Antonio Baptista | Oregon Health & Science University (original) (raw)

Papers by Antonio Baptista

Atmosphere Ocean, Jan 1, 1996

Canadian Journal of Fisheries and Aquatic Sciences, 2010

... analyses, to correctly assess restoration efforts and inform adaptive management experi-ments... more ... analyses, to correctly assess restoration efforts and inform adaptive management experi-ments in the freshwater environment (Anderson 1997; Hil ... By predicting conditions off the river mouth, the simulation capabilities made available by CORIE potentially provide an effective ...

AIAA Guidance, Navigation, and Control Conference and Exhibit, 2001

In this paper we present a method for optimal control of a nonlinear highly realistic helicopter ... more In this paper we present a method for optimal control of a nonlinear highly realistic helicopter model based on a combination of a neural network (NN) feedback
controller and a state-dependent Riccati equation (SDRE) controller. Optimization of the NN is performed within a receding horizon model predictive control (MPC)
framework, subject to dynamic and kinematic constraints. The SDRE controller utilizes a simplified 6DOF rigid body dynamic model, and augments the NN controller by providing an initial feasible solution and improving stability. While the SDRE control provides robustness based on a pseudo-linear formulation of the dynamics, the MPNC utilizes the highly accurate numerical helicopter model.

... António M. Baptista a , Corresponding Author Contact Information , E-mail The Corresponding A... more ... António M. Baptista a , Corresponding Author Contact Information , E-mail The Corresponding Author , Yinglong Zhang a , Arun Chawla a , Mike Zulauf a , Charles Seaton a , Edward P. Myers III a , b , John Kindle c , Michael Wilkin a , Michela Burla a and Paul J. Turner a. ...

Proteins, 2004

The tetraheme cytochrome c 3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reduci... more The tetraheme cytochrome c 3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c 3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using highresolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redoxcooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II. Proteins 2004;54:135-152.

The Journal of Physical Chemistry B, Apr 30, 2012

A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of s... more A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals. 1 To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl − and Cs + ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs + can be used to find the binding sites of cations like Na + and K + , which, unlike Cs + , have physiological and biotechnological roles. The Na + Cl − is more stable than the Cs + Cl − ion pair, decreasing the probability of interaction between Cl − and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium. a This methodology is described in detail in the Supporting Information. b The method that was used to randomly distribute the ions in these simulations is described in the Supporting Information. c To make sure that the ions that were initially randomly distributed in solution (far from the protein) would have enough time to reach the protein surface and explore a large number of binding sites, and given that in water simulations the enzyme is stable, five replicates of 50 ns were used, amounting to a total of 250 ns, which enables a good sampling.

Journal of the American Chemical Society, Mar 1, 2011

We present here the first comprehensive structural characterization of peptide dendrimers using m... more We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five thirdgeneration peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.

ABSTRACT Background/Question/Methods Many populations of Pacific salmon in modified watersheds ar... more ABSTRACT Background/Question/Methods Many populations of Pacific salmon in modified watersheds are not meeting recovery goals, and conservation efforts would benefit from a better understanding of factors limiting productivity. We combined field, laboratory, and modeling approaches to evaluate the relative importance of “bottom-up” (production-limited) and “top-down” (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined characteristics (length, mass, and condition) of juveniles (age 0+) collected in the coastal ocean during two periods (June and September) across 11 years (1998 to 2008). Interannual variation in marine growth during the summer was also estimated. The relationships between seasonal and interannual variation in juvenile attributes and environmental conditions within the river, plume, and coastal ocean during early marine residence were determined. Multi-model inference and regression analysis were used to evaluate which factors explained the most variation in subsequent adult returns. Results/Conclusions There was no evidence of direct resource limitation, i.e., juvenile body condition displayed a negative relationship with indicators of ocean productivity. Furthermore, mean body condition of juveniles after their first ocean summer was significantly lower during high survival years, which likely indicates top-down effects or competition. A multivariate model that incorporated key physical (plume volume during freshwater emigration) and biological (body condition of juveniles) variables and their interaction hindcast interannual variation in survival with a high level of accuracy (>95%). Our analysis provides evidence that top-down effects, such as selective mortality, or competition influence upper Columbia River summer/fall Chinook salmon juveniles during early marine residence. These observations also indicate that interannual variation in abundance for this population, which migrates >4000 ocean km, may be well-established by the end of their first ocean summer. Future research and management efforts should focus on evaluating potential predators and competitors and understanding how plume structure influences survival.

The Journal of Physical Chemistry B, Mar 1, 2006

A new implementation of the stochastic titration method for constant-pH molecular dynamics is pre... more A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.

Journal of Chemical Theory and Computation, 2015

Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effec... more Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effects on the structure and dynamics of soluble biomolecules like peptides and proteins. However, addressing such effects on lipid membrane assemblies has remained problematic until now, despite the important role played by lipid ionization at physiological pH in a plethora of biological processes. Modeling (de)protonation events in these systems requires a proper consideration of the physicochemical features of the membrane environment, including a sound treatment of solution ions. Here, we apply our recent CpHMD-L method to the study of pH effects on a 25% DMPA/DMPC bilayer membrane model, closely reproducing the correct lipid phases of this system, namely, gel-fluid coexistence at pH 4 and a fluid phase at pH 7. A significant transition is observed for the membrane ionization and mechanical properties at physiological pH, providing a molecular basis for the well-established role of phosphatidic acid (PA) as a key player in the regulation of many cellular events. Also, as reported experimentally, we observed pH-induced PA-PA lipid aggregation at acidic pH. By including the titration of anionic phospholipids, the current methodology makes possible to simulate lipid bilayers with increased realism. To the best of our knowledge, this is the first simulation study dealing with a continuous phospholipid bilayer with pH titration of all constituent lipids.

Journal of chemical information and modeling, Jan 26, 2015

Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl ch... more Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl chains that plays a crucial role in the formation and stabilization of the pulmonary surfactant reservoirs during the compression and expansion steps of the respiratory cycle. Although its function is known to be tightly related to its highly hydrophobic character and key interactions maintained with specific lipid components, much is left to understand about its molecular mechanism of action. Also, although it adopts a mainly helical structure while associated with the membrane, factors as pH variation and deacylation have been shown to affect its stability and function. In this work, the conformational behavior of both the acylated and deacylated SP-C isoforms was studied in a DPPC bilayer under different pH conditions using constant-pH molecular dynamics simulations. Our findings show that both protein isoforms are remarkably stable over the studied pH range, even though the acylated is...

Frontiers of Earth Science, 2015

The Journal of Physical Chemistry B, 2001

The present article discusses some aspects concerning the inclusion of proton isomerism in simula... more The present article discusses some aspects concerning the inclusion of proton isomerism in simulations of the global protonation equilibrium of protein molecules. In the context of continuum electrostatic methods, the usual basis for these simulations, this isomerism can be treated as a coexistence of tautomeric forms in equilibrium in a rigid structure; furthermore, it can be formally extended to nontitrable sites with proton isomerism, such as alcohol groups and water molecules. We follow the previously adopted approach of transforming the real system of tautomeric sites into a thermodynamically equivalent one of nontautomeric pseudosites, establishing a proper relation between the two systems. The necessary energetic and entropic modifications of model compound pK a values are also discussed. Additionally, we discuss the new entropy term, named tautomeric entropy, that results from the explicit inclusion of tautomerism in the simulations and how it can be computed together with the occupational entropy. Simulations using tautomerism were done for hen egg white lysozyme (HEWL) using a simple set of tautomers at dihedral energy minima. A very good overall prediction of pK a values was obtained, presumably the best in the literature for HEWL, using a high value for the dielectric constant assigned to the protein region, p . The explicit inclusion of water molecules treated under the extended tautomer formalism further improved the prediction, in contrast with previous works using rigid water molecules. In all calculations performed, the region with p ≈ 20 is shown the to be the optimal one. Some aspects of the somewhat controversial issue of the "proper" p value are also discussed.

Journal of Chemical Theory and Computation, 2015

Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose ionization a... more Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose ionization and, consequently, intermolecular interactions are strongly dependent on the solution pH. The titration curve of these molecules was already obtained using different experimental methods, which have shown the lipid bilayer assemblies to be stable between pH 7.0 and 9.0. In this work, we take advantage of our recent implementations of periodic boundary conditions in Poisson−Boltzmann calculations and ionic strength treatment in simulations of charged lipid bilayers, and we studied the ionization dependent behavior of an oleic acid bilayer using a new extension of the stochastic titration constant-pH MD method. With this new approach, we obtained titration curves that are in good agreement with the experimental data. Also, we were able to estimate the slope of the titration curve from charge fluctuations, which is an important test of thermodynamic consistency for the sampling in a constant-pH MD method. The simulations were performed for ionizations up to 50%, because an experimentally observed macroscopic transition to micelles occurs above this value. As previously seen for a binary mixture of a zwitterionic and an anionic lipid, we were able to reproduce experimental results with simulation boxes usually far from neutrality. This observation further supports the idea that a charged membrane strongly influences the ion distribution in its vicinity and that neutrality is achieved significantly far from the bilayer surface. The good results obtained with this extension of the stochastic titration constant-pH MD method strongly supports its usefulness to sample the coupling between configuration and protonation in these types of biophysical systems. This method stands now as a powerful tool to study more realistic lipid bilayers where pH can influence both the lipids and the solutes interacting with them.

Atmosphere Ocean, Jan 1, 1996

Canadian Journal of Fisheries and Aquatic Sciences, 2010

... analyses, to correctly assess restoration efforts and inform adaptive management experi-ments... more ... analyses, to correctly assess restoration efforts and inform adaptive management experi-ments in the freshwater environment (Anderson 1997; Hil ... By predicting conditions off the river mouth, the simulation capabilities made available by CORIE potentially provide an effective ...

AIAA Guidance, Navigation, and Control Conference and Exhibit, 2001

In this paper we present a method for optimal control of a nonlinear highly realistic helicopter ... more In this paper we present a method for optimal control of a nonlinear highly realistic helicopter model based on a combination of a neural network (NN) feedback
controller and a state-dependent Riccati equation (SDRE) controller. Optimization of the NN is performed within a receding horizon model predictive control (MPC)
framework, subject to dynamic and kinematic constraints. The SDRE controller utilizes a simplified 6DOF rigid body dynamic model, and augments the NN controller by providing an initial feasible solution and improving stability. While the SDRE control provides robustness based on a pseudo-linear formulation of the dynamics, the MPNC utilizes the highly accurate numerical helicopter model.

... António M. Baptista a , Corresponding Author Contact Information , E-mail The Corresponding A... more ... António M. Baptista a , Corresponding Author Contact Information , E-mail The Corresponding Author , Yinglong Zhang a , Arun Chawla a , Mike Zulauf a , Charles Seaton a , Edward P. Myers III a , b , John Kindle c , Michael Wilkin a , Michela Burla a and Paul J. Turner a. ...

Proteins, 2004

The tetraheme cytochrome c 3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reduci... more The tetraheme cytochrome c 3 is a small metalloprotein with ca. 13,000 Da found in sulfate-reducing bacteria, which is believed to act as a partner of hydrogenase. The three-dimensional structure of the oxidized and reduced forms of cytochrome c 3 from Desulfovibrio desulfuricans ATCC 27774 at pH 7.6 were determined using highresolution X-ray crystallography and were compared with the previously determined oxidized form at pH 4.0. Theoretical calculations were performed with both structures, using continuum electrostatic calculations and Monte Carlo sampling of protonation and redox states, in order to understand the molecular basis of the redox-Bohr and cooperativity effects related to the coupled transfer of electrons and protons. We were able to identify groups that showed redox-linked conformational changes. In particular, Glu61, His76, and propionate D of heme II showed important contributions to the redoxcooperativity, whereas His76, propionate A of heme I, and propionate D of heme IV were the key residues for the redox-Bohr effect. Upon reduction, an important movement of the backbone region surrounding hemes I and II was also identified, that, together with a few redox-linked conformational changes in side-chain residues, results in a significant decrease in the solvent accessibility of hemes I and II. Proteins 2004;54:135-152.

The Journal of Physical Chemistry B, Apr 30, 2012

A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of s... more A recent X-ray structure has enabled the location of chloride and cesium ions on the surface of subtilisin Carlsberg in acetonitrile soaked crystals. 1 To complement the previous study and analyze the system in solution, molecular dynamics (MD) simulations, in acetonitrile, were performed using this structure. Additionally, Cl − and Cs + ions were docked on the protein surface and this system was also simulated. Our results indicate that chloride ions tend to stay close to the protein, whereas cesium ions frequently migrate to the solvent. The distribution of the ions around the enzyme surface is not strongly biased by their initial locations. Replacing cesium by sodium ions showed that the distribution of the two cations is similar, indicating that Cs + can be used to find the binding sites of cations like Na + and K + , which, unlike Cs + , have physiological and biotechnological roles. The Na + Cl − is more stable than the Cs + Cl − ion pair, decreasing the probability of interaction between Cl − and subtilisin. The comparison of water and acetonitrile simulations indicates that the solvent influences the distribution of the ions. This work provides an extensive theoretical analysis of the interaction between ions and the model enzyme subtilisin in a nonaqueous medium. a This methodology is described in detail in the Supporting Information. b The method that was used to randomly distribute the ions in these simulations is described in the Supporting Information. c To make sure that the ions that were initially randomly distributed in solution (far from the protein) would have enough time to reach the protein surface and explore a large number of binding sites, and given that in water simulations the enzyme is stable, five replicates of 50 ns were used, amounting to a total of 250 ns, which enables a good sampling.

Journal of the American Chemical Society, Mar 1, 2011

We present here the first comprehensive structural characterization of peptide dendrimers using m... more We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five thirdgeneration peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles. A more detailed analysis is then performed using dissimilarity measures, principal coordinate analysis, and free energy landscapes, with the aim of identifying groups of similar conformations. The results point to a high conformational flexibility of these molecules, with no clear "folded state", although two markedly distinct behaviors were found: one of the dendrimers displayed mostly compact conformations clustered into distinct basins (rough landscape), while the remaining dendrimers displayed mainly noncompact conformations with no significant clustering (downhill landscape). This study brings new insight into the conformational behavior of peptide dendrimers and may provide better routes for their functional design. In particular, we propose a yet unsynthesized peptide dendrimer that might exhibit enhanced ability to coordinate aquocobalamin.

ABSTRACT Background/Question/Methods Many populations of Pacific salmon in modified watersheds ar... more ABSTRACT Background/Question/Methods Many populations of Pacific salmon in modified watersheds are not meeting recovery goals, and conservation efforts would benefit from a better understanding of factors limiting productivity. We combined field, laboratory, and modeling approaches to evaluate the relative importance of “bottom-up” (production-limited) and “top-down” (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined characteristics (length, mass, and condition) of juveniles (age 0+) collected in the coastal ocean during two periods (June and September) across 11 years (1998 to 2008). Interannual variation in marine growth during the summer was also estimated. The relationships between seasonal and interannual variation in juvenile attributes and environmental conditions within the river, plume, and coastal ocean during early marine residence were determined. Multi-model inference and regression analysis were used to evaluate which factors explained the most variation in subsequent adult returns. Results/Conclusions There was no evidence of direct resource limitation, i.e., juvenile body condition displayed a negative relationship with indicators of ocean productivity. Furthermore, mean body condition of juveniles after their first ocean summer was significantly lower during high survival years, which likely indicates top-down effects or competition. A multivariate model that incorporated key physical (plume volume during freshwater emigration) and biological (body condition of juveniles) variables and their interaction hindcast interannual variation in survival with a high level of accuracy (>95%). Our analysis provides evidence that top-down effects, such as selective mortality, or competition influence upper Columbia River summer/fall Chinook salmon juveniles during early marine residence. These observations also indicate that interannual variation in abundance for this population, which migrates >4000 ocean km, may be well-established by the end of their first ocean summer. Future research and management efforts should focus on evaluating potential predators and competitors and understanding how plume structure influences survival.

The Journal of Physical Chemistry B, Mar 1, 2006

A new implementation of the stochastic titration method for constant-pH molecular dynamics is pre... more A new implementation of the stochastic titration method for constant-pH molecular dynamics is presented, which introduces ionic strength effects in the simulations. In addition, the new implementation uses a faster molecular dynamics algorithm and an improved treatment of protonation events and of their effect on force field parameters. This new methodology is applied to a decalysine peptide, yielding very good quantitative agreement with experiments, both in terms of titration and helix-coil transition. The results show a significant dependence on ionic strength, illustrating the importance of including this parameter in constant-pH molecular dynamics simulations. Overall, the method seems to properly capture the protonation-conformation coupling and its dependence on ionic strength.

Journal of Chemical Theory and Computation, 2015

Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effec... more Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effects on the structure and dynamics of soluble biomolecules like peptides and proteins. However, addressing such effects on lipid membrane assemblies has remained problematic until now, despite the important role played by lipid ionization at physiological pH in a plethora of biological processes. Modeling (de)protonation events in these systems requires a proper consideration of the physicochemical features of the membrane environment, including a sound treatment of solution ions. Here, we apply our recent CpHMD-L method to the study of pH effects on a 25% DMPA/DMPC bilayer membrane model, closely reproducing the correct lipid phases of this system, namely, gel-fluid coexistence at pH 4 and a fluid phase at pH 7. A significant transition is observed for the membrane ionization and mechanical properties at physiological pH, providing a molecular basis for the well-established role of phosphatidic acid (PA) as a key player in the regulation of many cellular events. Also, as reported experimentally, we observed pH-induced PA-PA lipid aggregation at acidic pH. By including the titration of anionic phospholipids, the current methodology makes possible to simulate lipid bilayers with increased realism. To the best of our knowledge, this is the first simulation study dealing with a continuous phospholipid bilayer with pH titration of all constituent lipids.

Journal of chemical information and modeling, Jan 26, 2015

Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl ch... more Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl chains that plays a crucial role in the formation and stabilization of the pulmonary surfactant reservoirs during the compression and expansion steps of the respiratory cycle. Although its function is known to be tightly related to its highly hydrophobic character and key interactions maintained with specific lipid components, much is left to understand about its molecular mechanism of action. Also, although it adopts a mainly helical structure while associated with the membrane, factors as pH variation and deacylation have been shown to affect its stability and function. In this work, the conformational behavior of both the acylated and deacylated SP-C isoforms was studied in a DPPC bilayer under different pH conditions using constant-pH molecular dynamics simulations. Our findings show that both protein isoforms are remarkably stable over the studied pH range, even though the acylated is...

Frontiers of Earth Science, 2015

The Journal of Physical Chemistry B, 2001

The present article discusses some aspects concerning the inclusion of proton isomerism in simula... more The present article discusses some aspects concerning the inclusion of proton isomerism in simulations of the global protonation equilibrium of protein molecules. In the context of continuum electrostatic methods, the usual basis for these simulations, this isomerism can be treated as a coexistence of tautomeric forms in equilibrium in a rigid structure; furthermore, it can be formally extended to nontitrable sites with proton isomerism, such as alcohol groups and water molecules. We follow the previously adopted approach of transforming the real system of tautomeric sites into a thermodynamically equivalent one of nontautomeric pseudosites, establishing a proper relation between the two systems. The necessary energetic and entropic modifications of model compound pK a values are also discussed. Additionally, we discuss the new entropy term, named tautomeric entropy, that results from the explicit inclusion of tautomerism in the simulations and how it can be computed together with the occupational entropy. Simulations using tautomerism were done for hen egg white lysozyme (HEWL) using a simple set of tautomers at dihedral energy minima. A very good overall prediction of pK a values was obtained, presumably the best in the literature for HEWL, using a high value for the dielectric constant assigned to the protein region, p . The explicit inclusion of water molecules treated under the extended tautomer formalism further improved the prediction, in contrast with previous works using rigid water molecules. In all calculations performed, the region with p ≈ 20 is shown the to be the optimal one. Some aspects of the somewhat controversial issue of the "proper" p value are also discussed.

Journal of Chemical Theory and Computation, 2015

Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose ionization a... more Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose ionization and, consequently, intermolecular interactions are strongly dependent on the solution pH. The titration curve of these molecules was already obtained using different experimental methods, which have shown the lipid bilayer assemblies to be stable between pH 7.0 and 9.0. In this work, we take advantage of our recent implementations of periodic boundary conditions in Poisson−Boltzmann calculations and ionic strength treatment in simulations of charged lipid bilayers, and we studied the ionization dependent behavior of an oleic acid bilayer using a new extension of the stochastic titration constant-pH MD method. With this new approach, we obtained titration curves that are in good agreement with the experimental data. Also, we were able to estimate the slope of the titration curve from charge fluctuations, which is an important test of thermodynamic consistency for the sampling in a constant-pH MD method. The simulations were performed for ionizations up to 50%, because an experimentally observed macroscopic transition to micelles occurs above this value. As previously seen for a binary mixture of a zwitterionic and an anionic lipid, we were able to reproduce experimental results with simulation boxes usually far from neutrality. This observation further supports the idea that a charged membrane strongly influences the ion distribution in its vicinity and that neutrality is achieved significantly far from the bilayer surface. The good results obtained with this extension of the stochastic titration constant-pH MD method strongly supports its usefulness to sample the coupling between configuration and protonation in these types of biophysical systems. This method stands now as a powerful tool to study more realistic lipid bilayers where pH can influence both the lipids and the solutes interacting with them.