Molecular dynamics simulations of the anchoring and tilting of the lung-surfactant peptide SP-B1-25 in palmitic acid monolayers

Simulated Breathing: Application of Molecular Dynamics Simulations to Pulmonary Lung Surfactant

In this review, we delve into the topic of the pulmonary surfactant (PS) system, which is present in the respiratory system. The total composition of the PS has been presented and explored, from the types of cells involved in its synthesis and secretion, down to the specific building blocks used, such as the various lipid and protein components. The lipid and protein composition varies across species and between individuals, but ultimately produces a PS monolayer with the same role. As such, the composition has been investigated for the ways in which it imposes function and confers peculiar biophysical characteristics to the system as a whole. Moreover, a couple of theories/models that are associated with the functions of PS have been addressed. Finally, molecular dynamic (MD) simulations of pulmonary surfactant have been emphasized to not only showcase various group’s findings, but also to demonstrate the validity and importance that MD simulations can have in future research exploring the PS monolayer system.

Prednisolone adsorption on lung surfactant models: insights on the formation of nanoaggregates, monolayer collapse and prednisolone spreading

The adsorption of prednisolone on a lung surfactant model was successfully performed using coarse grained molecular dynamics.

Computer simulations of lung surfactant

Lung surfactant lines the gas-exchange interface in the lungs and reduces the surface tension, which is necessary for breathing. Lung surfactant consists mainly of lipids with a small amount of proteins and forms a monolayer at the air-water interface connected to bilayer reservoirs. Lung surfactant function involves transfer of material between the monolayer and bilayers during the breathing cycle. Lipids and proteins are organized laterally in the monolayer; selected species are possibly preferentially transferred to bilayers. The complex 3D structure of lung surfactant and the exact roles of lipid organization and proteins remain important goals for research. We review recent simulation studies on the properties of lipid monolayers, monolayers with phase coexistence, monolayer-bilayer transformations, lipid-protein interactions, and effects of nanoparticles on lung surfactant. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

The influence of the surface composition of mixed monolayer films on the evaporation coefficient of water

The influence of mixed component organic surface films on the evaporation rate of water from an aqueous droplet is reported.

Investigation of Mixed Surfactant Films at Water Surface Using Molecular Dynamics Simulations

Multicomponent Langmuir monolayers are important models of organic coatings of naturally occurring water-vapor interfaces such as the surfaces of oceans or aerosol particles. We investigated mixed monolayers comprised of palmitic acid, C15H31COOH (PA) and 1-bromoalkanes of different chain length (C5, C10, and C16) at the air-water interface employing classical molecular dynamics simulations. Different composition ratios and lateral compression of the monolayers were considered. The structural parameters, such as density profiles, and deuterium order parameter, evaluated as functions of composition and the lateral film packing, provide microscopic information about organization and dynamics of the mixed monolayers. Simulations demonstrate that stable and well mixed monolayers are formed by the mixtures of PA and BrC16H33 (BrCl6), whereas the two considered shorter bromoalkanes, BrC5H11 (BrC5) and BrC10H21 (BrC10), do not form stable films. This is in accord with earlier experimental studies. Under high lateral pressures, in PA/BrC10 mixed systems molecules of the bromoalkane readily flip in the monolayer and subsequently leave the film, while the molecules of the longer BrC16 are expelled from the PA film but no flipping occurs. These results suggest that the film collapse under pressure is preceded by squeezing-out of bromoalkanes from the PA monolayer.

Effects of surface pressure on the properties of Langmuir monolayers and interfacial water at the air-water interface

The effects of surface pressure on the physical properties of Langmuir monolayers of palmitic acid (PA) and dipalmitoylphosphatidic acid (DPPA) at the air/water interface are investigated through molecular dynamics simulations with atomistic force fields. The structure and dynamics of both monolayers and interfacial water are compared across the range of surface pressures at which stable monolayers can form. For PA monolayers at T = 300 K, the untilted condensed phase with a hexagonal lattice structure is found at high surface pressure, while the uniformly tilted condensed phase with a centered rectangular lattice structure is observed at low surface pressure, in agreement with the available experimental data. A state with uniform chain tilt but no periodic spatial ordering is observed for DPPA monolayers on a Na(+)/water subphase at both high and low surface pressures. The hydrophobic acyl chains of both monolayers pack efficiently at all surface pressures, resulting in a very small number of gauche defects. The analysis of the hydrogen-bonding structure/dynamics at the monolayer/water interface indicates that water molecules hydrogen-bonded to the DPPA head groups reorient more slowly than those hydrogen-bonded to the PA head groups, with the orientational dynamics becoming significantly slower at high surface pressure. Possible implications for physicochemical processes taking place on marine aerosols in the atmosphere are discussed.

Molecular dynamics of dibenz[a,h]anthracene and its metabolite interacting with lung surfactant phospholipid bilayers

Dibenz[a,h]anthracene and its metabolite may form aggregates, which have implications in the clearance process of the lung surfactant phospholipid bilayers.

Protein modeling and molecular dynamics simulation of the two novel surfactant proteins SP-G and SP-H

Surfactant proteins are well known from the human lung where they are responsible for the stability and flexibility of the pulmonary surfactant system. They are able to influence the surface tension of the gas–liquid interface specifically by directly interacting with single lipids. This work describes the generation of reliable protein structure models to support the experimental characterization of two novel putative surfactant proteins called SP-G and SP-H. The obtained protein models were complemented by predicted posttranslational modifications and placed in a lipid model system mimicking the pulmonary surface. Molecular dynamics simulations of these protein-lipid systems showed the stability of the protein models and the formation of interactions between protein surface and lipid head groups on an atomic scale. Thereby, interaction interface and strength seem to be dependent on orientation and posttranslational modification of the protein. The here presented modeling was fundamental for experimental localization studies and the simulations showed that SP-G and SP-H are theoretically able to interact with lipid systems and thus are members of the surfactant protein family.

Structural modelling and dynamics of proteins for insights into drug interactions

Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural rearrangements during ligand entry, ligand binding and protein-protein interactions. Hence, the knowledge of protein structure and, importantly, the dynamic behaviour of the structure are critical for understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour can be performed by combinations of structure modelling and molecular dynamics simulations. The simulations also need to be sensitive to the constraints of the environment in which the protein resides. Standard computational methods now exist in this field to support the experimental effort of solving protein structures. This review presents a comprehensive overview of the basis of the calculations and the well-established computational methods used to generate and understand protein structure and function and the study of their dynamic behaviour with the reference to lung-related targets.

Lung surfactant protein SP-B promotes formation of bilayer reservoirs from monolayer and lipid transfer between the interface and subphase

We investigated the possible role of SP-B proteins in the function of lung surfactant. To this end, lipid monolayers at the air/water interface, bilayers in water, and transformations between them in the presence of SP-B were simulated. The proteins attached bilayers to monolayers, providing close proximity of the reservoirs with the interface. In the attached aggregates, SP-B mediated establishment of the lipid-lined connection similar to the hemifusion stalk. Via this connection, a lipid flow was initiated between the monolayer at the interface and the bilayer in water in a surface-tension-dependent manner. On interface expansion, the flow of lipids to the monolayer restored the surface tension to the equilibrium spreading value. SP-B induced formation of bilayer folds from the monolayer at positive surface tensions below the equilibrium. In the absence of proteins, lipid monolayers were stable at these conditions. Fold nucleation was initiated by SP-B from the liquid-expanded monolayer phase by local bending, and the proteins lined the curved perimeter of the growing fold. No effect on the liquid-condensed phase was observed. Covalently linked dimers resulted in faster kinetics for monolayer folding. The simulation results are in line with existing hypotheses on SP-B activity in lung surfactant and explain its molecular mechanism.

Critical structural and functional roles for the N-terminal insertion sequence in surfactant protein B analogs

Background

Surfactant protein B (SP-B; 79 residues) belongs to the saposin protein superfamily, and plays functional roles in lung surfactant. The disulfide cross-linked, N- and C-terminal domains of SP-B have been theoretically predicted to fold as charged, amphipathic helices, suggesting their participation in surfactant activities. Earlier structural studies with Mini-B, a disulfide-linked construct based on the N- and C-terminal regions of SP-B (i.e., ∼residues 8–25 and 63–78), confirmed that these neighboring domains are helical; moreover, Mini-B retains critical in vitro and in vivo surfactant functions of the native protein. Here, we perform similar analyses on a Super Mini-B construct that has native SP-B residues (1–7) attached to the N-terminus of Mini-B, to test whether the N-terminal sequence is also involved in surfactant activity.

Methodology/Results

FTIR spectra of Mini-B and Super Mini-B in either lipids or lipid-mimics indicated that these peptides share similar conformations, with primary α-helix and secondary β-sheet and loop-turns. Gel electrophoresis demonstrated that Super Mini-B was dimeric in SDS detergent-polyacrylamide, while Mini-B was monomeric. Surface plasmon resonance (SPR), predictive aggregation algorithms, and molecular dynamics (MD) and docking simulations further suggested a preliminary model for dimeric Super Mini-B, in which monomers self-associate to form a dimer peptide with a “saposin-like” fold. Similar to native SP-B, both Mini-B and Super Mini-B exhibit in vitro activity with spread films showing near-zero minimum surface tension during cycling using captive bubble surfactometry. In vivo, Super Mini-B demonstrates oxygenation and dynamic compliance that are greater than Mini-B and compare favorably to full-length SP-B.

Conclusion

Super Mini-B shows enhanced surfactant activity, probably due to the self-assembly of monomer peptide into dimer Super Mini-B that mimics the functions and putative structure of native SP-B.

Molecular dynamics simulation study of a pulmonary surfactant film interacting with a carbonaceous nanoparticle

This article reports an all-atom molecular dynamics simulation to study a model pulmonary surfactant film interacting with a carbonaceous nanoparticle. The pulmonary surfactant is modeled as a dipalmitoylphosphatidylcholine monolayer with a peptide consisting of the first 25 residues from surfactant protein B. The nanoparticle model with a chemical formula C188H53 was generated using a computational code for combustion conditions. The nanoparticle has a carbon cage structure reminiscent of the buckyballs with open ends. A series of molecular-scale structural and dynamical properties of the surfactant film in the absence and presence of nanoparticle are analyzed, including radial distribution functions, mean-square displacements of lipids and nanoparticle, chain tilt angle, and the surfactant protein B peptide helix tilt angle. The results show that the nanoparticle affects the structure and packing of the lipids and peptide in the film, and it appears that the nanoparticle and peptide repel each other. The ability of the nanoparticle to translocate the surfactant film is one of the most important predictions of this study. The potential of mean force for dragging the particle through the film provides such information. The reported potential of mean force suggests that the nanoparticle can easily penetrate the monolayer but further translocation to the water phase is energetically prohibitive. The implication is that nanoparticles can interact with the lung surfactant, as supported by recent experimental data by Bakshi et al.

The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations

The aqueous lining of the lung surface exposed to the air is covered by lung surfactant, a film consisting of lipid and protein components. The main function of lung surfactant is to reduce the surface tension of the air-water interface to the low values necessary for breathing. This function requires the exchange of material between the lipid monolayer at the interface and lipid reservoirs under dynamic compression and expansion of the interface during the breathing cycle. We simulated the reversible exchange of material between the monolayer and lipid reservoirs under compression and expansion of the interface. We used a mixture of dipalmitoyl-phosphatidylcholine, palmitoyl-oleoyl-phosphatidylglycerol, cholesterol, and surfactant-associated protein C as a functional analog of mammalian lung surfactant. In our simulations, the monolayer collapses into the water subphase on compression and forms bilayer folds. On monolayer reexpansion, the material is transferred from the folds back to the interface. The simulations indicate that the connectivity of the bilayer aggregates to the monolayer is necessary for the reversibility of the monolayer-bilayer transformation. The simulations also show that bilayer aggregates are unstable in the air subphase and stable in the water subphase.

New insights into lung surfactant monolayers using vibrational sum frequency generation spectroscopy

At the air-water interface, interfacial molecular structure, intermolecular interactions, film relaxation and film respreading of model lung surfactant monolayers were studied using vibrational sum frequency generation (VSFG) spectroscopy combined with a Langmuir film balance. Chain-perdeuterated dipalmitoylphosphatidylcholine (DPPC-d62), palmitoyloleoyl-phosphatidylglycerol (POPG), palmitic acid (PA) and tripalmitin were investigated. In the DPPC-d62-PA binary monolayer, PA showed a condensing effect on the DPPC chains. On the contrary, in the DPPC-d62-POPG binary monolayer, POPG showed a fluidizing effect on the DPPC chains. In the ternary monolayer system of DPPC-d62-POPG-PA, the balance between the fluidizing and the condensing effect was also observed. In addition, the film relaxation behavior of DPPC-d62 and the enhanced film stability of DPPC-d62 caused by the addition of tripalmitin were observed. Real-time VSFG was also employed to study the respreading properties of a complex lung surfactant mixture containing DPPC-d62, POPG, PA and KL4 (a mimic of SP-B) peptide, which revealed DPPC enrichment after film compression.

Under the microscope: single molecule symposium at the University of Michigan, 2006

In recent years, a revolution has occurred in the basic sciences, which exploits novel single molecule detection and manipulation tools to track and analyze biopolymers in unprecedented detail. A recent Gordon Research Conference style meeting, hosted by the University of Michigan, highlighted current status and future perspectives of this rising field as researchers begin to integrate it with mainstream biology and nanotechnology.

DPPC Langmuir monolayer at the air-water interface: probing the tail and head groups by vibrational sum frequency generation spectroscopy

Dipalmitoylphosphatidylcholine (DPPC) is the predominant lipid component in lung surfactant. In this study, the Langmuir monolayer of deuterated dipalmitoylphosphatidylcholine (DPPC-d62) in the liquid-expanded (LE) phase and the liquid-condensed (LC) phase has been investigated at the air-water interface with broad bandwidth sum frequency generation (BBSFG) spectroscopy combined with a Langmuir film balance. Four moieties of the DPPC molecule are probed by BBSFG: the terminal methyl (CD3) groups of the tails, the methylene (CD2) groups of the tails, the choline methyls (CH3) in the headgroup, and the phosphate in the headgroup. BBSFG spectra of the four DPPC moieties provide information about chain conformation, chain orientation, headgroup orientation, and headgroup hydration. These results provide a comprehensive picture of the DPPC phase behavior at the air-water interface. In the LE phase, the DPPC hydrocarbon chains are conformationally disordered with a significant number of gauche configurations. In the LC phase, the hydrocarbon chains are in an all-trans conformation and are tilted from the surface normal by 25 degrees. In addition, the orientations of the tail terminal methyl groups are found to remain nearly unchanged with the variation of surface area. Qualitative analysis of the BBSFG spectra of the choline methyl groups suggests that these methyl groups are tilted but lie somewhat parallel to the surface plane in both the LE and LC phases. The dehydration of the phosphate headgroup due to the LE-LC phase transition is observed through the frequency blue shift of the phosphate symmetric stretch in the fingerprint region. In addition, implications for lung surfactant function from this work are discussed.