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Protein Modelling

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The Protein Modelling Laboratory works on molecular modelling of proteins using physical methods. Our areas of work range from basic research in modelling methodologies to applications with biotechnological and biomedical interest. 

 

 

Cláudio M. Soares
Professor Associado
PhD 1994 in Theoretical Biochemistry, Univ. Lisboa / Uppsala University

Phone (+351) 214469610 | Extension 1610
claudio@itqb.unl.pt

 

Research Interests

The Protein Modelling Laboratory works on molecular modelling of proteins using physical methods. Our areas of work range from basic research in modelling methodologies to applications with biotechnological and biomedical interest. Modelling redox proteins and redox chains is one of our research interests, and one of the most relevant examples is the work on hydrogenases, which are enzymes that catalyse the reversible molecular hydrogen cleavage into electrons and protons. We study molecular hydrogen permeation towards the internal active site, using molecular dynamics simulations, as well as proton transfer within the protein, using continuum electrostatic and Monte Carlo calculations. In collaboration with other groups at ITQB we are trying to understand the mechanism of laccases at the molecular level, as well as their engineering. Studying enzymes in non-aqueous solvents is another important area in our laboratory, with focus on the molecular mechanisms of enzyme hydration, enantioselectivity, imprinting and catalysis. The non-aqueous solvents studied include ionic liquids, and we were the first to simulate protein molecules within this media, clarifying the molecular reasons for stability. ABC transporters constitute a new topic to our laboratory. Our first work on the subject was on the NBD1-NBD association in CTFR, the chloride transporter involved in cystic fibrosis, one of the most common genetic diseases. We built structural models for this association, responsible for ATP hydrolysis, and used them to understand the effect of mutations on disease causing genotypes. To study how these molecular machines work, we turn to prokaryotic ABC transporters and in particular NBD dimers. We recently published a paper on the conformational changes involved in ATP hydrolysis, and their consequences on substrate translocation. Other studies on complete transporters are on the way.

 

Group Members

  • Bruno Victor, Post-doc
  • Ana Sofia Oliveira, PhD student
  • Diana Lousa, PhD student
  • João M. Damas, PhD student
  • Carla Baltazar, Research Student
  • Joana Vaz, Research Student (also affiliated with the Structural Genomics lab)

 

Selected Publications

  1. Oliveira, ASF, Baptista, AM, Soares, CM (2010) “Insights into the ATP-hydrolysis mechanism of an ABC-transporter: conformational changes in the NBD dimer of MJ0796”, J Phys Chem B, 114, 5486-5496.
  2. Micaelo, NM, Soares, CM (2008) “Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies”. J.Phys.Chem.B, 112, 2566-2572
  3. Teixeira V. H., Baptista A. M. and Soares C. M. (2006). “Pathways of H2 toward the active site of [NiFe]-hydrogenase.” Biophysical Journal 91(6): 2035-2045

 

Laboratory's Website

For further information please visit the laboratory's website

 

Modelação de Proteínas  (PT)

O Laboratório de Modelação de Proteínas desenvolve investigação na área da simulação física de proteínas, tentando compreender processos biológicos utilizando meios computacionais, ou em colaboração com grupos de investigação experimental. O objectivo final destas investigações é a compreensão da Vida ao nível molecular e atómico, pela simulação dos seus mais pequenos componentes. O trabalho do Laboratório de Modelação de Proteínas centra-se no estudo de proteínas envolvidas em cadeias transportadoras de electrões, e em processos com interesse biotecnológico e biomédico. 

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