Molecular dynamics simulations on the Tre1 G protein-coupled receptor: Exploring the role of the arginine of the NRY motif in Tre1 structure

Abstract Background: The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an aspartic acid or glutamic acid in transmembrane 6. The Drosophila melanogaster GPCR Trapped in endoderm-1 (Tre1) is required for normal primordial germ cell migration. In a mutant form of the protein, Tre1sctt, eight amino acids RYILIACH are missing, resulting in a severe disruption of primordial germ cell development. The impact of the loss of these amino acids on Tre1 structure is unknown. Since the missing amino acids in Tre1sctt include the arginine that is part of the D/E/NRY motif in Tre1, molecular dynamics simulations were performed to explore the hypothesis that these amino acids are involved in salt bridge formation and help maintain Tre1 structure. Results: Structural predictions of wild type Tre1 (Tre1+) and Tre1sctt were subjected to over 250 ns of molecular dynamics simulations. The ability of the model systems to form a salt bridge between the arginine of the D/E/NRY motif and an aspartic acid residue in transmembrane 6 was analyzed. The results indicate that a stable salt bridge can form in the Tre1+ systems and a weak salt bridge or no salt bridge, using an alternative arginine, is likely in the Tre1sctt systems. Conclusions: The weak salt bridge or lack of a salt bridge in the Tre1sctt systems could be one possible explanation for the disrupted function of Tre1sctt in primordial germ cell migration. These results provide a framework for studying the importance of the arginine of the D/E/NRY motif in the structure and function of other GPCRs that are involved in cell migration, such as CXCR4 in the mouse, zebrafish, and chicken

Characterization of 3D Voronoi Tessellation Nearest Neighbor Lipid Shells Provides Atomistic Lipid Disruption Profile of Protein Containing Lipid Membranes

Quantifying protein-induced lipid disruptions at the atomistic level is a challenging problem in membrane biophysics. Here we propose a novel 3D Voronoi tessellation nearest-atom-neighbor shell method to classify and characterize lipid domains into discrete concentric lipid shells surrounding membrane proteins in structurally heterogeneous lipid membranes. This method needs only the coordinates of the system and is independent of force fields and simulation conditions. As a proof-of-principle, we use this multiple lipid shell method to analyze the lipid disruption profiles of three simulated membrane systems: phosphatidylcholine, phosphatidylcholine/cholesterol, and beta-amyloid/phosphatidylcholine/cholesterol. We observed different atomic volume disruption mechanisms due to cholesterol and beta-amyloid. Additionally, several lipid fractional groups and lipid-interfacial water did not converge to their control values with increasing distance or shell order from the protein. This volume divergent behavior was confirmed by bilayer thickness and chain orientational order calculations. Our method can also be used to analyze high-resolution structural experimental data

Elucidating the Binding Pockect of the GPR119 Receptor, a Type 2 Diabetes Target

An in-house homology model of the GPR119 receptor was used to identify residues which may affect ligand binding and ligand-dependent activity through computational and experimental studies. In a docking study comparing an agonist and its inverse agonist structural analog, Leu5.43169, L6.52242 and Ser1.324 appear to be involved in ligand binding. These residues were mutated experimentally to test the predictions of the homology model. The in vitro studies indicate that Leu5.43169 and Ser1.324 mutations cause ten-fold and six-fold decreases in ligand-induced cAMP formation, indicating their importance in ligand-induced activation. Leu6.52242 mutations show minimal effect in cAMP production, indicating a lesser involvement in ligand binding. MD simulations of the homology model bound to an agonist indicate that Leu5.43169 has an indirect effect in ligand binding, via interactions with Phe6.51241, whereas Leu6.52242 is not facing the binding pocket. Ser1.324 seems to interact occasionally with the ligand headgroup

A machine learning assessment of the two states model for lipid bilayer phase transitions

We have adapted a set of classification algorithms, also known as Machine Learning, to the identification of fluid and gel domains close to the main transition of dipalmitoyl-phosphatidylcholine (DPPC) bilayers. Using atomistic molecular dynamics conformations in the low and high temperature phases as learning sets, the algorithm was trained to categorize individual lipid configurations as fluid or gel, in relation with the usual two-states phenomenological description of the lipid melting transition. We demonstrate that our machine can learn and sort lipids according to their most likely state without prior assumption regarding the nature of the order parameter of the transition. Results from our machine learning approach provides strong support in favor of a two-states model approach of membrane fluidity

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

1,4-dioxane is a cytotoxic B2 type human carcinogen, a serious water pollutant produced solely by industrial activity. The effect of 1,4-dioxane on phospholipid membrane models composed by DPPC and its branched isomer (IPPC) was investigated using MD simulations. Clear and polluted membranes were compared by membrane parameters such as APL, VPL, compressibility modulus, membrane thickness and orderliness of lipid tails. While neat systems significantly differ from each other, the presence of the pollutant has the same effect on both types of lipid membranes: high density of dioxane appears at the vicinity of ester groups which pushes away lipid headgroups from each other, leading to an overall change in lipid structure: APL and VPL grows, while the orderliness of lipid tails, membrane thickness and compressibility modulus decreases. Orientational preferences of water and dioxane molecules were also investigated and different membrane regions have been specified according to the stance of water molecules. Free energy profile for 1,4-dioxane penetration mechanism into DPPC membranes was carried out using metadynamics for two different concentrations of the pollutant (c1=7.51 g/dm3 , c2=75.10 g/dm3 ), which showed that the higher the concentration is, the lower the free energy of penetration gets. Only a small free energy barrier was found in the headgroup region and accumulation of dioxane is thermodynamically unfavored in the middle of the bilayer. The penetration mechanism has been described in detail based on the orientational preference of 1,4-dioxane molecules and the free energy profiles

Entropie‐dominierte Selbstorganisationsprozesse birnenförmiger Teilchensysteme

The ambition to recreate highly complex and functional nanostructures found in living organisms marks one of the pillars of today‘s research in bio- and soft matter physics. Here, self-assembly has evolved into a prominent strategy in nanostructure formation and has proven to be a useful tool for many complex structures. However, it is still a challenge to design and realise particle properties such that they self-organise into a desired target configuration. One of the key design parameters is the shape of the constituent particles. This thesis focuses in particular on the shape sensitivity of liquid crystal phases by addressing the entropically driven colloidal self-assembly of tapered ellipsoids, reminiscent of „pear-shaped“ particles. Therefore, we analyse the formation of the gyroid and of the accompanying bilayer architecture, reported earlier in the so-called pear hard Gaussian overlap (PHGO) approximation, by applying various geometrical tools like Set-Voronoi tessellation and clustering algorithms. Using computational simulations, we also indicate a method to stabilise other bicontinuous structures like the diamond phase. Moreover, we investigate both computationally and theoretically(density functional theory) the influence of minor variations in shape on different pearshaped particle systems, including the stability of the PHGO gyroid phase. We show that the formation of the gyroid is due to small non-additive properties of the PHGO potential. This phase does not form in pears with a „true“ hard pear-shaped potential. Overall our results allow for a better general understanding of necessity and sufficiency of particle shape in regards to colloidal self-assembly processes. Furthermore, the pear-shaped particle system sheds light on a unique collective mechanism to generate bicontinuous phases. It suggests a new alternative pathway which might help us to solve still unknown characteristics and properties of naturally occurring gyroid-like nano- and microstructures.Ein wichtiger Bestandteil der heutigen Forschung in Bio- und Soft Matter Physik besteht daraus, Technologien zu entwickeln, um hoch komplexe und funktionelle Strukturen, die uns aus der Natur bekannt sind, nachzubilden. Hinsichtlich dessen ist vor allem die Methode der Selbstorganisation von Mikro- und Nanoteilchen hervorzuheben, durch die eine Vielzahl verschiedener Strukturen erzeugt werden konnten. Jedoch stehen wir bei diesem Verfahren noch immer vor der Herausforderung, Teilchen mit bestimmten Eigenschaften zu entwerfen, welche die spontane Anordnung der Teilchen in eine gewünschte Struktur bewirken. Einer der wichtigsten Designparameter ist dabei die Form der Bausteinteilchen. In dieser Dissertation konzentrieren wir uns besonders auf die Anfälligkeit von Flüssigkristallphasen bezüglich kleiner Änderungen der Teilchenform und nutzen dabei das Beispiel der Selbstorganisation von Entropie-dominierter Kolloide, die dem Umriss nach verjüngten Ellipsoiden oder "Birnen" ähneln. Mit Hilfe von geometrischen Werkzeugen wie z.B. Set-Voronoi Tessellation oder Cluster-Algorithmen analysieren wir insbesondere die Entstehung der Gyroidphase und der dazugehörigen Bilagenformation, welche bereits in Systemen von harten Birnen, die durch das pear hard Gaussian overlap (PHGO) Potential angenähert werden, entdeckt wurden. Des Weiteren zeigen wir durch Computersimulationen eine Strategie auf, um andere bikontinuierliche Strukturen, wie die Diamentenphase, zu stabilisieren. Schlussendlich betrachten wir sowohl rechnerisch (durch Simulationen) als auch theoretisch (durch Dichtefunktionaltheorie) die Auswirkungen kleiner Abweichungen der Teilchenform auf das Verhalten des kolloiden, birnenförmigen Teilchensystems, inklusive der Stabilität der PHGO Gyroidphase. Wir zeigen, dass die Entstehung des Gyroids auf kleinen nicht-additiven Eigenschaften des PHGO Birnenmodells beruhen. In ''echten'' harten Teilchensystemen entwickelt sich diese Struktur nicht. Insgesamt ermöglichen unsere Ergebnisse einen besseren Einblick auf das Konzept von notwendiger und hinreichender Teilchenform in Selbstorganistationsprozessen. Die birnenförmigen Teilchensysteme geben außerdem Aufschluss über einen ungewöhnlichen, kollektiven Mechanismus, um bikontinuierliche Phasen zu erzeugen. Dies deutet auf einen neuen, alternativen Konstruktionsweg hin, der uns möglicherweise hilft, noch unbekannte Eigenschaften natürlich vorkommender, gyroidähnlicher Nano- und Mikrostrukturen zu erklären

Binding of Aβ peptide creates lipid density depression in DMPC bilayer

AbstractUsing isobaric–isothermal replica exchange molecular dynamics and all-atom explicit water model we study the impact of Aβ monomer binding on the equilibrium properties of DMPC bilayer. We found that partial insertion of Aβ peptide into the bilayer reduces the density of lipids in the binding “footprint” and indents the bilayer thus creating a lipid density depression. Our simulations also reveal thinning of the bilayer and a decrease in the area per lipid in the proximity of Aβ. Although structural analysis of lipid hydrophobic core detects disordering in the orientations of lipid tails, it also shows surprisingly minor structural perturbations in the tail conformations. Finally, partial insertion of Aβ monomer does not enhance water permeation through the DMPC bilayer and even causes considerable dehydration of the lipid–water interface. Therefore, we conclude that Aβ monomer bound to the DMPC bilayer fails to perturb the bilayer structure in both leaflets. Limited scope of structural perturbations in the DMPC bilayer caused by Aβ monomer may constitute the molecular basis of its low cytotoxicity

Structure formation and identification in geometrically driven soft matter systems

Subdividing space through interfaces leads to many space partitions that are relevant to soft matter self-assembly. Prominent examples include cellular media, e.g. soap froths, which are bubbles of air separated by interfaces of soap and water, but also more complex partitions such as bicontinuous minimal surfaces. Using computer simulations, this thesis analyses soft matter systems in terms of the relationship between the physical forces between the system’s constituents and the structure of the resulting interfaces or partitions. The focus is on two systems, copolymeric self-assembly and the so-called Quantizer problem, where the driving force of structure formation, the minimisation of the free-energy, is an interplay of surface area minimisation and stretching contributions, favouring cells of uniform thickness. In the first part of the thesis we address copolymeric phase formation with sharp interfaces. We analyse a columnar copolymer system “forced” to assemble on a spherical surface, where the perfect solution, the hexagonal tiling, is topologically prohibited. For a system of three-armed copolymers, the resulting structure is described by solutions of the so-called Thomson problem, the search of minimal energy configurations of repelling charges on a sphere. We find three intertwined Thomson problem solutions on a single sphere, occurring at a probability depending on the radius of the substrate. We then investigate the formation of amorphous and crystalline structures in the Quantizer system, a particulate model with an energy functional without surface tension that favours spherical cells of equal size. We find that quasi-static equilibrium cooling allows the Quantizer system to crystallise into a BCC ground state, whereas quenching and non-equilibrium cooling, i.e. cooling at slower rates then quenching, leads to an approximately hyperuniform, amorphous state. The assumed universality of the latter, i.e. independence of energy minimisation method or initial configuration, is strengthened by our results. We expand the Quantizer system by introducing interface tension, creating a model that we find to mimic polymeric micelle systems: An order-disorder phase transition is observed with a stable Frank-Caspar phase. The second part considers bicontinuous partitions of space into two network-like domains, and introduces an open-source tool for the identification of structures in electron microscopy images. We expand a method of matching experimentally accessible projections with computed projections of potential structures, introduced by Deng and Mieczkowski (1998). The computed structures are modelled using nodal representations of constant-mean-curvature surfaces. A case study conducted on etioplast cell membranes in chloroplast precursors establishes the double Diamond surface structure to be dominant in these plant cells. We automate the matching process employing deep-learning methods, which manage to identify structures with excellent accuracy

Entropically driven self-assembly of pear-shaped nanoparticles

This thesis addresses the entropically driven colloidal self-assembly of pear-shaped particle ensembles, including the formation of nanostructures based on triply periodic minimal surfaces, in particular of the Ia3d gyroid. One of the key results is that the formation of the Ia3d gyroid, re-ported earlier in the so-called pear hard Gaussian overlap (PHGO) approximation and confirmed here, is due to a slight non-additivity of that potential; this phase does not form in pears with true hard-core potential. First, we computationally study the PHGO system and present the phase diagram of pears with an aspect ratio of 3 in terms of global density and particle shape (degree of taper), containing gyroid, isotropic, nematic and smectic phases. We confirm that it is adequate to interpret the gyroid as a warped smectic bilayer phase. The collective behaviour to arrange into interdigitated sheets with negative Gauss curvature, from which the gyroid results, is investigated through correlations of (Set-)Voronoi cells and local curvature. This geometric arrangement within the bilayers suggests a fundamentally different stabilisation mechanism of the pear gyroid phase compared to those found in both lipid-water and di-block copolymer systems forming the Ia3d gyroid. The PHGO model is only an approximation for hard-core interactions, and we additionally investigate, by much slower simulations, pear-assemblies with true hard-core interactions (HPR). We find that HPR phase diagram only contains isotropic and nematic phases, but neither gyroid nor smectic phases. To understand this shape sensitivity more profoundly, the depletion interactions of both models are studied in two pear-shaped colloids dissolved in a hard sphere solvent. The HPR particles act as one would expect from a geometric analysis of the excluded-volume minimisation, whereas the PHGO particles show deviations from this expectation. These differences are attributed to the unusual angle dependency of the (non-additive) contact function and, more so, to small overlaps induced by the approximation. For the PHGO model, we further demonstrate that the addition of a small concentration of hard spheres ("solvent") drives the system towards a Pn3m diamond phase. This result is explained by the greater spatial heterogeneity of the diamond geometry compared to the gyroid where additional material is needed to relieve packing frustration. In contrast to copolymer systems, however, the solvent mostly aggregates near the diamond minimal surface, driven by the non-additivity of the PHGO pears. At high solvent concentrations, the mixture phase separates into “inverse” micelle-like structures with the blunt ends at the micellar centres and thin ends pointing out-wards. The micelles themselves spontaneously cluster, indicative of a hierarchical self-assembly process for bicontinuous structures. Finally, we develop a density functional for hard solids of revolution (including pears) within the framework of fundamental measure theory. It is applied to low-density ensembles of pear-shaped particles, where we analyse their response near a hard substrate. A complex orientational ordering close to the wall is predicted, which is directly linked to the particle shape and gives insight into adsorption processes of asymmetric particles. This predicted behaviour and the differences between the PHGO and HPR model are confirmed by MC simulations

On Bilayer Deformation Energetics With and Without Gramicidin A Channel

Lipid membranes are not simply passive barriers. Embedded proteins are coupled to the membrane and can deform the surrounding bilayer, which incurs an energetic penalty. To minimize these penalties, proteins are known to tilt, aggregate, and experience major conformation changes. The degree to which the protein is influenced by the bilayer is dependent on the bilayer material properties and protein-bilayer coupling strength, for example. In this dissertation, the effects of bilayer material properties and protein-bilayer coupling are detailed using gramicidin A channel. This simple channel experiences one major conformational change, its transmembrane dimerization, which produces a bilayer deformation if the bilayer and dimer do not have the same hydrophobic lengths. Herein, molecular dynamics simulations are used to describe bilayer material properties, channel-bilayer coupling, and general lipid energetics with and without gramicidin A