(530) 752-6700 – Office
(530) 754-0325 – Lab
Office 2315 GBSF
Ph.D. in Physics, University of Barcelona, Spain 1998
Biomedical Engineering Graduate Group
Biophysics Graduate Group
Computational Characterization and Exploitation of Biological Networks Initiative
Modeling of biological networks and cellular processes
Cells use networks of interactions between molecules and macromolecular assemblies to sense and respond to their environment. Biological networks are extensively regulated and control fundamental cellular processes, including gene expression and signal transduction, in all types of organisms, from bacteria to humans. Disruption of the regulation mechanisms is responsible for many human diseases, such a cancer, diabetes, and autoimmune disorders.
Leonor Saiz’s research involves the study of the dynamics of biological networks at the cellular and molecular level. Dr. Saiz group combines computational and theoretical approaches together with experimental data to (1) understand how cellular behavior arises from the physical properties and interactions of the cellular components; and to (2) infer detailed molecular properties, such as the in vivo DNA mechanics, from the cellular physiology. By developing novel methodologies that consider multiple spatial and temporal scales and multiple levels of biological organization, including atomic, molecular, and cellular, our work has provided new avenues to integrate the molecular properties of cellular components directly into the dynamics of cellular networks. We focus on gene regulation and signal transduction networks, as well as their combined networks, to understand their regulatory mechanisms for proper cell function and how regulation is disrupted in cancer and other diseases. The work of Leonor Saiz group is highly interdisciplinary, drawing from techniques and tools from physics, chemistry, mathematics, computer science, biomedicine, and engineering. The ultimate goal is to understand and follow the impact of molecular perturbations in the cellular components, such as a mutation in a protein or interventions with small molecules or drugs, through the different cellular processes up to the cellular behavior; one of the major challenges of modern biomedical sciences.
L. Saiz and J. M. G. Vilar, Protein-protein/DNA interaction networks: versatile macromolecular structures for the control of gene expression, IET Systems Biology, 2, 247-255 (2008).
L. Saiz and J. M. G. Vilar, Ab initio thermodynamic modeling of distal multisite transcription regulation, Nucleic Acids Research, 36, 726-731 (2008).
L. Saiz and J.M.G. Vilar, Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes, PLoS One, 2(4): e355. doi:10.1371/journal.pone.0000355 (2007).
J.M.G. Vilar and L. Saiz, Multiprotein DNA looping, Phys. Rev. Lett., 96: 238103 (2006).
L. Saiz and J.M.G. Vilar, DNA looping: the consequences and its control, Current Opinion in Structural Biology, 16: 344-350 (2006).
L. Saiz and J.M.G. Vilar, Stochastic dynamics of macromolecular-assembly networks, Nature/EMBO Molecular Systems Biology, 2, doi:10.1038/msb4100061 (2006).
S. Vemparala, L. Saiz, R.G. Eckenhoff, and M.L. Klein, Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles, Biophys. J., 91: 2815-2825 (2006).
L. Saiz, J.M. Rubi, and J.M.G. Vilar, Inferring the in vivo looping properties of DNA, Proc. Natl. Acad. Sci. USA, 102: 17642-17645 (2005).
J.M.G. Vilar and L. Saiz, DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise, Current Opinion in Genetics & Development, 15: 136-144 (2005).
L. Saiz and M.L. Klein, The transmembrane domain of the acetylcholine receptor: Insights from simulations on synthetic peptide models, Biophys. J., 88: 959-970 (2005).
M. Pickholz, L. Saiz, and M.L. Klein, Concentration effects of volatile anesthetics on the properties of model membranes: A coarse-grain approach, Biophys. J., 88: 1524-2534 (2005).
L. Saiz and M.L. Klein, Computer simulation studies of model biological membranes, Acc. Chem. Res., 35: 482-489 (2002).
L. Saiz and M.L. Klein, Influence of highly polyunsaturated lipid acyl chains of biomembranes on the NMR order parameters, J. Am. Chem. Soc., 123: 7381-7387 (2001).
L. Saiz and M.L. Klein, Structural properties of a highly polyunsaturated lipid bilayer from molecular dynamics simulations, Biophys. J., 81: 204-216 (2001).
Major Research Interests
Computational and theoretical approaches to the study of biological networks at the cellular and molecular level. Multiscale and multilevel approaches to study biomolecular processes. Assembly of macromolecular complexes on DNA, membranes, and scaffols. Statistical mechanics basis of gene regulation and signal transduction. Noise in cellular processes. In vivo biomolecular mechanics. Molecular biophysics: membranes, membrane associated proteins, and their interactions with small molecules and drugs.