Biomedical subjects

D Peter Tieleman

Publications and source records attributed to D Peter Tieleman.

At least 19 recordsLinked to original sources

PubMed2007

Simulation of the coupling between nucleotide binding and transmembrane domains in the ATP binding cassette transporter BtuCD.

The nucleotide-induced structural rearrangements in ATP binding cassette (ABC) transporters, leading to substrate translocation, are largely unknown. We have modeled nucleotide binding and release in the vitamin B(12) importer BtuCD using perturbed elastic network calculations and biased molecular dynamics simulations. Both models predict that nucleotide release decreases the tilt between the two transmembrane domains and opens the cytoplasmic gate. Nucleotide binding has the opposite effect. The observed coupling may be relevant for all ABC transporters because of the conservation of nucleotide binding domains and the shared role of ATP in ABC transporters. The rearrangements in the cytoplasmic gate region do not provide enough space for B(12) to diffuse from the transporter pore into the cytoplasm, which could suggest that peristaltic forces are needed to exclude B(12) from the transporter pore.

ATP-Binding Cassette Transporters↗

PubMed2007

Modifying the OPLS-AA force field to improve hydration free energies for several amino acid side chains using new atomic charges and an off-plane charge model for aromatic residues.

The hydration free energies of amino acid side chains are an important determinant of processes that involve partitioning between different environments, including protein folding, protein complex formation, and protein-membrane interactions. Several recent papers have shown that calculated hydration free energies for polar and aromatic residues (Trp, His, Tyr, Asn, Gln, Asp, Glu) in several common molecular dynamics force fields differ significantly from experimentally measured values. We have attempted to improve the hydration energies for these residues by modifying the partial charges of the OPLS-AA force field based on natural population analysis of density functional theory calculations. The resulting differences between calculated hydration free energies and experimental results for the seven side chain analogs are less than 0.1 kcal/mol. Simulations of the synthetic Trp-rich peptide Trpzip2 show that the new charges lead to significantly improved geometries for interacting Trp-side chains. We also investigated an off-plane charge model for aromatic rings that more closely mimics their electronic configuration. This model results in an improved free energy of hydration for Trp and a somewhat altered benzene-sodium potential of mean force with a more favorable energy for direct benzene-sodium contact.

Amino Acids↗

PubMed2006

Opening and closing motions in the periplasmic vitamin B12 binding protein BtuF.

BtuF is the periplasmic binding protein (PBP) in the vitamin B(12) uptake system in Escherichia coli where it is associated with the ABC transporter BtuCD. When the ligand binds, PBPs generally display large conformational changes, commonly termed the Venus flytrap mechanism. BtuF belongs to a group of PBPs that, on the basis of crystal structures, does not appear to display such behavior. Using 480 ns multicopy molecular dynamics simulations of apo and holo forms of the protein, we investigate the dynamics of BtuF. We find BtuF to be more flexible than previously assumed, displaying clear opening and closing motions which are more pronounced in the apo form. The protein behavior is compatible with a PBP functional model that postulates a closed conformation for the ligand-bound state, whereas the empty form fluctuates between open and closed conformations. Elastic network normal-mode analysis suggests that all BtuF-like PBPs are capable of similar opening and closing motions. It also makes the typical Venus flytrap domain motions a likely common means of how PBP-ABC transporter interaction could occur.

Escherichia coli↗

PubMed2006

Nanopore-facilitated, voltage-driven phosphatidylserine translocation in lipid bilayers--in cells and in silico.

Nanosecond, megavolt-per-meter pulses--higher power but lower total energy than the electroporative pulses used to introduce normally excluded material into biological cells--produce large intracellular electric fields without destructively charging the plasma membrane. Nanoelectropulse perturbation of mammalian cells causes translocation of phosphatidylserine (PS) to the outer face of the cell, intracellular calcium release, and in some cell types a subsequent progression to apoptosis. Experimental observations and molecular dynamics (MD) simulations of membranes in pulsed electric fields presented here support the hypothesis that nanoelectropulse-induced PS externalization is driven by the electric potential that appears across the lipid bilayer during a pulse and is facilitated by the poration of the membrane that occurs even during pulses as brief as 3 ns. MD simulations of phospholipid bilayers in supraphysiological electric fields show a tight association between PS externalization and membrane pore formation on a nanosecond time scale that is consistent with experimental evidence for electropermeabilization and anode-directed PS translocation after nanosecond electric pulse exposure, suggesting a molecular mechanism for nanoelectroporation and nanosecond PS externalization: electrophoretic migration of the negatively charged PS head group along the surface of nanometer-diameter electropores initiated by field-driven alignment of water dipoles at the membrane interface.

Biological Transport↗

PubMed2006

Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop.

The potential of mean force (PMF) of a phospholipid in a bilayer is a key thermodynamic property that describes the energetic cost of localized lipid defects. We have calculated the PMF by umbrella sampling using molecular dynamics simulations. The profile has a deep minimum at the equilibrium position in the bilayer and steeply rises for displacements both deeper into the bilayer and moving away from the bilayer. As the lipid loses contact with the bilayer, the profile abruptly flattens without a significant barrier. The calculated free energy difference of 80 kJ/mol between the minimum of the PMF and the value in water agrees well with the free energy difference calculated from the experimentally measured critical micelle concentration. Significant water/lipid defects form when a lipid is forced into the bilayer interior, in the form of a small water pore that spans the membrane. The energy required to form such a water pore is also found to be 80 kJ/mol. On the basis of this energy, we estimate the lipid flip-flop rate and permeability rate of sodium ions. The resulting rates are in good agreement with experimental measurements, suggesting lipid flip-flop and basal permeability of ions are pore mediated.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2006

The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter.

The nucleotide binding domains (NBDs) are the energy supplying subunits of ATP-binding cassette (ABC) proteins. They power transport by binding and hydrolyzing ATP. Tracing the pathway between different conformational states of the NBDs during ATP binding, hydrolysis, and release has, however, proven difficult. We have used molecular dynamics simulations to study the ATP-driven association of the NBDs of the maltose ABC transporter, MalK, based on the crystal structures of its open and semiopen dimers. When MgATP was introduced into the binding pockets, the semiopen dimer transitioned to a closed conformation, whereas the open dimer evolved to a semiopen state. In the absence of docked MgATP, however, the twin NBDs of both the open and semiopen starting configurations drifted further apart. Both the presence of MgATP and direct cross-interface protein-protein hydrogen bonds, primarily involving the D-loop, quite likely play a key role in initiating closure. The simulations of the MgATP-docked semiopen form indicate that completion of closure is driven mainly by cross-interface contacts between the gamma-phosphate of ATP and residues in the signature motif. Our simulations also give insight into possible interactions of MalK with the regulatory proteins MalT and enzyme IIA(glc).

ATP-Binding Cassette Transporters↗

PubMed2006

Nanopore formation and phosphatidylserine externalization in a phospholipid bilayer at high transmembrane potential.

Atomic-resolution molecular dynamics simulations of lipid bilayers containing 7% phosphatidylserine (PS) on one leaflet are consistent with experimental observations of membrane poration and PS externalization in living cells exposed to nanosecond, megavolt-per-meter electric pulses. Nanometer-diameter aqueous pores develop within nanoseconds after application of an electric field of 450 mV/nm, and electrophoretic transport of the anionic PS headgroup along the newly constructed hydrophilic pore surface commences even while pore formation is still in progress.

Cell Membrane Permeability↗

PubMed2006

Computer simulation of the distribution of hexane in a lipid bilayer: spatially resolved free energy, entropy, and enthalpy profiles.

The partitioning behavior of small molecules in lipid bilayers is important in a variety of areas including membrane protein folding and pharmacology. However, the inhomogeneous nature of lipid bilayers on a nanometer length scale complicates experimental studies of membrane partitioning. To gain more insight in the partitioning of a small molecule into the lipid bilayer, we have carried out atomistic computer simulations of hexane in a dioleoyl phosphatidylcholine model membrane. We have been able to obtain spatially resolved free energy, entropy, enthalpy, and heat capacity profiles based on umbrella sampling calculations at three different temperatures. In agreement with experiment, hexane partitions preferentially to the center of the bilayer. This process is driven almost entirely by a favorable entropy change, consistent with the hydrophobic effect. In contrast, partitioning to the densest region of the acyl chains is dominated by a favorable enthalpy change with a small entropy change, which is consistent with the "nonclassical" hydrophobic effect or "bilayer" effect. We explain the features of the entropy and enthalpy profiles in terms of density and free volume in the system.

Computer Simulation↗

PubMed2006

Computer simulations of transport through membranes: passive diffusion, pores, channels and transporters.

A key function of biological membranes is to provide mechanisms for the controlled transport of ions, nutrients, metabolites, peptides and proteins between a cell and its environment. We are using computer simulations to study several processes involved in transport. In model membranes, the distribution of small molecules can be accurately calculated; we are making progress towards understanding the factors that determine the partitioning behaviour in the inhomogeneous lipid environment, with implications for drug distribution, membrane protein folding and the energetics of voltage gating. Lipid bilayers can be simulated at a scale that is sufficiently large to study significant defects, such as those caused by electroporation. Computer simulations of complex membrane proteins, such as potassium channels and ATP-binding cassette (ABC) transporters, can give detailed information about the atomistic dynamics that form the basis of ion transport, selectivity, conformational change and the molecular mechanism of ATP-driven transport. This is illustrated in the present review with recent simulation studies of the voltage-gated potassium channel KvAP and the ABC transporter BtuCD.

ATP-Binding Cassette Transporters↗

PubMed2006

Computer simulations of ABC transporter components.

Current computer simulation techniques provide robust tools for studying the detailed structure and functional dynamics of proteins, as well as their interaction with each other and with other biomolecules. In this minireview, we provide an illustration of recent progress and future challenges in computer modeling by discussing computational studies of ATP-binding cassette (ABC) transporters. ABC transporters have multiple components that work in a well coordinated fashion to enable active transport across membranes. The mechanism by which members of this superfamily execute transport remains largely unknown. Molecular dynamics simulations initiated from high-resolution crystal structures of several ABC transporters have proven to be useful in the investigation of the nature of conformational coupling events that may drive transport. In addition, fruitful efforts have been made to predict unknown structures of medically relevant ABC transporters, such as P-glycoprotein, using homology-based computational methods. The various techniques described here are also applicable to gaining an atomically detailed understanding of the functional mechanisms of proteins in general.

ATP-Binding Cassette Transporters↗

PubMed2005

Computer simulation of partitioning of ten pentapeptides Ace-WLXLL at the cyclohexane/water and phospholipid/water interfaces.

BACKGROUND: Peptide-membrane interactions play a key role in the binding, partitioning and folding of membrane proteins, the activity of antimicrobial and fusion peptides, and a number of other processes. To gain a better understanding of the thermodynamics of such interactions, White and Wimley created an interfacial hydrophobicity scale based of the transfer free energy from water to octanol or lipid bilayers of a series of synthetic peptapeptides (Ace-WLXLL, with X being any of the twenty natural amino acids) (White and Wimley (1996) Nat. Struct. Biol. 3, 842-848). In this study, we performed molecular dynamics simulations of a representative set of ten of these peptides (X = D, K, R, N, A, T, S, I, F and W) in two membrane mimetic interfaces: water-cyclohexane (10 ns) and a fully solvated dioleoylphosphatidylcholine (DOPC) bilayer (50 ns) using both constant pressure and constant area ensembles. We focus on partitioning of the ten peptides at the cyclohexane/water and lipid/water interfaces. RESULTS: The peptides rapidly equilibrate (< 2 ns) and partition at the cyclohexane/water interface. The X3 guest residue assumes average orientations that depend on the nature of the side chain. At the DOPC/water interface, dynamics is much slower and convergence is difficult to achieve on a 50 ns timescale. Nonetheless, all peptides partition to the lipid/water interface with distributions with widths of 1-2 nm. The peptides assume a broad range of side chain and backbone orientations and have only a small effect on the area of the unit cell. On average, hydrophobic guest residues partition deeper into the hydrophobic core than hydrophilic residues. In some cases the peptides penetrate sufficiently deep to somewhat affect the distribution of the C=C double bond in DOPC. The relative distribution of the X3 guest residue compared to W1 and L5 is similar in the water/cyclohexane and water/lipid simulations. Snapshots show mostly extended backbone conformations in both environments. There is little difference between simulations at a constant area of 0.66 nm2 and simulations at constant pressure that approximately yield the same average area of 0.66 nm2. CONCLUSION: These peptides were designed to assume extended conformations, which is confirmed by the simulations. The distribution of the X3 side chain depends on its nature, and can be determined from molecular dynamics simulations. The time scale of peptide motion at a phospholipids-water interface is too long to directly calculate the experimentally measured hydrophobicity scale to test and improve the simulation parameters. This should be possible at the water/cyclohexane interface and likely will become feasible in the future for the phospholipids/water case.

Amino Acid Sequence↗

PubMed2005

Mechanism of helix nucleation and propagation: microscopic view from microsecond time scale MD simulations.

Microsecond time scale molecular dynamics simulations of the 13-residue peptide RN24 were carried out to investigate the mechanism of helix nucleation and propagation. An extended and an ideal alpha-helical conformation were used as starting structures. NOE-derived interatomic distances were compared with distances calculated from the simulations, showing good agreement between experimental and simulation results. Based on almost 200 helix nucleation events observed, beta-turn and 3(10)-helix play an important role in helix nucleation; in most cases, helix nucleation is preceded by the formation of a short-lived beta-turn (60% probability) or 3(10)-helix (20% probability), and the conversion from beta-turn to alpha-turn involves bifurcated hydrogen bonds. Helix propagation in RN24 appears to occur preferentially from the N-terminus to the C-terminus, and helix unfolding preferentially in the opposite direction.

C-Peptide↗

PubMed2005

The role of extra-membranous inter-helical loops in helix-helix interactions.

The effect of a short loop connecting two transmembrane alpha-helices was studied using molecular dynamics simulations. Helices F and G from bacteriorhodopsin and two corresponding polyalanine helices were embedded in octane and POPC membranes in a transmembrane configuration both with and without the inter-helical loop. The results indicate that the membrane environment and the sequence of the loop are more influential on the dynamics and structure of the motif than the presence of a loop as such, at least for the time-scales investigated. The four residues in the FG loop are stabilized by four hydrogen bonds. These hydrogen bonds are not present in the polyalanine loop, causing it to be more flexible than the FG loop. This effect was observed independently of the protein environment, stressing the importance of the sequence. The structural analysis indicates that the loop has weak stabilizing properties in all environments. The stabilization due to the presence of the loop was strongest in a simulation of the FG fragment in a membrane-mimetic octane slab. In the simulations of the helix-loop-helix motif embedded in an explicit lipid bilayer model, the lipid bilayer interface compensates to a large extent for the absence of the loop.

Amino Acid Motifs↗

PubMed2005

Molecular models of lipopeptide detergents: large coiled-coils with hydrocarbon interiors.

We have constructed molecular models of octameric micelles formed by a recently developed lipopeptide detergent consisting of a single amphipathic alpha-helix coupled to two acyl chains at either end of the helix. The models explain the experimentally observed aggregation behavior of peptides with different acyl chain lengths. The octameric micelles form a unique coiled-coil structure, with the acyl chains in a nearly frozen conformation inside the cylindrical assemblies. Two extreme models with helices either all parallel or in an alternating orientation suggest that the alternating orientation is energetically more favorable. The models suggest several new directions for further diversifying this new class of detergents for the structural studies of membrane proteins.

Detergents↗

PubMed2005

Self-association of transmembrane alpha-helices in model membranes: importance of helix orientation and role of hydrophobic mismatch.

Interactions between transmembrane helices play a key role in almost all cellular processes involving membrane proteins. We have investigated helix-helix interactions in lipid bilayers with synthetic tryptophan-flanked peptides that mimic the membrane spanning parts of membrane proteins. The peptides were functionalized with pyrene to allow the self-association of the helices to be monitored by pyrene fluorescence and Trp-pyrene fluorescence resonance energy transfer (FRET). Specific labeling of peptides at either their N or C terminus has shown that helix-helix association occurs almost exclusively between antiparallel helices. Furthermore, computer modeling suggested that antiparallel association arises primarily from the electrostatic interactions between alpha-helix backbone atoms. We propose that such interactions may provide a force for the preferentially antiparallel association of helices in polytopic membrane proteins. Helix-helix association was also found to depend on the lipid environment. In bilayers of dioleoylphosphatidylcholine, in which the hydrophobic length of the peptides approximately matched the bilayer thickness, association between the helices was found to require peptide/lipid ratios exceeding 1/25. Self-association of the helices was promoted by either increasing or decreasing the bilayer thickness, and by adding cholesterol. These results indicate that helix-helix association in membrane proteins can be promoted by unfavorable protein-lipid interactions.

Computer Simulation↗

PubMed2005

A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein.

The uptake of nutrients is essential for the survival of bacterial cells. Many specialized systems have evolved, such as the maltose-dependent ABC transport system that transfers oligosaccharides through the cytoplasmic membrane. The maltose/maltodextrin-binding protein (MBP) serves as an initial high-affinity binding component in the periplasm that delivers the bound sugar into the cognate ABC transporter MalFGK(2). We have investigated the domain motions induced by the binding of the ligand maltotriose into the binding cleft using molecular dynamics simulations. We find that MBP is predominantly in the open state without ligand and in the closed state with ligand bound. Oligosaccharide binding induces a closure motion (30.0 degrees rotation), whereas ligand removal leads to domain opening (32.6 degrees rotation) around a well-defined hinge affecting key areas relevant for chemotaxis and transport. Our simulations suggest that a "hook-and-eye" motif is involved in the binding. A salt bridge between Glu-111 and Lys-15 forms that effectively locks the protein-ligand complex in a semiclosed conformation inhibiting any further opening and promoting complete closure. This previously unrecognized feature seems to secure the ligand in the binding site and keeps MBP in the closed conformation and suggests a role in the initial steps of substrate transport.

Amino Acid Motifs↗

PubMed2004

2H-NMR study and molecular dynamics simulation of the location, alignment, and mobility of pyrene in POPC bilayers.

The alignment of pyrene in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer was investigated using two different approaches, namely solid-state (2)H-NMR spectroscopy and molecular dynamics (MD) simulations. Quadrupolar splittings from (2)H-NMR spectra of deuterated pyrene-d(10) in an oriented lipid bilayer give information about the orientation of C-D bonds with respect to the membrane normal. From MD simulations, geometric information is accessible via trajectories. By defining molecular and bond order parameters, the data from MD trajectories and NMR spectra can be compared straightforwardly. To ensure that the results from both methods are comparable, parameters of the experimental and the simulation setup were chosen to be as similar as possible. From simulations, we saw that pyrene prefers a position inside the lipid membrane near the headgroups and has no tendency to diffuse from one monolayer of the membrane to the other. The results from simulation and NMR show that the normal of the molecular plane is aligned nearly perpendicular to the bilayer normal. The long axis of pyrene lies preferentially parallel to the bilayer normal within a range of +/-30 degrees . The results from the two different methods are remarkably consistent. The good agreement can be explained by the fact that the different kind of motions of a pyrene molecule are already averaged within a few nanoseconds, which is the timescale covered by the MD simulation.

Computer Simulation↗

PubMed2004

Computer simulations of membrane proteins.

Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.

Bacterial Proteins↗