Refine
Document Type
- Doctoral Thesis (6)
- Article (5)
- Postprint (3)
Language
- English (14)
Keywords
- molecular dynamics (14) (remove)
Biomembranes are constantly remodeled and in cells, these processes are controlled and modulated by an assortment of membrane proteins. Here, it is shown that such remodeling can also be induced by photoresponsive molecules. The morphological control of giant vesicles in the presence of a water-soluble ortho-tetrafluoroazobenzene photoswitch (F-azo) is demonstrated and it is shown that the shape transformations are based on an increase in membrane area and generation of spontaneous curvature. The vesicles exhibit budding and the buds can be retracted by using light of a different wavelength. In the presence of F-azo, the membrane area can increase by more than 5% as assessed from vesicle electrodeformation. To elucidate the underlying molecular mechanism and the partitioning of F-azo in the membrane, molecular dynamics simulations are employed. Comparison with theoretically calculated shapes reveals that the budded shapes are governed by curvature elasticity, that the spontaneous curvature can be decomposed into a local and a nonlocal contribution, and that the local spontaneous curvature is about 1/(2.5 mu m). The results show that exo- and endocytotic events can be controlled by light and that these photoinduced processes provide an attractive method to change membrane area and morphology.
Biomembranes are constantly remodeled and in cells, these processes are controlled and modulated by an assortment of membrane proteins. Here, it is shown that such remodeling can also be induced by photoresponsive molecules. The morphological control of giant vesicles in the presence of a water-soluble ortho-tetrafluoroazobenzene photoswitch (F-azo) is demonstrated and it is shown that the shape transformations are based on an increase in membrane area and generation of spontaneous curvature. The vesicles exhibit budding and the buds can be retracted by using light of a different wavelength. In the presence of F-azo, the membrane area can increase by more than 5% as assessed from vesicle electrodeformation. To elucidate the underlying molecular mechanism and the partitioning of F-azo in the membrane, molecular dynamics simulations are employed. Comparison with theoretically calculated shapes reveals that the budded shapes are governed by curvature elasticity, that the spontaneous curvature can be decomposed into a local and a nonlocal contribution, and that the local spontaneous curvature is about 1/(2.5 mu m). The results show that exo- and endocytotic events can be controlled by light and that these photoinduced processes provide an attractive method to change membrane area and morphology.
Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.
The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.
Aluminum oxide is an Earth-abundant geological material, and its interaction with water is of crucial importance for geochemical and environmental processes. Some aluminum oxide surfaces are also known to be useful in heterogeneous catalysis, while the surface chemistry of aqueous oxide interfaces determines the corrosion, growth and dissolution of such materials. In this doctoral work, we looked mainly at the (0001) surface of α-Al 2 O 3 and its reactivity towards water. In particular, a great focus of this work is dedicated to simulate and address the vibrational spectra of water adsorbed on the α-alumina(0001) surface in various conditions and at different coverages. In fact, the main source of comparison and inspiration for this work comes from the collaboration with the “Interfacial Molecular Spectroscopy” group led by Dr. R. Kramer Campen at the Fritz-Haber Institute of the MPG in Berlin. The expertise of our project partners in surface-sensitive Vibrational Sum Frequency (VSF) generation spectroscopy was crucial to develop and adapt specific simulation schemes used in this work. Methodologically, the main approach employed in this thesis is Ab Initio Molecular Dynamics (AIMD) based on periodic Density Functional Theory (DFT) using the PBE functional with D2 dispersion correction. The analysis of vibrational frequencies from both a static and a dynamic, finite-temperature perspective offers the ability to investigate the water / aluminum oxide interface in close connection to experiment.
The first project presented in this work considers the characterization of dissociatively adsorbed deuterated water on the Al-terminated (0001) surface. This particular structure is known from both experiment and theory to be the thermodynamically most stable surface termination of α-alumina in Ultra-High Vacuum (UHV) conditions. Based on experiments performed by our colleagues at FHI, different adsorption sites and products have been proposed and identified for D 2 O. While previous theoretical investigations only looked at vibrational frequencies of dissociated OD groups by staticNormal Modes Analysis (NMA), we rather employed a more sophisticated approach to directly assess vibrational spectra (like IR and VSF) at finite temperature from AIMD. In this work, we have employed a recent implementation which makes use of velocity-velocity autocorrelation functions to simulate such spectral responses of O-H(D) bonds. This approach allows for an efficient and qualitatively accurate estimation of Vibrational Densities of States (VDOS) as well as IR and VSF spectra, which are then tested against experimental spectra from our collaborators.
In order to extend previous work on unimolecularly dissociated water on α-Al 2 O 3 , we then considered a different system, namely, a fully hydroxylated (0001) surface, which results from the reconstruction of the UHV-stable Al-terminated surface at high water contents. This model is then further extended by considering a hydroxylated surface with additional water molecules, forming a two-dimensional layer which serves as a potential template to simulate an aqueous interface in environmental conditions. Again, employing finite-temperature AIMD trajectories at the PBE+D2 level, we investigated the behaviour of both hydroxylated surface (HS) and the water-covered structure derived from it (known as HS+2ML). A full range of spectra, from VDOS to IR and VSF, is then calculated using the same methodology, as described above. This is the main focus of the second project, reported in Chapter 5. In this case, comparison between theoretical spectra and experimental data is definitely good. In particular, we underline the nature of high-frequency resonances observed above 3700 cm −1 in VSF experiments to be associated with surface OH-groups, known as “aluminols” which are a key fingerprint of the fully hydroxylated surface.
In the third and last project, which is presented in Chapter 6, the extension of VSF spectroscopy experiments to the time-resolved regime offered us the opportunity to investigate vibrational energy relaxation at the α-alumina / water interface. Specifically, using again DFT-based AIMD simulations, we simulated vibrational lifetimes for surface aluminols as experimentally detected via pump-probe VSF. We considered the water-covered HS model as a potential candidate to address this problem. The vibrational (IR) excitation and subsequent relaxation is performed by means of a non-equilibrium molecular dynamics scheme. In such a scheme, we specifically looked at the O-H stretching mode of surface aluminols. Afterwards, the analysis of non-equilibrium trajectories allows for an estimation of relaxation times in the order of 2-4 ps which are in overall agreement with measured ones.
The aim of this work has been to provide, within a consistent theoretical framework, a better understanding of vibrational spectroscopy and dynamics for water on the α-alumina(0001) surface,ranging from very low water coverage (similar to the UHV case) up to medium-high coverages, resembling the hydroxylated oxide in environmental moist conditions.
Glycosylphosphatidylinositols (GPIs) are highly complex glycolipids that serve as membrane anchors to a large variety of eukaryotic proteins. These are covalently attached to a group of peripheral proteins called GPI-anchored proteins (GPI-APs) through a post-translational modification in the endoplasmic reticulum. The GPI anchor is a unique structure composed of a glycan, with phospholipid tail at one end and a phosphoethanolamine linker at the other where the protein attaches. The glycan part of the GPI comprises a conserved pseudopentasaccharide core that could branch out to carry additional glycosyl or phosphoethanolamine units. GPI-APs are involved in a diverse range of cellular processes, few of which are signal transduction, protein trafficking, pathogenesis by protozoan parasites like the malaria- causing parasite Plasmodium falciparum. GPIs can also exist freely on the membrane surface without an attached protein such as those found in parasites like Toxoplasma gondii, the causative agent of Toxoplasmosis. These molecules are both structurally and functionally diverse, however, their structure-function relationship is still poorly understood. This is mainly because no clear picture exists regarding how the protein and the glycan arrange with respect to the lipid layer. Direct experimental evidence is rather scarce, due to which inconclusive pictures have emerged, especially regarding the orientation of GPIs and GPI-APs on membrane surfaces and the role of GPIs in membrane organization. It appears that computational modelling through molecular dynamics simulations would be a useful method to make progress. In this thesis, we attempt to explore characteristics of GPI anchors and GPI-APs embedded in lipid bilayers by constructing molecular models at two different resolutions – all-atom and coarse-grained.
First, we show how to construct a modular molecular model of GPIs and GPI-anchored proteins that can be readily extended to a broad variety of systems, addressing the micro-heterogeneity of GPIs. We do so by creating a hybrid link to which GPIs of diverse branching and lipid tails of varying saturation with their optimized force fields, GLYCAM06 and Lipid14 respectively, can be attached. Using microsecond simulations, we demonstrate that GPI prefers to “flop-down” on the membrane, thereby, strongly interacting with the lipid heads, over standing upright like a “lollipop”. Secondly, we extend the model of the GPI core to carry out a systematic study of the structural aspects of GPIs carrying different side chains (parasitic and human GPI variants) inserted in lipid bilayers. Our results demonstrate the importance of the side branch residues as these are the most accessible, and thereby, recognizable epitopes. This finding qualitatively agrees with experimental observations that highlight the role of the side branches in immunogenicity of GPIs and the specificity thereof. The overall flop-down orientation of the GPIs with respect to the bilayer surface presents the side chain residues to face the solvent. Upon attaching the green fluorescent protein (GFP) to the GPI, it is seen to lie in close proximity to the bilayer, interacting both with the lipid heads and glycan part of the GPI. However the orientation of GFP is sensitive to the type of GPI it is attached to. Finally, we construct a coarse-grained model of the GPI and GPI-anchored GFP using a modified version of the MARTINI force-field, using which the timescale is enhanced by at least an order of magnitude compared to the atomistic system.
This study provides a theoretical perspective on the conformational behavior of the GPI core and some of its branched variations in presence of lipid bilayers, as well as draws comparisons with experimental observations. Our modular atomistic model of GPI can be further employed to study GPIs of variable branching, and thereby, aid in designing future experiments especially in the area of vaccines and drug therapies. Our coarse-grained model can be used to study dynamic aspects of GPIs and GPI-APs w.r.t plasma membrane organization. Furthermore, the backmapping technique of converting coarse-grained trajectory back to the atomistic model would enable in-depth structural analysis with ample conformational sampling.
Acting during phase II metabolism, sulfotransferases (SULTs) serve detoxification by transforming a broad spectrum of compounds from pharmaceutical, nutritional, or environmental sources into more easily excretable metabolites. However, SULT activity has also been shown to promote formation of reactive metabolites that may have genotoxic effects. SULT subtype 1E1 (SULT1E1) was identified as a key player in estrogen homeostasis, which is involved in many physiological processes and the pathogenesis of breast and endometrial cancer. The development of an in silico prediction model for SULT1E1 ligands would therefore support the development of metabolically inert drugs and help to assess health risks related to hormonal imbalances. Here, we report on a novel approach to develop a model that enables prediction of substrates and inhibitors of SULT1E1. Molecular dynamics simulations were performed to investigate enzyme flexibility and sample protein conformations. Pharmacophores were developed that served as a cornerstone of the model, and machine learning techniques were applied for prediction refinement. The prediction model was used to screen the DrugBank (a database of experimental and approved drugs): 28% of the predicted hits were reported in literature as ligands of SULT1E1. From the remaining hits, a selection of nine molecules was subjected to biochemical assay validation and experimental results were in accordance with the in silico prediction of SULT1E1 inhibitors and substrates, thus affirming our prediction hypotheses.
Membrane adhesion is a fundamental biological process in which membranes are attached to neighboring membranes or surfaces. Membrane adhesion emerges from a complex interplay between the binding of membrane-anchored receptors/ligands and the membrane properties. In this work, we study membrane adhesion mediated by lipid-anchored saccharides using microsecond-long full-atomistic molecular dynamics simulations. Motivated by neutron scattering experiments on membrane adhesion via lipid-anchored saccharides, we investigate the role of LeX, Lac1, and Lac2 saccharides and membrane fluctuations in membrane adhesion.
We study the binding of saccharides in three different systems: for saccharides in water, for saccharides anchored to essentially planar membranes at fixed separations, and for saccharides anchored to apposing fluctuating membranes. Our simulations of two saccharides in water indicate that the saccharides engage in weak interactions to form dimers. We find that the binding occurs in a continuum of bound states instead of a certain number of well-defined bound structures, which we term as "diffuse binding".
The binding of saccharides anchored to essentially planar membranes strongly depends on separation of the membranes, which is fixed in our simulation system. We show that the binding constants for trans-interactions of two lipid-anchored saccharides monotonically decrease with increasing separation. Saccharides anchored to the same membrane leaflet engage in cis-interactions with binding constants comparable to the trans-binding constants at the smallest membrane separations. The interplay of cis- and trans-binding can be investigated in simulation systems with many lipid-anchored saccharides. For Lac2, our simulation results indicate a positive cooperativity of trans- and cis-binding. In this cooperative binding the trans-binding constant is enhanced by the cis-interactions. For LeX, in contrast, we observe no cooperativity between trans- and cis-binding. In addition, we determine the forces generated by trans-binding of lipid-anchored saccharides in planar membranes from the binding-induced deviations of the lipid-anchors. We find that the forces acting on trans-bound saccharides increase with increasing membrane separation to values of the order of 10 pN.
The binding of saccharides anchored to the fluctuating membranes results from an interplay between the binding properties of the lipid-anchored saccharides and membrane fluctuations. Our simulations, which have the same average separation of the membranes as obtained from the neutron scattering experiments, yield a binding constant larger than in planar membranes with the same separation. This result demonstrates that membrane fluctuations play an important role at average membrane separations which are seemingly too large for effective binding. We further show that the probability distribution of the local separation can be well approximated by a Gaussian distribution. We calculate the relative membrane roughness and show that our results are in good agreement with the roughness values reported from the neutron scattering experiments.
This thesis studies strong, completely charged polyelectrolyte brushes. Extensive molecular dynamics simulations are performed on different polyelectrolyte brush systems using local compute servers and massively parallel supercomputers. The full Coulomb interaction of charged monomers, counterions, and salt ions is treated explicitly. The polymer chains are anchored by one of their ends to a uncharged planar surface. The chains are treated under good solvent conditions. Monovalent salt ions (1:1 type) are modelled same as counterions. The studies concentrate on three different brush systems at constant temperature and moderate Coulomb interaction strength (Bjerrum length equal to bond length): The first system consists of a single polyelectrolyte brush anchored with varying grafting density to a plane. Results show that chains are extended up to about 2/3 of their contour length. The brush thickness slightly grows with increasing anchoring density. This slight dependence of the brush height on grafting density is in contrast to the well known scaling result for the osmotic brush regime. That is why the result obtained by simulations has stimulated further development of theory as well as new experimental investigations on polyelectrolyte brushes. This observation can be understood on a semi-quantitative level using a simple scaling model that incorporates excluded volume effects in a free-volume formulation where an effective cross section is assigned to the polymer chain from where couterions are excluded. The resulting regime is called nonlinear osmotic brush regime. Recently this regime was also obtained in experiments. The second system studied consists of polyelectrolyte brushes with added salt in the nonlinear osmotic regime. Varying salt is an important parameter to tune the structure and properties of polyelectrolytes. Further motivation is due to a theoretical scaling prediction by Pincus for the salt dependence of brush thickness. In the high salt limit (salt concentration much larger than counterion concentration) the brush height is predicted to decrease with increasing external salt, but with a relatively weak power law showing an exponent -1/3. There is some experimental and theoretical work that confirms this prediction, but there are other results that are in contradiction. In such a situation simulations are performed to validate the theoretical prediction. The simulation result shows that brush thickness decreases with added salt, and indeed is in quite good agreement with the scaling prediction by Pincus. The relation between buffer concentration and the effective ion strength inside the brush at varying salt concentration is of interest both from theoretical as well as experimental point of view. The simulation result shows that mobile ions (counterions as well as salt) distribute nonhomogeneously inside and outside of the brush. To explain the relation between the internal ion concentration with the buffer concentration a Donnan equilibrium approach is employed. Modifying the Donnan approach by taking into account the self-volume of polyelectrolyte chains as indicated above, the simulation result can be explained using the same effective cross section for the polymer chains. The extended Donnan equilibrium relation represents a interesting theoretical prediction that should be checked by experimental data. The third system consist of two interacting polyelectrolyte brushes that are grafted to two parallel surfaces. The interactions between brushes are important, for instance, in stabilization of dispersions against flocculation. In the simulations pressure is evaluated as a function of separation D between the two grafting planes. The pressure behavior shows different regimes for decreasing separation. This behavior is in qualitative agreement with experimental data. At relatively weak compression the pressure behavior obtained in the simulation agrees with a 1/D power law predicted by scaling theory. Beyond that the present study could supply new insight for understanding the interaction between polyelectrolyte brushes.
To determine whether Förster resonance energy transfer (FRET) measurements can provide quantitative distance information in single-molecule fluorescence experiments on polypeptides, we measured FRET efficiency distributions for donor and acceptor dyes attached to the ends of freely diffusing polyproline molecules of various lengths. The observed mean FRET efficiencies agree with those determined from ensemble lifetime measurements but differ considerably from the values expected from Förster theory, with polyproline treated as a rigid rod. At donor–acceptor distances much less than the Förster radius R0, the observed efficiencies are lower than predicted, whereas at distances comparable to and greater than R0, they are much higher. Two possible contributions to the former are incomplete orientational averaging during the donor lifetime and, because of the large size of the dyes, breakdown of the point-dipole approximation assumed in Förster theory. End-to-end distance distributions and correlation times obtained from Langevin molecular dynamics simulations suggest that the differences for the longer polyproline peptides can be explained by chain bending, which considerably shortens the donor–acceptor distances.