Molecular Modelling and Simulation


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    The study of biologically relevant macromolecules has been for quite some time a challenge for researchers. In recent years, molecular modeling and simulation is the field of research that probably has more enthusiastically contributed with information at the atomic level.
    Here, at the MMS Group, we are very interested in the study of the dynamic properties of proteins and lipid bilayers under different conditions of pH, ionic strength, temperature, redox potential and solvent composition. In particular, we are currently engaged in the following projects:


    Inclusion of pH effects in molecular modelling of lipid bilayers

    The lipid bilayer is the basic structural component of biological membranes. Membrane protein function is often strongly affected by the chemical and physical properties of the bilayer, which in turn depend on the composition of lipids and their complex interactions at the molecular level. Kyotorphin A detailed description of a lipid bilayer at the atomic level has to take in consideration all important factors that affect in some way the membrane behavior and stability. pH is recognizably one of these factors even though it is usually forgotten due to the high complexity in terms of modeling. Changes in pH are usually associated with (de)protonation in key titrable groups present in the polar head of some phospholipids that constitute the bilayer. The resulting changes in the electrostatic environment will influence strongly the very structure of the bilayer allowing for the appearance of certain phenomena, like lipid phase transition and microdomain formation. Our objective is to apply the constant-pH MD methodology to the study of lipid protonation in bilayers.


    Cardiolipin-rich lipid bilayers: the "acid-anion" formation at neutral pH


    Cardiolipins (CLs) constitute an exceptional class of lipids. Unlike most of the other lipid types, CLs are anionic lipids with four acyl chains. CLs have two acidic sites that can be ionized. The protonation state of CLs is still a matter of debate and both single and double charged CLs have been proposed. This uncertainty seems to arise from difficulties in determining its charge, since it depends on pH and on environmental factors such as the concentration of CLs. A high pKa2 (>7.0) has been proposed on a potentiometric titration and has been associated with an internal "acid-anion" conformation. This high pKa value, inevitably influences our understanding of its conformation in bilayers. These features are very important in the ability of CL to play its role in ATP synthesis. Disruption of the molecule's key features that allow for this mechanism can result in the inability for CL to perform its biological function. Inefficient CLs have been associated with the Barth's syndrome disease. Even though many of these theories and mechanisms have been proposed over 25 years ago, there are still many questions regarding the way lipids exchange protons in their bilayer environment. One major hurdle is that many of the studies performed are technically very difficult to perform in a biological membrane or, sometimes, even in a simple bilayer model. Molecular modeling has also not been able to help us rationalize these mechanisms mainly due to limitations in the available methodologies. Our approach aims to solve this problem.


    Study of the folding properties of peptide dendrimers

    Dendrimer

    Peptide dendrimers are a specific kind of dendrimers which are formed by alternating functional amino acids with branching diamino acids (see Figure). One major advantage of peptide dendrimer over de novo linear peptides in mimicking protein structure/function is the ability to predict and control their folded structure. Most dendritic peptides are topologically constrained to adopt a more globular shape. In this way, simple protein-like structures can be created where functions such as catalysis or molecular recognition occur by constructive interactions between amino acids as in natural proteins.


    Study of the pH induced misfolding and possible reversibility of the human prion protein

    The human prion protein (hPrP) is associated with the Creutzfeldt-Jakob disease and other amyloid diseases known as transmissible spongiform encephalopathies. The normal form of PrP is monomeric and solube but can be transformed Prion Protein into a misfolded beta-rich form (see Figure) which aggregates and forms amyloid fibrils. This transition can be induced by decreasing the pH and is thought to be caused "in vivo" by the low pH of endosomes. We are currently studying the possible reversibility of this transition using constant-pH MD simulations of misfolded hPrP conformations at neutral pH.


    Charge parameterization in united atom force fields using QM and QM/MM methodologies

    Cytochrome c3
    DesulfoVibrio Vulgaris Hildenborough cytochrome c3 (DvHc3) is a small (~14 kDa) globular and monomeric tetraheme protein (see Figure). It is constituted by 107 residues plus four hemes covalently bound to cysteines in the polypeptide chain together with bis-histidinyl axial ligation. DvHc3 redox titration using constant-(pH/E) MD revealed very strong electrostatic interactions between the 4 heme groups in the protein, which should be very sensitive to charge parameterization. The objective of this project is to improve this charge parameterization using QM and QM/MM methodologies in order to successfully model the different redox states in constant-(pH,E) MD simulations of multihemic cytochromes.



    Selected Publications: (for a complete list check my personal webpage)


  • pKa values of titrable amino acids at the water/membrane interface, V. H. Teixeira, D. Vila-Viçosa, P. B. P. S. Reis, M. Machuqueiro, J. Chem. Theory Comput., 2016, Accepted http://dx.doi.org/10.1021/acs.jctc.5b01114.

  • Constant-pH molecular dynamics study of kyotorphin in an explicit bilayer, P. R. Magalhães, M. Machuqueiro, A. M. Baptista, Biophys. J., 2015, 108, 2282-2290.

  • Constant-pH MD simulations of an oleic acid bilayer, D. Vila-Viçosa, V. H. Teixeira, H. A. F. Santos, A. M. Baptista, M. Machuqueiro, J. Chem. Theory Comput., 2015, 11, 2367-2376.

  • Molecular details of INH-C10 binding to wt KatG and to its S315T mutant, V. H. Teixeira, C. Ventura, R. Leitão, C. Rafols, E. Bosch, F. Martins, M. Machuqueiro, Mol. Pharmaceutics, 2015, 12, 898-909.

  • Treatment of ionic strength in biomolecular simulations of charged lipid bilayers, D. Vila-Viçosa, V. H. Teixeira, H. A. F. Santos, A. M. Baptista, M. Machuqueiro, J. Chem. Theory Comput., 2014, 10, 5483-5492.

  • Influence of activated carbons porous structure on iopamidol adsorption, A. S. Mestre, M. Machuqueiro, M. Silva, R. Freire, I. M. Fonseca, S. C. S. Santos, M. J. Calhorda, A. P. Carvalho, A.P., Carbon, 2014, 77, 607-615.

  • Protonation of DMPC in a bilayer environment using a linear response approximation, V. H. Teixeira, D. Vila-Viçosa, A. M. Baptista, M. Machuqueiro, J. Chem. Theory Comput., 2014, 10, 2176-2184.

  • A simulated intermediate state for folding and aggregation provides insights into ΔN6 β2-microglobulin amyloidogenic behavior, S. G. Estácio, H. Krobath, D. Vila-Viçosa, M. Machuqueiro, E. I. Shakhnovich, P. F. N. Faísca, PLoS Comput. Biol., 2014, 10, e1003606.

  • Conformational Study of GSH and GSSG Using Constant-pH Molecular Dynamics Simulations, D. Vila-Viçosa, V. H. Teixeira, H. A. F. Santos, M. Machuqueiro, J. Phys Chem. B, 2013, 117, 7507-7517.

  • Charge Parametrization of the DvH-c3 Heme Group: Validation Using Constant-(pH,E) Molecular Dynamics Simulations, J. Henriques, P. J. Costa, M. J. Calhorda, M. Machuqueiro, J. Phys. Chem. B, 2013, 117, 70-82.

  • Reversibility of Prion Misfolding: Insights from Constant-pH Molecular Dynamics Simulations, D. Vila-Viçosa, S. R. R. Campos, A. M. Baptista, M. Machuqueiro, J. Phys. Chem. B, 2012, 116, 8812-8821.

  • Indenyl ring slippage in crown thioether complexes [IndMo(CO)2L]+ and C-S activation of trithiacyclononane: Experimental and theoretical studies, C. A. Gamelas, N. A. G. Bandeira, C. C. L. Pereira, M. J. Calhorda, E. Herdtweck, M. Machuqueiro, C. C. Romão, L. F. Veiros, Dalton Trans., 2011, 40, 10513.

  • Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations, Filipe, L. C. S., Machuqueiro, M., Baptista, A. M., J. Am. Chem. Soc., 2011, 133, 5042-5052.

  • Molecular Dynamics at Constant pH and Reduction Potential: Application to Cytochrome c3, M. Machuqueiro, A. M. Baptista, J. Am. Chem. Soc. 2009, 131, 12586-12594.


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