Dynamics of biological processes

Dynamics of biological processes

Gustavo Fuertes Vives

Gustavo Fuertes Vives — Project head

About us

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

We are particularly interested in transcription factors that interact with specific sequences of DNA in a light-dependent manner. We employ a combination of computational (density functional theory, quantum mechanics/molecular mechanics) and time-resolved structural biology techniques, including spectroscopy (infrared, Raman and fluorescence), diffraction (X-ray crystallography) and scattering (small-angle X-ray scattering). This Project has a close collaboration with the “Intermolecular Recognition of Proteins and Nucleic Acids” Project and the “Structure of Medically and Biotechnologically Important Enzymes” Project.

Together with the ELI Beamlines laser facility (Dolni Brezany, Czech Republic), we are part of the ELIBIO (Structural Dynamics of Biomolecular Systems) Project.

Objectives

  • Elucidation of the sequence of molecular events leading to the formation of protein/DNA complexes upon photoexcitation.
  • Development of molecular engineering tools for the site-specific labeling of proteins.
  • Development of computational tools for the analysis of photoinduced processes in proteins and nucleic acids.

Publications

2018

Schneider B, Boaeikova P, Necasova I, Cech P, Svozil D, Cerny J. A DNA structural alphabet provides new insight into DNA flexibility. Acta Crystallogr D Struct Biol. 2018;74(Pt 1):52-64. Epub 2018/01/27. doi: 10.1107/S2059798318000050.

Zahradnik J, Kolenko P, Palyzova A, Cerny J, Kolarova L, Kyslikova E, et al. The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form. PLoS One. 2018;13(4):e0195299. Epub 2018/04/10. doi: 10.1371/journal.pone.0195299.

Fuertes, G.; Banterle, N.; Ruff, K. M.; Chowdhury, A.; Pappu, R. V.; Svergun, D. I.; Lemke, E. A. Comment on “Innovative Scattering Analysis Shows That Hydrophobic Disordered Proteins Are Expanded in Water.” Science 2018, 361 (6405). https://doi.org/10.1126/science.aau8230

2017

Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, et al. Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements. Proc Natl Acad Sci U S A. 2017;114(31):E6342-E51. Epub 2017/07/19. doi: 10.1073/pnas.1704692114.

Schneider B, Bozikova P, Cech P, Svozil D, Cerny J. A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle. Genes (Basel). 2017;8(10). Epub 2017/10/24. doi: 10.3390/genes8100278.

Nguyen HTH, Andrikopoulos PC, Bim D, Rulisek L, Dang A, Turecek F. Radical Reactions Affecting Polar Groups in Threonine Peptide Ions. Journal of Physical Chemistry B. 2017;121(27):6557-69. doi: 10.1021/acs.jpcb.7b04661.

Liu Y, Guchhait B, Siebert T, Fingerhut BP, Elsaesser T. Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations. Struct Dyn. 2017;4(4):044015. Epub 2017/04/14. doi: 10.1063/1.4980075.

2016

Crosas E, Castellvi A, Crespo I, Fulla D, Gil-Ortiz F, Fuertes G, et al. Uridine as a new scavenger for synchrotron-based structural biology techniques. J Synchrotron Radiat. 2017;24(Pt 1):53-62. Epub 2016/12/24. doi: 10.1107/S1600577516018452.

2015

Cerny, Jiri; Biedermannova, Lada; Mikulecky, Pavel; Zahradnik, Jiri; Charnavets, Tatsiana; Sebo, Peter; Schneider, Bohdan; Redesigning Protein Cavities as a Strategy for Increasing Affinity in Protein-Protein Interaction: Interferon-gamma Receptor 1 as a Model; BIOMED RESEARCH INTERNATIONAL; 10.1155/2015/716945; 2015; IF = 1.579

Team

Gustavo Fuertes Vives

Gustavo Fuertes Vives

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

gustavo.fuertes@ibt.cas.cz
+420325873739
doc. Ing. Bohdan Schneider, CSc.

doc. Ing.
Bohdan Schneider, CSc.

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

bohdan.schneider@ibt.cas.cz
+420325873766
Aditya Suresh Chaudhari

Aditya Suresh Chaudhari

PhD Student

adityasuresh.chaudhari@ibt.cas.cz
+420325873739