohdan Schneider, CSc., DSc

prof. Ing.
Bohdan Schneider, CSc., DSc

Director, Institute of Biotechnology CAS,
Head of Structural Biology and Protein Engineering Program,
Head of the Intermolecular Recognition of Proteins and Nucleic Acids Group

bohdan.schneider@ibt.cas.cz
+420325873701
Aditya Suresh Chaudhari Aditya Suresh Chaudhari

Aditya Suresh Chaudhari

Postdoc

adityasuresh.chaudhari@ibt.cas.cz
+420325873741
Aditi Chatterjee Aditi Chatterjee

Aditi Chatterjee

PhD student

aditi.chatterjee@ibt.cas.cz
+420325873741
Mgr. Phuong Ngoc Pham Mgr. Phuong Ngoc Pham
Jiří Kozma Jiří Kozma

Teaching

Are you interested in working on a project to gain molecular insights into the biology of photoactive proteins?

Currently, there are opportunities to join our team as a PhD student, Master's student or Bachelor's. Students will have the opportunity to work on multidisciplinary projects and to train in wet and dry lab approaches to study light-induced phenomena in biomolecules like electron / proton / energy transfer, conformational changes, folding transitions, allosterism and hierarchical assembly. Students are expected to be highly motivated to work on challenging research questions in an international team and collaborative environment.

Please contact Gustavo Fuertes to discuss your project ideas. Applicants are encouraged to get in touch with additional suggestions of project directions.

Alumni

thesis author thesis name thesis type term
Aditya Suresh Chaudhari Structural dynamics of the light-sensitive transcription factor EL222 Ph.D. 10/2018-11/2023
Annemarie Klette Recovery kinetics of EL222 Internship (DAAD Rise Worldwide) 08-10/2023
Carolina Filipe Rodrigues Compilation of the properties of genetically encoded non-canonical amino acidcs for the future development of a database Erasmus+ internship 03-07/2023
Heba Halimeh Electronic structure calculations and spectroscopy of biologically relevant chromophores Internship (DAAD Rise Worldwide) 08-10/2022
Edel Cunill Semanat Monitoring light-induced biological phenomena by advanced optical microscopy methods Visiting scholar 07-12/2021
Gina Göritz Preparation and spectroscopic analysis of variants of the light-sensitive protein EL222 Erasmus+ internship 10/2020-03/2021
Natalie Huhn Photobiology of the "non-canonical" DNA-binding EL222 protein Internship (DAAD Rise Worldwide) 08-09/2019
Catarina Alexandra Oliveira Domingos Photobiology of light-sensitive transcription factors Master 03-07/2019

Offered topics

thesis author thesis name thesis type
Aditi Chatterjee Vibrational structural biology of “non-canonical” photoreceptors PhD (IN PROGRESS)
Beatriz Palma Recovery kinetics of EL222 Erasmus+ internship (IN PROGRESS)
Photoxenoprotein engineering for time-resolved structural biology Internship (DAAD Rise Worldwide)

Collaboration

BIOCEV

This Project has a close collaboration with the “Intermolecular Recognition of Proteins and Nucleic Acids” (Bohdan Schneider), “Structure of Medically and Biotechnologically Important Enzymes” (Jan Dohnalek), and "Structural Bioinformatics of Proteins" (Jiri Cerny) Projects. We make extensive use of in-house facilities like the Center of Molecular Structure, the Imaging Methods Core Facility, and the Service Technology Laboratory.

Czech Republic.

Together with the ELI Beamlines laser facility (Institute of Physics CAS, Dolni Brezany), we are part of the ELIBIO (Structural Dynamics of Biomolecular Systems) Project led by Janos Hajdu. The ELIBIO team explores new frontiers in light and optics to create breakthrough science in biology, chemistry and physics.

Overseas.

Our group has access to large-scale research infrastructures to perform cutting-edge experiments including SANS (Institute Laue Langevin, France), SAXS (the European Molecular Biology Laboratory, Germany) and time-resolved spectroscopy (LaserLab Amsterdam, The Netherlands). We have exciting collaborations with research groups worldwide:

- Janos Hajdu (ELI Beamlines, Czech Republic): Principal investigator of ELIBIO Project

- C.S. Raman (University of Maryland, USA): CO-binding transcription factors (CooA)

- S. Padmanabhan “Padhu” (Institute of Physical Chemistry Rocasolano CSIC, Spain): Cobalamin-binding transcription factors (CarH)

- Frank Bernhard (University of Frankfurt, Germany): Cell-free protein expression

- Pau Bernadó (Centre de Biochimie Structurale, France): Site-specific isotopic labelling

- Bernhard Brutscher (Institut de Biologie Structurale, France): laser-triggered NMR spectroscopy

- Anne Martel (Institut Laue Langevin, France): Small-angle neutron scattering

- Miroslav Kloz (ELI ERIC, Czech Republic): Ultrafast spectroscopy

- Víctor Lórenz-Fonfría (University of Valencia, Spain): Maximum entropy and Bayesian methods

- Andreas Möglich (University of Bayreuth, Germany): Photobiochemistry