A study on the mode of action of clinically relevant antimicrobial peptides

Tese de doutoramento, Bioquímica (Biofísica Molecular), Universidade de Lisboa, Faculdade de Ciências, 2010The antimicrobial peptides (AMPs) omiganan (ILRWPWWPWRRK– NH2) and BP100 (KKLFKKILKYL–NH2) were biophysically studied with bacterial and mammalian cell membrane models, essentially using optical spectroscopy techniques. Peptide-membrane binding was interpreted under a Nernst partition formalism. Both peptides strongly prefer the anionic bacterial membrane models over the zwitterionic mammalian ones, justifying, at least in part, higher antibacterial than hemolytic activities. Deviations to the expected binding behavior were observed at high bound peptide-to-lipid (P:L) ratios in the membrane whenever anionic models were used. These deviations could be ascribed to membrane saturation and occurred with both peptides. The saturation threshold could be identified for both peptides; the obtained critical P:L ratios were also consistent with membrane surface charge neutralization. Disruptive events were observed above the saturation threshold: internalization into the membrane (omiganan), leakage, membrane aggregation, membrane surface charge neutralization, and structural reorganization (BP100). The plausibility of high membrane coverage was evaluated using a mathematical model devised to estimate the extent of binding under physiological conditions. Not only is saturation a possible phenomenon but it was also shown to be a potential requirement for peptide activity. This hypothesis could be verified using the model with published data on several AMPs. The model could be further adapted to provide a means to predict, from simple biophysical parameters (a binding constant and a critical P:L ratio), the peptide concentration at which antibacterial activity is triggered. Different methods to implement this prediction are presented.In vivo measurements using BP100 with Escherichia coli were carried out to further test the correlation between membrane saturation and bacterial death. A suitable method to determine the occurrence of binding saturation with bacteria could not be devised. Nonetheless, bacterial surface charge did become neutralized by the peptide at the same concentrations that caused loss of viability, supporting a connection between the phenomena.Fundação para a Ciência e Tecnologia / Foundation for Science and Technology - SFRH/BD/24778/2005; Portuguese National Conference of Rector

Localization Preference of Antimicrobial Peptides on Liquid-Disordered Membrane Domains

We performed coarse-grained simulations of the antimicrobial peptides Magainin-2, BP100, MSI-103, and MSI-78 on a phase-separated membrane to study their preference for the different domains. All the peptides displayed a clear preference for the liquid-disordered (Ld) phase over the liquid-ordered (Lo) one. For BP100, MSI-103, and MSI-78 there was a further preference of the peptides for the domain interface. The peptides' preference toward the disordered phase was shown to reflect a penalization of lipid-lipid interaction enthalpy in the Lo phase, when in the vicinity of peptides. Similar results were observed at the two studied concentrations, although Ld phase saturation at the higher concentration drove some of the peptide excess to the Lo phase. Magainin-2 and MSI-103 were found to dimerize, in agreement with available experimental data. Interestingly, at high concentrations of Magainin-2 toroidal pores spontaneously formed in the Ld phase. We performed additional simulations to characterize this phenomenon, which is likely related to Magainin-2's membranolytic action

The mechanism of action of antimicrobial peptides : lipid vesicles vs. bacteria

Copyright © 2012 Melo and Castanho. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in other forums, provided the original authors and source are credited and subject to any copyright notices concerning any third-party graphics etc.The authors acknowledge the European FP7-PEOPLE-2009-IEF-254559 grant to Manuel N. Melo and the Fundação para a Ciência e a Tecnologia (Portugal) project PTDC/QUI-BIQ/112929/2009

Room for improvement in the initial martini 3 parameterization of peptide interactions

Funding Information: We thank T. Cordeiro for bringing to our attention the coiled coil system that motivated part of this study. J.K.S. acknowledges an internship sponsored by Fundação Luso-Americana para o Desenvolvimento through its Study in Portugal Network. M.N.M. thanks Fundação para a Ciência e a Tecnologia, Portugal for fellowship CEECIND/04124/2017 , and for funding project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020 . Publisher Copyright: © 2023 The AuthorsThe Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.publishersversionpublishe

Two decades of Martini:Better beads, broader scope

The Martini model, a coarse-grained force field for molecular dynamics simulations, has been around for nearly two decades. Originally developed for lipid-based systems by the groups of Marrink and Tieleman, the Martini model has over the years been extended as a community effort to the current level of a general-purpose force field. Apart from the obvious benefit of a reduction in computational cost, the popularity of the model is largely due to the systematic yet intuitive building-block approach that underlies the model, as well as the open nature of the development and its continuous validation. The easy implementation in the widely used Gromacs software suite has also been instrumental. Since its conception in 2002, the Martini model underwent a gradual refinement of the bead interactions and a widening scope of applications. In this review, we look back at this development, culminating with the release of the Martini 3 version in 2021. The power of the model is illustrated with key examples of recent important findings in biological and material sciences enabled with Martini, as well as examples from areas where coarse-grained resolution is essential, namely high-throughput applications, systems with large complexity, and simulations approaching the scale of whole cells. This article is categorized under: Software > Molecular Modeling Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Computational Biochemistry and Biophysics

Pitfalls of the Martini Model

R.A. thanks The Netherlands Organisation for Scientific Research NWO (Graduate Programme Advanced Materials, No. 022.005.006) for financial support. S.T. thanks the European Commission for financial support via a Marie Skłodowska-Curie Actions Individual Fellowship (MicroMod-PSII, grant agreement 748895).The computational and conceptual simplifications realized by coarse-grain (CG) models make them a ubiquitous tool in the current computational modeling landscape. Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. However, there are certain inherent limitations to this approach, which we investigate in detail in this work. We first study the consequences of the absence of specific cross Lennard-Jones parameters between different particle sizes. We show that this lack may lead to artificially high free energy barriers in dimerization profiles. We then look at the effect of deviating too far from the standard bonded parameters, both in terms of solute partitioning behavior and solvent properties. Moreover, we show that too weak bonded force constants entail the risk of artificially inducing clustering, which has to be taken into account when designing elastic network models for proteins. These results have implications for the current use of the Martini CG model and provide clear directions for the reparametrization of the Martini model. Moreover, our findings are generally relevant for the parametrization of any other building block based force field.publishersversionpublishe

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License

Charge-dependent interactions of monomeric and filamentous actin with lipid bilayers

The cytoskeletal protein actin polymerizes into filaments that are essential for the mechanical stability of mammalian cells. In vitro experiments showed that direct interactions between actin filaments and lipid bilayers are possible and that the net charge of the bilayer as well as the presence of divalent ions in the buffer play an important role. In vivo, colocalization of actin filaments and divalent ions are suppressed, and cells rely on linker proteins to connect the plasma membrane to the actin network. Little is known, however, about why this is the case and what microscopic interactions are important. A deeper understanding is highly beneficial, first, to obtain understanding in the biological design of cells and, second, as a possible basis for the building of artificial cortices for the stabilization of synthetic cells. Here, we report the results of coarse-grained molecular dynamics simulations of monomeric and filamentous actin in the vicinity of differently charged lipid bilayers. We observe that charges on the lipid head groups strongly determine the ability of actin to adsorb to the bilayer. The inclusion of divalent ions leads to a reversal of the binding affinity. Our in silico results are validated experimentally by reconstitution assays with actin on lipid bilayer membranes and provide a molecular-level understanding of the actin-membrane interaction.</p