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Susana’s research experience

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PhD candidate

Feb 2014  to present
Theoretical and Computational Chemistry Group
Institut of Advanced Chemistry of Catalonia (IQAC), Spanish Council for Scientific Research (CSIC)
Barcelona, Spain
Thesis title: Structural and computational study of the intrinsically disordered protein p15PAF
Supervisor: Dr. Ramon Crehuet, IQAC-CSIC
Tutor: Dr. Fermín Huarte Larrañaga, University of Barcelona
Collaborator: Dr. Alfredo De Biasio, University of Leicester
Theme: Description of intrinsically disordered proteins by integrating NMR and SAXS data into simulations coarse grained

Three short scientific stays abroad with Pau Bernadó, Rohit V. Pappu and João P.G.L.M. Rodrigues (see bellow)

Molecular dynamics (MDs) studies of the human Proliferating Cell Nuclear Antigen (PCNA) with Gromacs

MDs studies of the human PCNA sliding on DNA with Gromacs

Study of the molecular mechanism of PCNA sliding on DNA by the combination of experimental (Nuclear Magnetic Resonance and Crystallography) and computational (MD) data

MDs studies of the interaction between PCNA and the intrinsically disordered protein p15PAF (PCNA Associated Factor p15) with Gromacs

MDs studies of the human PCNA sliding on DNA in the presence of p15PAF with Gromacs

Improvement of the SAXS (Small-angle X-ray scattering) theoretical curve provided by the CRYSOL program. Optimization of the calculation of the theoretical curve of SAXS for intrinsically disordered proteins

Cooperativity studies in α-helix formation in polyAlanine peptides of different lengths using theoretically calculated NMR parameters, such as the RDCs (Residual Dipolar Couplings) using the Flexible-Meccano

PhD student in international training

Sep 2018 (2 weeks)
Michael Levitt Lab
Group of Structural Biology, School of Medicine, Stanford University
Stanford, CA, USA
Supervisor: Dr. João P.G.L.M. Rodrigues
Collaborator: Dr. João M. C. Teixeira
Theme: Simulation of a multicomponent system with OpenMM

PDB file preparation via pdb-tools pipeline, optimization of calculation conditions and molecular dynamic calculations with OpenMM: application to the case of a system with three different components (globular protein, intrinsically disordered protein and DNA)

PhD student in international training

Sep 2016 to Dec 2016 (3 months)
Pappu Lab
Laboratory of Computational Biophysics and Molecular Engineering, Department of Biomedical Engineering, Washington University in Saint Louis
Saint Louis, MO, USA
Supervisor: Dr. Rohit V. Pappu
Collaborator: Dr. Lucía Beatriz Chemes, National University of San Martín, Argentina
Theme: Function studies of the disordered linker of Adenovirus early region 1A protein (E1A)

Optimization of calculation conditions and molecular dynamic calculations of intrinsically disordered regions with Campari: application to the case of different E1A linker of different viral species

Analysis of molecular dynamics and different parameters obtained with Campari

Study of the correlation between sequence length and chain dimensions in intrinsically disordered regions

Study of the sequence properties influence (composition and patterning) on the dimensions of an intrinsically disordered region

PhD student in international training

Apr 2015 to Jul 2015 (4 months)
Structure and function of highly flexible proteins Group
Department of Structural Biology, Structural Biochemistry Center (CBS), National Center for Scientific Research (CNRS)
Montpellier, France
Supervisor: Dr. Pau Bernadó
Theme: NMR studies on the effect of high pressure on intrinsically disordered protein

Ensemble characterization of the unstructured C-terminal domain of the Beta-2 Adrenergic Receptor (b2ar)

Assignment of high-pressure NMR spectra of the b2ar’s C-ter domain

Assignment of high-pressure NMR spectra of the b2ar’s C-ter domain with MTSL paramagnetic tag

Calculation of Paramagnetic Relaxation Enhancement values of b2ar’s C-ter domain

Calculation of Paramagnetic Relaxation Enhancement values of b2ar’s C-ter domain with MTSL paramagnetic tag

Study of the different populations of conformers of b2ar’s C-ter domain at different pressures

Study of the effect of pressure at the structural level on an intrinsically disordered protein

Research assistant

Jan 2012 to Jan 2014 (2 years and 1 month)
Organometallic Compounds in the Environment Group
Institute of Environmental Assessment and Water Research (IDAEA), Spanish Council for Scientific Research (CSIC)
Barcelona, Spain
Supervisor: Dr. Sergi Diez
Theme: The Audouin seagull (Larus audouinii) as a mercury biomarker in the protected area of ​​the Delta del Ebro Natural Park

Protocol design and optimization for liquid-liquid extraction of methylmercury in biological and environmental samples and subsequent determination of mercury by atomic absorption spectroscopy (AAS)

Correlation studies of the amount of mercury in the Ebro River and the activity of the Ercros factory in the town of Flix

Study of the mercury uptake into the food chain: Audouin’s gull eggs as a biomarker

Study of the mercury/methylmercury ratio and correlation with the order of egg deposition in the laying of Audouin’s gull

Correlation studies of the amount of mercury in Audouin’s gull eggs and the kind of diet of the mother

Correlation studies of the amount of mercury in Audouin’s gull eggs and the feeding site of the mother

Researcher

Apr 2008 to Jun 2011 (3 years and 3 months)
Víctor Muñoz’s Group (currently in UC Merced – Muñoz Lab)
Department of Physical-Chemical Biology, Biological Research Center (CIB), Spanish Council for Scientific Research (CSIC)
Madrid, Spain
Supervisor: Dr. Eva de Alba
Theme: Structural and biophysics studies of programmed cell death

Optimization of protocols for cloning, expression and purification of proteins

Optimization of protein purification protocols with a high degree of aggregation

Study of the disruption of protein aggregates with different methods

Protein aggregation studies by NMR and analytical ultracentrifugation

Optimization of the sample preparation protocol for NMR of protein transmembrane domains by the use of detergents and other membrane mimics

Tuning of samples and various 1D, 2D, 3D and 4D NMR experiments, acquisition of 1D, 2D, 3D and 4D NMR experiments and structural determination of the cytosolic domain of the Harakiri protein, the transmembrane domain of Harakiri protein and the NLRP3 protein

Biophysical and structural study of the interacting death domain BH3 of different members of Bcl-2 family

Biophysical and structural study of protein transmembrane domains of different members of BH3-only subfamily of Bcl-2 family

Structural and functional study of tryptophan in protein transmembrane domains

Study and characterization of the interaction between Diva protein and Harakiri protein, two Bcl-2 members

Management of purchases of laboratory material and reagents

Maintenance and set-up of laboratory equipment

Research assistant

Aug 2007 to Mar 2008 (8 months)
Enrique Villar’s Group
Department of Biochemistry and Molecular Biology, University of Salamanca
Salamanca, Spain
Supervisor: Dr. Valery L. Shnyrov
Theme: Thermal stability of peroxidase from Chamaerops excelsa palm tree

Extraction and purification of vegetable proteins

Determination of the isoelectric point (pI) of proteins

Acid-base and temperature protein titrations by UV-visible spectroscopy, fluorescence spectroscopy and circular dichroism (CD)

Molecular kinetics studies of enzymes

Biophysical study and protein stability of peroxidases

Pregaduate student in training

Oct 2006 to Jul 2007 (10 months)
Protein NMR Group
Department of Biological Physics Chemistry, Institute of Physical Chemistry “Rocasolano” (IQFR), Spanish Council for Scientific Research (CSIC)
Madrid, Spain
Supervisor: Dr. María Ángeles Jiménez and Dr. José Manuel Pérez Cañadillas
Theme: NMR study of vascular endothelial growth factor (VEGF), signalling protein involved in vasculogenesis and angiogenesis

Design and synthesis of plasmids aimed at the overexpression of proteins in the cytosol, in the periplasmic space and for the excretion to the extracellular medium in different bacterial strains of E. coli, design and synthesis of plasmids for the expression and stabilization of rapid degradation proteins

Protein cloning, expression and purification

Refolding of proteins

Pregaduate student in training

Sep 2006 (1 month)
1st Program of Initiation to Research in Chemistry-Physics and Chemistry-Biological Physics
Protein NMR Group
Department of Biological Physics Chemistry, Institute of Physical Chemistry “Rocasolano” (IQFR), Spanish Council for Scientific Research (CSIC)
Madrid, Spain
Supervisor: Dr. María Ángeles Jiménez and Dr. Marta Bruix
Theme: Structural determination of proteins by NMR

NMR study of β-hairpins folded peptides

Other work experience

Pregaduate student in apprenticeship in Company

Jun 2005 to Aug 2005 (3 months)
Apprenticeship Program in Company of the University of Salamanca
Aquimisa, S.L.
Department of Physical Chemistry
Salamanca, Spain
Supervisor: Ana María López Oreja
Theme: Physic-chemical analysis, quality control and traceability control

Physic-chemical analysis of food samples from different Spanish supermarkets, agricultural products of the region and waters of different origins (rivers, sewage treatment plants, industries, water wells), and quality control of the Protected Designation of Origin “Jamón de Guijuelo”

With a scholarship awarded by the Regional Government (Junta de Castilla y León)

Private tutoring

Sep 2000 to Jun 2005 (5 school years)
Private teacher
Salamanca, Spain

I taught private classes in physics, chemistry and mathematics to more than ten primary and secondary students.

I taught private classes in two academies. The subjects were physics, chemistry and mathematics for primary and secondary students, and Organic Chemistry, Physical Chemistry and Physics for university students.

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