Massimo Marchi - Academia.edu (original) (raw)
Papers by Massimo Marchi
![Research paper thumbnail of Comment on “Efficient stress relaxation in molecular dynamics simulations of semiflexiblen-alkanes” [Phys. Rev. E.58, 6766 (1998)]](https://attachments.academia-assets.com/97161302/thumbnails/1.jpg)
](Physical Review E, 2001
Contrary to the findings of Mülders, Toxvaerd, and Kneller ͓Phys. Rev. E 58, 6766 ͑1998͔͒ ͑MTK͒, ... more Contrary to the findings of Mülders, Toxvaerd, and Kneller ͓Phys. Rev. E 58, 6766 ͑1998͔͒ ͑MTK͒, we are unable to discern any difference in the behavior of long chain alkanes simulated by molecular dynamics at constant pressure using either atomic or molecular scaling schemes. This result confirms our previous study ͓M. Marchi and P. Procacci, J. Chem. Phys. 109, 5194 ͑1998͔͒ on hydrated proteins published at the same time as the MTK's paper. This Comment indicates that errors in the calculation of the pressure tensor might be responsible for at least a part of the MTKs results.
Langmuir, 2016
The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We... more The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water to surfactant number ratios ranging from W o = to 16. The aggregation number, i.e., the number of DOPC molecules per reverse micelle, is determined to fit experimental light-scattering measurements of the reverse micelle diameter. The simulated reverse micelles are found to be approximately spherical. Larger reverse micelles (W o > 4) exhibit a layered structure with a water core and the hydration structure of DOPC phosphate headgroups is similar to that found in phospholipid membranes. In contrast, the structure of smaller reverse micelles (W o ≤ 4) cannot be described as a series of concentric layers successively containing water, surfactant headgroups, and surfactant tails, and the headgroups are only partly hydrated and frequently present in the core. The dynamics of water molecules within the phospholipid reverse micelles slow down as the reverse micelle size decreases, in agreement with prior studies on AOT and Igepal reverse micelles. However, the average water reorientation dynamics in DOPC reverse micelles is found to be much slower than in AOT and Igepal reverse micelles with the same W o ratio. This is explained by the smaller water pool and by the stronger interactions between water and the charged headgroups, as confirmed by the redshift of the computed infrared lineshape with decreasing W o .
Journal of Physical Chemistry, 1996
To assess the feasibility of high-pressure simulation of biomolecular systems, we discuss some pr... more To assess the feasibility of high-pressure simulation of biomolecular systems, we discuss some practical aspects of molecular dynamics simulation techniques at constant pressure and temperature. We compare the extended Lagrangian (EL) method, initially developed by Andersen 1 for sampling from well-defined statistical mechanical ensembles, with the method by Berendsen et al., 2 where temperature and/or pressure are kept constant by weakly coupling (WC) the system to external thermal and pressure baths. We examine the convergence of the volume and of its fluctuations (related to the system compressibility) in both approaches and compute the statistical efficiency of the two methods. Also, the influence on computed observables and fluctuations of the adjustable parameters entering the equation of motions in both approaches is discussed. Systems of increasing complexity from liquid argon to a solvated protein are examined. Remarkably, we find that observables such as volume and enthalpy obtained by extended Lagrangian and weak coupling simulations at the same thermodynamic point are within statistical error of each other. However, for values of the pressure and temperature coupling parameters used commonly in simulation of biomolecules, the statistical inefficiency of the WC approach is higher than for the EL method. This was confirmed in the study of the solvated protein. We find also that at equal computational expense the compressibility is calculated from fluctuation formulas and finite differences with similar precisions. Finally, we observe that when the solvated protein undergoes a sudden pressure increase, the volume relaxes involving two time scales: a slower one with a half-time close to 20 ps due probably to the protein internal relaxation and a faster one with a half-time of about 300 fs attributed to the solvent water. Thus, the equilibration to a new pressure of a solvated protein is 2 orders of magnitude slower than for water but occurs on a time scale manageable by current molecular dynamics simulation techniques.
The Journal of Physical Chemistry B, 2004
The Journal of Physical Chemistry B, 2011
This paper deals with the development and validation of new potential parameter sets, based on th... more This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-Dodecyl-ß-maltoside (C 12 G 2), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure and hydration of the C 12 G 2 anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M. et al. J. Comp. Chem. 2002, 23, 1236-1243). We find that our CHARMM and GLYCAM parameter sets yields similar results in case of properties related to the micelle structure, but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C 12 G 2 micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 Å and 25.4 Å for the αand β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7-11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in αor βanomers.
Proceedings of the National Academy of Sciences, 1996
Constant pressure and temperature molecular dynamics techniques have been employed to investigate... more Constant pressure and temperature molecular dynamics techniques have been employed to investigate the changes in structure and volumes of two globular proteins, superoxide dismutase and lysozyme, under pressure. Compression (the relative changes in the proteins' volumes), computed with the Voronoi technique, is closely related with the so-called protein intrinsic compressibility, estimated by sound velocity measurements. In particular, compression computed with Voronoi volumes predicts, in agreement with experimental estimates, a negative bound water contribution to the apparent protein compression. While the use of van der Waals and molecular volumes underestimates the intrinsic compressibilities of proteins, Voronoi volumes produce results closer to experimental estimates. Remarkably, for two globular proteins of very different secondary structures, we compute identical (within statistical error) protein intrinsic compressions, as predicted by recent experimental studies. Chan...
Langmuir, 2006
We used constant pressure (P) 0.1 MPa) and temperature (T) 298 K) molecular dynamics simulations ... more We used constant pressure (P) 0.1 MPa) and temperature (T) 298 K) molecular dynamics simulations to study the structures and dynamics of small size reverse micelles (RMs) with poly(ethylene glycol) alkyl ether (C m E n) surfactants. The water-to-surfactant molar ratio was 3, with decane as the apolar solvent. We focused on the effect of the two possible imposed conformations (trans vs gauche) for the surfactant headgroups on RMs structures and water dynamics. For this purpose, we built up two RMs, which only differ by their surfactant headgroup conformations. The results obtained for the two RMs were compared to what is known in the literature. Here, we show that the surfactant headgroup conformation affects mainly the water-related properties such as the water core size, the area per surfactant headgroup, the headgroup hydration, and the water core translational diffusion. The properties computed for the RM with the surfactant in trans conformation fit better with the experimental data than the gauche conformation. We further show that the surfactant hydrophilic headgroup plays a crucial role in the micellar structures, favors the entrapment of the micellar water, and reduces strongly their diffusion compared to the bulk water.
Langmuir, 2004
Hydration of a spherical micelles of C12E6 in solution is studied by molecular dynamics simulatio... more Hydration of a spherical micelles of C12E6 in solution is studied by molecular dynamics simulation. The interface is found to be separated in an inner part composed of water and hydrophobic and hydrophilic moieties and an outer part with hydrophilic moiety and water only. Hydration numbers in the inner and in the outer parts are in excellent agreement with experimental data from various different methods. Temperature dehydration occurs in the inner region only and is related to the presence of water molecules directly in contact with the hydrophobic core at low temperature. † Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'E Ä tudes.
Journal of the American Chemical Society, 2006
Journal of the American Chemical Society, 2002
This paper is concerned with the dynamics of water around a small globular protein. Dipolar secon... more This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of lysozyme is 3-7 times slower than that in the bulk depending on how the hydration shell is defined in the calculation. We have also verified that the dynamics of water translational diffusion in the vicinity of lysozyme have retardations similar to rotational relaxation. This is a common assumption in nuclear magnetic relaxation dispersion (NMRD) studies to derive residence times. In contrast to bulk water dynamics, surface water is in a dispersive diffusion regime or subdiffusion. Very good agreement of dipolar second-rank relaxation time with NMRD estimates is obtained by using appropriate dimensions of the hydration shell. Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P.
Journal of Computational Chemistry, 1997
Journal of Computational Chemistry, 2009
We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FO... more We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.
Journal of Computational Chemistry, 2002
This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, ... more This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.
Journal of Chemical Theory and Computation, 2012
The European Physical Journal E, 2010
Chemical Physics Letters, 2009
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
Biophysical Journal, 2012
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2014
In this paper, we describe molecular dynamics simulation results of the interactions between four... more In this paper, we describe molecular dynamics simulation results of the interactions between four peptides (mTM10, mTM16, TM17 and KTM17) with micelles of dodecylphosphocholine (DPC) and dodecyl-β-Dmaltoside (DDM). These peptides represent three transmembrane fragments (TM10, 16 and 17) from the MSD1 and MSD2 membrane-spanning domains of an ABC membrane protein (hMRP1), which play roles in the protein functions. The peptide-micelle complex structures, including the tryptophan accessibility and dynamics were compared to circular dichroism and fluorescence studies obtained in water, trifluoroethanol and with micelles. Our work provides additional results not directly accessible by experiments that give further support to the fact that these peptides adopt an interfacial conformation within the micelles. We also show that the peptides are more buried in DDM than in DPC, and consequently, that they have a larger surface exposure to water in DPC than in DDM. As noted previously by simulations and experiments we have also observed formation of cation-π bonds between the phosphocholine DPC headgroup and Trp peptide residue. Concerning the peptide secondary structures (SS), we find that in TFE their initial helical conformations are maintained during the simulation, whereas in water their initial SS are lost after few nanoseconds of simulation. An intermediate situation is observed with micelles, where the peptides remain partially folded and more structured in DDM than in DPC. Finally, our results show no sign of β-strand structure formation as invoked by far-UV CD experiments even when three identical peptides are simulated either in water or with micelles.
Physical Review E, 2001
Contrary to the findings of Mülders, Toxvaerd, and Kneller ͓Phys. Rev. E 58, 6766 ͑1998͔͒ ͑MTK͒, ... more Contrary to the findings of Mülders, Toxvaerd, and Kneller ͓Phys. Rev. E 58, 6766 ͑1998͔͒ ͑MTK͒, we are unable to discern any difference in the behavior of long chain alkanes simulated by molecular dynamics at constant pressure using either atomic or molecular scaling schemes. This result confirms our previous study ͓M. Marchi and P. Procacci, J. Chem. Phys. 109, 5194 ͑1998͔͒ on hydrated proteins published at the same time as the MTK's paper. This Comment indicates that errors in the calculation of the pressure tensor might be responsible for at least a part of the MTKs results.
Langmuir, 2016
The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We... more The structure and dynamics of phospholipid reverse micelles are studied by molecular dynamics. We report all-atom unconstrained simulations of 1,2-dioleoyl-sn-phosphatidylcholine (DOPC) reverse micelles in benzene of increasing sizes, with water to surfactant number ratios ranging from W o = to 16. The aggregation number, i.e., the number of DOPC molecules per reverse micelle, is determined to fit experimental light-scattering measurements of the reverse micelle diameter. The simulated reverse micelles are found to be approximately spherical. Larger reverse micelles (W o > 4) exhibit a layered structure with a water core and the hydration structure of DOPC phosphate headgroups is similar to that found in phospholipid membranes. In contrast, the structure of smaller reverse micelles (W o ≤ 4) cannot be described as a series of concentric layers successively containing water, surfactant headgroups, and surfactant tails, and the headgroups are only partly hydrated and frequently present in the core. The dynamics of water molecules within the phospholipid reverse micelles slow down as the reverse micelle size decreases, in agreement with prior studies on AOT and Igepal reverse micelles. However, the average water reorientation dynamics in DOPC reverse micelles is found to be much slower than in AOT and Igepal reverse micelles with the same W o ratio. This is explained by the smaller water pool and by the stronger interactions between water and the charged headgroups, as confirmed by the redshift of the computed infrared lineshape with decreasing W o .
Journal of Physical Chemistry, 1996
To assess the feasibility of high-pressure simulation of biomolecular systems, we discuss some pr... more To assess the feasibility of high-pressure simulation of biomolecular systems, we discuss some practical aspects of molecular dynamics simulation techniques at constant pressure and temperature. We compare the extended Lagrangian (EL) method, initially developed by Andersen 1 for sampling from well-defined statistical mechanical ensembles, with the method by Berendsen et al., 2 where temperature and/or pressure are kept constant by weakly coupling (WC) the system to external thermal and pressure baths. We examine the convergence of the volume and of its fluctuations (related to the system compressibility) in both approaches and compute the statistical efficiency of the two methods. Also, the influence on computed observables and fluctuations of the adjustable parameters entering the equation of motions in both approaches is discussed. Systems of increasing complexity from liquid argon to a solvated protein are examined. Remarkably, we find that observables such as volume and enthalpy obtained by extended Lagrangian and weak coupling simulations at the same thermodynamic point are within statistical error of each other. However, for values of the pressure and temperature coupling parameters used commonly in simulation of biomolecules, the statistical inefficiency of the WC approach is higher than for the EL method. This was confirmed in the study of the solvated protein. We find also that at equal computational expense the compressibility is calculated from fluctuation formulas and finite differences with similar precisions. Finally, we observe that when the solvated protein undergoes a sudden pressure increase, the volume relaxes involving two time scales: a slower one with a half-time close to 20 ps due probably to the protein internal relaxation and a faster one with a half-time of about 300 fs attributed to the solvent water. Thus, the equilibration to a new pressure of a solvated protein is 2 orders of magnitude slower than for water but occurs on a time scale manageable by current molecular dynamics simulation techniques.
The Journal of Physical Chemistry B, 2004
The Journal of Physical Chemistry B, 2011
This paper deals with the development and validation of new potential parameter sets, based on th... more This paper deals with the development and validation of new potential parameter sets, based on the CHARMM36 and GLYCAM06 force fields, to simulate micelles of the two anomeric forms (α and β) of N-Dodecyl-ß-maltoside (C 12 G 2), a surfactant widely used in the extraction and purification of membrane proteins. In this context, properties such as size, shape, internal structure and hydration of the C 12 G 2 anomer micelles were thoroughly investigated by molecular dynamics simulations and the results compared with experiments. Additional simulations were also performed with the older CHARMM22 force field for carbohydrates (Kuttel, M. et al. J. Comp. Chem. 2002, 23, 1236-1243). We find that our CHARMM and GLYCAM parameter sets yields similar results in case of properties related to the micelle structure, but differ for other properties such as the headgroup conformation or the micelle hydration. In agreement with experiments, our results show that for all model potentials the β-C 12 G 2 micelles have a more pronounced ellipsoidal shape than those containing α anomers. The computed radius of gyration is 20.2 Å and 25.4 Å for the αand β-anomer micelles, respectively. Finally, we show that depending on the potential the water translational diffusion of the interfacial water is 7-11.5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in αor βanomers.
Proceedings of the National Academy of Sciences, 1996
Constant pressure and temperature molecular dynamics techniques have been employed to investigate... more Constant pressure and temperature molecular dynamics techniques have been employed to investigate the changes in structure and volumes of two globular proteins, superoxide dismutase and lysozyme, under pressure. Compression (the relative changes in the proteins' volumes), computed with the Voronoi technique, is closely related with the so-called protein intrinsic compressibility, estimated by sound velocity measurements. In particular, compression computed with Voronoi volumes predicts, in agreement with experimental estimates, a negative bound water contribution to the apparent protein compression. While the use of van der Waals and molecular volumes underestimates the intrinsic compressibilities of proteins, Voronoi volumes produce results closer to experimental estimates. Remarkably, for two globular proteins of very different secondary structures, we compute identical (within statistical error) protein intrinsic compressions, as predicted by recent experimental studies. Chan...
Langmuir, 2006
We used constant pressure (P) 0.1 MPa) and temperature (T) 298 K) molecular dynamics simulations ... more We used constant pressure (P) 0.1 MPa) and temperature (T) 298 K) molecular dynamics simulations to study the structures and dynamics of small size reverse micelles (RMs) with poly(ethylene glycol) alkyl ether (C m E n) surfactants. The water-to-surfactant molar ratio was 3, with decane as the apolar solvent. We focused on the effect of the two possible imposed conformations (trans vs gauche) for the surfactant headgroups on RMs structures and water dynamics. For this purpose, we built up two RMs, which only differ by their surfactant headgroup conformations. The results obtained for the two RMs were compared to what is known in the literature. Here, we show that the surfactant headgroup conformation affects mainly the water-related properties such as the water core size, the area per surfactant headgroup, the headgroup hydration, and the water core translational diffusion. The properties computed for the RM with the surfactant in trans conformation fit better with the experimental data than the gauche conformation. We further show that the surfactant hydrophilic headgroup plays a crucial role in the micellar structures, favors the entrapment of the micellar water, and reduces strongly their diffusion compared to the bulk water.
Langmuir, 2004
Hydration of a spherical micelles of C12E6 in solution is studied by molecular dynamics simulatio... more Hydration of a spherical micelles of C12E6 in solution is studied by molecular dynamics simulation. The interface is found to be separated in an inner part composed of water and hydrophobic and hydrophilic moieties and an outer part with hydrophilic moiety and water only. Hydration numbers in the inner and in the outer parts are in excellent agreement with experimental data from various different methods. Temperature dehydration occurs in the inner region only and is related to the presence of water molecules directly in contact with the hydrophobic core at low temperature. † Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'E Ä tudes.
Journal of the American Chemical Society, 2006
Journal of the American Chemical Society, 2002
This paper is concerned with the dynamics of water around a small globular protein. Dipolar secon... more This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of lysozyme is 3-7 times slower than that in the bulk depending on how the hydration shell is defined in the calculation. We have also verified that the dynamics of water translational diffusion in the vicinity of lysozyme have retardations similar to rotational relaxation. This is a common assumption in nuclear magnetic relaxation dispersion (NMRD) studies to derive residence times. In contrast to bulk water dynamics, surface water is in a dispersive diffusion regime or subdiffusion. Very good agreement of dipolar second-rank relaxation time with NMRD estimates is obtained by using appropriate dimensions of the hydration shell. Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P.
Journal of Computational Chemistry, 1997
Journal of Computational Chemistry, 2009
We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FO... more We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.
Journal of Computational Chemistry, 2002
This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, ... more This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.
Journal of Chemical Theory and Computation, 2012
The European Physical Journal E, 2010
Chemical Physics Letters, 2009
This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are encouraged to visit: http://www.elsevier.com/copyright
Biophysical Journal, 2012
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2014
In this paper, we describe molecular dynamics simulation results of the interactions between four... more In this paper, we describe molecular dynamics simulation results of the interactions between four peptides (mTM10, mTM16, TM17 and KTM17) with micelles of dodecylphosphocholine (DPC) and dodecyl-β-Dmaltoside (DDM). These peptides represent three transmembrane fragments (TM10, 16 and 17) from the MSD1 and MSD2 membrane-spanning domains of an ABC membrane protein (hMRP1), which play roles in the protein functions. The peptide-micelle complex structures, including the tryptophan accessibility and dynamics were compared to circular dichroism and fluorescence studies obtained in water, trifluoroethanol and with micelles. Our work provides additional results not directly accessible by experiments that give further support to the fact that these peptides adopt an interfacial conformation within the micelles. We also show that the peptides are more buried in DDM than in DPC, and consequently, that they have a larger surface exposure to water in DPC than in DDM. As noted previously by simulations and experiments we have also observed formation of cation-π bonds between the phosphocholine DPC headgroup and Trp peptide residue. Concerning the peptide secondary structures (SS), we find that in TFE their initial helical conformations are maintained during the simulation, whereas in water their initial SS are lost after few nanoseconds of simulation. An intermediate situation is observed with micelles, where the peptides remain partially folded and more structured in DDM than in DPC. Finally, our results show no sign of β-strand structure formation as invoked by far-UV CD experiments even when three identical peptides are simulated either in water or with micelles.