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António M. Baptista Lab

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The Molecular Simulation Laboratory uses theoretical and computational methods to study the atomic-level determinants of the properties of (bio)chemical molecules. The methods are based on physical principles and intend to derive/simulate molecular behavior from those principles.

 

António M. Baptista
Principal Investigador
PhD in 1998, UNL, Portugal

Phone (+351) 214469619
Extension 1619
baptista@itqb.unl.pt

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Research Interests

We put a strong emphasis on the development of novel methods tailored for biomolecules, which are then applied to cases of biological interest. Many of our studies focus on the study of processes with an electrostatic basis, such as the structural consequences of the uptake/release of protons and electrons in proteins.

A major line of work is the inclusion in simulation methods of experimentally important parameters that are essentially electrostatic, such as pH, ionic strength and reduction potential of the solution. This made possible the detailed study of the structural changes induced by pH on several peptides and proteins, as well as the investigation of the coupling between protons and electrons in several redox proteins.

Other investigated subjects include protein folding/misfolding, peptide dendrimers, characterization of energy landscapes, ligand-induced structural effects, protein partition in two-phase aqueous systems, and the interaction of peptides and proteins with biological membranes

 

Group Members

  • Sara Campos, postdoctoral fellow
  • Dragana Barros, postdoctoral fellow
  • Pedro Magalhães, PhD student

 

Selected Publications

  1. Filipe, L. C. S., Machuqueiro, M., Baptista, A. M. (2011) "Unfolding the conformational behavior of peptide dendrimers: Insights from molecular dynamics simulations." Journal of the American Chemical Society, 133:5042-5052.
  2. Campos, S. R. R., Machuqueiro, M., Baptista, A. M. (2010) "Constant-pH molecular dynamics simulations reveal a β-rich form of the human prion protein." J. Phys. Chem. B, 114:12692-12700.
  3. Machuqueiro, M., Baptista, A. M. (2009) "Molecular dynamics at constant pH and reduction potential: application to cytochrome c3."  Journal of the American Chemical Society 131(35):12586-12594.

     

Laboratory's Website

For further information please visit the laboratory's website

 

Simulação Molecular (PT)

O Laboratório de Simulação Molecular estuda o funcionamento das moléculas usando métodos computacionais. Esses métodos baseiam-se nas leis físicas que governam os átomos e moléculas, permitindo simular o seu comportamento. Tais simulações tornam possível investigar processos cujo estudo experimental é difícil, demorado, ou mesmo impossível. Assim, por exemplo, se quisermos entender a nível molecular de que modo uma proteína realiza a sua tarefa no nosso organismo, a simulação pode dar-nos pistas sobre quais as partes da proteína directamente envolvidas nessa tarefa, bem como as consequências da modificação dessas partes. Uma das principais linhas de trabalho do Laboratório de Simulação Molecular é o desenvolvimento de métodos computacionais para estudar o efeito do pH no comportamento das moléculas. Esses e outros métodos são depois usados para entender as bases moleculares de vários processos de interesse biológico, médico ou tecnológico.

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