Biomedical subjects

Thomas B Woolf

Publications and source records attributed to Thomas B Woolf.

At least 19 recordsLinked to original sources

PubMed2007

How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations.

Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.

Alanine↗

PubMed2007

Insights into protein structure and function from disorder-complexity space.

Intrinsically disordered proteins have a wide variety of important functional roles. However, the relationship between sequence and function in these proteins is significantly different than that for well-folded proteins. In a previous work, we showed that the propensity to be disordered can be recognized based on sequence composition alone. Here that analysis is furthered by examining the relationship of disorder propensity to sequence complexity, where the metrics for these two properties depend only on composition. The distributions of 40 amino acid peptides from both ordered and disordered proteins are graphed in this disorder-complexity space. An analysis of Swiss-Prot shows that most peptides have high complexity and relatively low disorder. However, there are also an appreciable number of low complexity-high disorder peptides in the database. In contrast, there are no low complexity-low disorder peptides. A similar analysis for peptides in the PDB reveals a much narrower distribution, with few peptides of low complexity and high disorder. In this case, the bounds of the disorder-complexity distribution are well defined and might be used to evaluate the likelihood that a peptide can be crystallized with current methods. The disorder-complexity distributions of individual proteins and sets of proteins grouped by function are also examined. Among individual proteins, there is an enormous variety of distributions that in some cases can be rationalized with regard to function. Groups of functionally related proteins are found to have distributions that are similar within each group but show notable differences between groups. Finally, a pattern matching algorithm is used to search for proteins with particular disorder-complexity distributions. The results suggest that this approach might be used to identify relationships between otherwise dissimilar proteins.

Algorithms↗

PubMed2006

Interaction of protegrin-1 with lipid bilayers: membrane thinning effect.

Protegrins (PG) are important in defending host tissues, preventing infection via an attack on the membrane surface of invading microorganisms. Protegrins have powerful antibiotic abilities, but the molecular-level mechanisms underlying the interactions of their beta-sheet motifs with the membrane are not known. Protegrin-1 (PG-1) is composed of 18 amino acids with a high content of basic residues and two disulfide bonds. Here we focused on the stability of PG-1 at the amphipathic interface in lipid bilayers and on the details of the peptide-membrane interactions. We simulated all-atom models of the PG-1 monomer with explicit water and lipid bilayers composed of both homogeneous POPC (palmitoyl-oleyl-phosphatidylcholine) lipids and a mixture of POPC/POPG (palmitoyl-oleyl-phosphatidylglycerol) (4:1) lipids. We observed that local thinning of the lipid bilayers mediated by the peptide is enhanced in the lipid bilayer containing POPG, consistent with experimental results of selective membrane targeting. The beta-hairpin motif of PG-1 is conserved in both lipid settings, whereas it is highly bent in aqueous solution. The conformational dynamics of PG-1, especially the highly charged beta-hairpin turn region, are found to be mostly responsible for disturbing the membrane. Even though the eventual membrane disruption requires PG-1 oligomers, our simulations clearly show the first step of the monomeric effects. The thinning effects in the bilayer should relate to pore/channel formation in the lipid bilayer and thus be responsible for further defects in the membrane caused by oligomer.

Antimicrobial Cationic Peptides↗

PubMed2006

Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling.

We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.

Alanine↗

PubMed2005

Folding is not required for bilayer insertion: replica exchange simulations of an alpha-helical peptide with an explicit lipid bilayer.

We implement the replica exchange molecular dynamics algorithm to study the interactions of a model peptide (WALP-16) with an explicitly represented DPPC membrane bilayer. We observe the spontaneous, unbiased insertion of WALP-16 into the DPPC bilayer and its folding into an alpha-helix with a transbilayer orientation. The free energy surface suggests that the insertion of the peptide into the DPPC bilayer precedes secondary structure formation. Although the peptide has some propensity to form a partially helical structure in the interfacial region of the DPPC/water system, this state is not a productive intermediate but rather an off-pathway trap for WALP-16 insertion. Equilibrium simulations show that the observed insertion/folding pathway mirrors the potential of mean force (PMF). Calculation of the enthalpic and entropic contributions to this PMF show that the surface bound conformation of WALP-16 is significantly lower in energy than other conformations, and that the insertion of WALP-16 into the bilayer without regular secondary structure is enthalpically unfavorable by 5-10 kcal/mol/residue. The observed insertion/folding pathway disagrees with the dominant conceptual model, which is that a surface-bound helix is an obligatory intermediate for the insertion of alpha-helical peptides into lipid bilayers. In our simulations, the observed insertion/folding pathway is favored because of a large (>100 kcal/mol) increase in system entropy that occurs when the unstructured WALP-16 peptide enters the lipid bilayer interior. The insertion/folding pathway that is lowest in free energy depends sensitively on the near cancellation of large enthalpic and entropic terms. This suggests the possibility that intrinsic membrane peptides may have a diversity of insertion/folding behaviors depending on the exact system of peptide and lipid under consideration.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Using non-Gaussian density functional fits to improve relative free energy calculations.

The accurate and reliable computation of relative free energy differences remains an important long-term goal. Major stumbling blocks for achieving this goal reflect the difficulty of sampling in a known fashion along the reaction coordinate and of maximally combining information that has been collected from the simulation along the reaction coordinate. In this paper we examine the utility of a probability density functional type fit to the distribution of work events collected during a nonequilibrium sample along the reaction coordinate. This approach can readily be generalized to equilibrium sampling and has the potential to estimate the quality of a relative free energy estimate as data are being collected. The method may have the greatest utility for nonequilibrium sampling where non-Gaussian work distributions are generally present that are strongly dominated by rare event sampling in the tail region. We believe that the approach can be used to augment the design and the error analysis of relative free energy computations thus improving the ability to reliably and with known accuracy compute a relative free energy.

Journal Article↗

PubMed2005

Mesoscopic simulation of adsorption of peptides in a hydrophobic chromatography system.

Mesoscopic simulations using Langevin dipoles on a lattice for the solvent and calculated partial charges for the solute have been used to estimate free energies of adsorption from data on reversed-phase chromatography on nine protected peptides covering a wide range of structures. There is a single parameter, the effective solvent dipole moment, that is fit to data for one peptide and used to predict properties of the other eight peptides. Good agreement of adsorption chemical potentials, including order of chromatographic retention times, is found for calculations that are Boltzmann-averaged over a set of orientations. In addition, the results suggest that there are preferential orientations for each peptide at the model hydrophobic chromatographic surface. Estimation methods for adsorption based on molecular descriptors and hydrophobicity scales are shown to be unreliable for these systems. With refinements and extensions, this simulation method should be applicable to solvents containing salt, such as in hydrophobic interaction chromatography, and to larger solutes including proteins.

Adsorption↗

PubMed2004

Atomistic simulations of biologically realistic transmembrane potential gradients.

We present all-atom molecular dynamics simulations of biologically realistic transmembrane potential gradients across a DMPC bilayer. These simulations are the first to model this gradient in all-atom detail, with the field generated solely by explicit ion dynamics. Unlike traditional bilayer simulations that have one bilayer per unit cell, we simulate a 170 mV potential gradient by using a unit cell consisting of three salt-water baths separated by two bilayers, with full three-dimensional periodicity. The study shows that current computational resources are powerful enough to generate a truly electrified interface, as we show the predicted effect of the field on the overall charge distribution. Additionally, starting from Poisson's equation, we show a new derivation of the double integral equation for calculating the potential profile in systems with this type of periodicity.

Biophysics↗

PubMed2004

Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein.

Intrinsically disordered proteins are an important class of proteins with unique functions and properties. Here, we have applied a support vector machine (SVM) trained on naturally occurring disordered and ordered proteins to examine the contribution of various parameters (vectors) to recognizing proteins that contain disordered regions. We find that a SVM that incorporates only amino acid composition has a recognition accuracy of 87+/-2%. This result suggests that composition alone is sufficient to accurately recognize disorder. Interestingly, SVMs using reduced sets of amino acids based on chemical similarity preserve high recognition accuracy. A set as small as four retains an accuracy of 84+/-2%; this suggests that general physicochemical properties rather than specific amino acids are important factors contributing to protein disorder.

Amino Acid Sequence↗

PubMed2004

Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films.

The dynamic phase behavior of a classical Heisenberg spin system with a bilinear exchange anisotropy in a planar thin film geometry has been investigated by Monte Carlo simulations using different forms for the stochastic dynamics. In simulations of the dynamic phase transition (DPT) in films subject to a pulsed oscillatory external field with competing surface fields, both Glauber and Metropolis dynamics show a continuous DPT. But while the field amplitude dependence of the DPT is similar in both cases, the transition region for the DPT as a function of temperature is more extended with Metropolis dynamics. The difference arises from a decoupling of the surface and bulk responses of the film near the dynamic phase transition with Metropolis dynamics that is not evident for Glauber dynamics.

Journal Article↗

PubMed2004

Using overlap and funnel sampling to obtain accurate free energies from nonequilibrium work measurements.

Two concepts are presented for accurate nonequilibrium work free-energy measurements, realized both in molecular simulation and experiment. First, the need for an intermediate important to both the reference and the target systems (overlap) is indicated. Second, the use of a soft path from each end point to the intermediate (funnel) is demonstrated. Schemes implementing these concepts dramatically improve efficiency and accuracy of free energy calculations, as shown by calculation of the free energy of ion charging in water, and the free energy change in mutation of an adenosine molecule.

Adenosine↗

PubMed2004

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods.

A challenge in free energy calculation for complex molecular systems by computer simulation is to obtain a reliable estimate within feasible computational time. In this study, we suggest an answer to this challenge by exploring a simple method, overlap sampling (OS), for producing reliable free-energy results in an efficient way. The formalism of the OS method is based on ensuring sampling of important overlapping phase space during perturbation calculations. This technique samples both forward and reverse free energy perturbation (FEP) to improve the free-energy calculation. It considers the asymmetry of the FEP calculation and features an ability to optimize both the precision and the accuracy of the measurement without affecting the simulation process itself. The OS method is tested at two optimization levels: no optimization (simple OS), and full optimization (equivalent to Bennett's method), and compared to conventional FEP techniques, including the widely used direct FEP averaging method, on three alchemical mutation systems: (a) an anion transformation in water solution, (b) mutation between methanol and ethane, and (c) alchemical change of an adenosine molecule. It is consistently shown that the reliability of free-energy estimates can be greatly improved using the OS techniques at both optimization levels, while the performance of Bennett's method is particularly striking. In addition, the efficiency of a calculation can be significantly improved because the method is able to (a) converge to the right answer quickly, and (b) work for large perturbations. The basic two-stage OS method can be extended to admit additional stages, if needed. We suggest that the OS method can be used as a general perturbation technique for computing free energy differences in molecular simulations.

Journal Article↗

PubMed2004

Tools for channels: moving towards molecular calculations of gating and permeation in ion channel biophysics.

Recent X-ray structures of voltage gated potassium channels provide an exciting opportunity to connect molecular structures with measured biological function. Two of the most important connections for these channels are: first, to the molecular basis behind selectivity and the associated free energy profile underlying ionic current flow and, second, to a true molecular understanding of the large-scale conformational transitions that underlie voltage dependent gating. But, existing computational tools need to be further developed to reach these goals. In this contribution to the symposia on sampling methods we outline our dynamic importance sampling method for sampling large-scale conformational transitions as well as our studies with non-equilibrium work events and equilibrium overlap sampling (OS) methods for sampling events related to the calculation of relative free energies.

Algorithms↗

PubMed2004

Changes in phosphatidylcholine headgroup tilt and water order induced by monovalent salts: molecular dynamics simulations.

The association between monovalent salts and neutral lipid bilayers is known to influence global bilayer structural properties such as headgroup conformational fluctuations and the dipole potential. The local influence of the ions, however, has been unknown due to limited structural resolution of experimental methods. Molecular dynamics simulations are used here to elucidate local structural rearrangements upon association of a series of monovalent Na(+) salts to a palmitoyl-oleoyl-phosphatidylcholine bilayer. We observe association of all ion types in the interfacial region. Larger anions, which are meant to rationalize data regarding a Hofmeister series of anions, bind more deeply within the bilayer than either Cl(-) or Na(+). Although the simulations are able to reproduce experimentally measured quantities, the analysis is focused on local properties currently invisible to experiments, which may be critical to biological systems. As such, for all ion types, including Cl(-), we show local ion-induced perturbations to headgroup tilt, the extent and direction of which is sensitive to ion charge and size. Additionally, we report salt-induced ordering of the water well beyond the interfacial region, which may be significant in terms of hydration repulsion between stacked bilayers.

Computer Simulation↗

PubMed2004

How environment supports a state: molecular dynamics simulations of two states in bacteriorhodopsin suggest lipid and water compensation.

The light-driven proton pump bacteriorhodopsin (bR) is a transmembrane protein that uses large conformational changes for proton transfer from the cytoplasmic to the extracellular regions. Crystal structures, due to their solvent conditions, do not resolve the effect of lipid molecules on these protein conformational changes. To begin to understand the molecular details behind such large conformational changes, we simulated two conformations of wild-type bacteriorhodopsin, one of the dark-adapted state and the second of an intermediate (M(O)) state, each within an explicit dimyristoyl-phosphatidylcholine (DMPC) lipid bilayer. The simulations included all-hydrogen and all-atom representations of protein, lipid, and water and were performed for 20 ns. We investigate the equilibrium properties and the dynamic motions of the two conformations in the lipid setting. We note that the conformational state of the M(O) intermediate bR remains markedly different from the dark-adapted bR state in that the M(O) intermediate shows rearrangement of the cytoplasmic portions of helices C, F, and G, and nearby loops. This difference in the states remained throughout the simulations, and the results are stable on the molecular dynamics timescale and provide an illustration of the changes in both lipid and water that help to stabilize a particular state. Our analysis focuses on how the environment adjusts to these two states and on how the dynamics of the helices, loops, and water molecules can be related to the pump mechanism of bacteriorhodopsin. For example, water generally behaves in the same manner on the extracellular sides of both simulations but is decreased in the cytoplasmic region of the M(O) intermediate. We suspect that the different water behavior is closely related to the fluctuations of microcavities volume in the protein interior, which is strongly coupled to the collective motion of the protein. Our simulation result suggests that experimental observation can be useful to verify a decreased number of waters in the cytoplasmic regions of the late-intermediate stages by measuring the rate of water exchange with the interior of the protein.

Bacteriorhodopsins↗

PubMed2003

Insights into the molecular mechanism of membrane fusion from simulation: evidence for the association of splayed tails.

We present coarse-grained simulations of fusion between two liposomes from which a detailed picture of lipid movements emerges. In these simulations the bilayers dilate at the contact edge, and the resulting increase in the area per lipid produces a tilting of the individual molecules as predicted. Fusion is initiated when some of these tilted lipids splay their aliphatic tails, such that the molecules are shared between the opposing leaflets. Multiple splayed lipids subsequently associate with their aliphatic tails in contact, which produces a new hydrophobic core. As the tails extend into a more parallel conformation the two outer leaflets become contiguous to produce a hemifused structure. The results have interesting implications for biological membrane fusion and suggest new possibilities for designing molecules that control fusion.

Computer Simulation↗

PubMed2003

Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change.

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.

Animals↗

PubMed2003

Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.

The recent determination of crystal structures for several important membrane proteins opens the way for comparative modeling of their membrane-spanning regions. However, the ability to predict correctly the structures of loop regions, which may be critical, for example, in ligand binding, remains a considerable challenge. To meet this challenge, accurate scoring methods have to discriminate between candidate conformations of an unknown loop structure. Some success in loop prediction has been reported for globular proteins; however, the proximity of membrane protein loops to the lipid bilayer casts doubt on the applicability of the same scoring methods to this problem. In this work, we develop "decoy libraries" of non-native folds generated, using the structures of two membrane proteins, with molecular dynamics and Monte Carlo techniques over a range of temperatures. We introduce a new approach for decoy library generation by constructing a flat distribution of conformations covering a wide range of Calpha-root-mean-square deviation (RMSD) from the native structure; this removes possible bias in subsequent scoring stages. We then score these decoy conformations with effective energy functions, using increasingly more cpu-intensive implicit solvent models, including (1) simple Coulombic electrostatics with constant or distance-dependent dielectrics; (2) atomic solvation parameters; (3) the effective energy function (EEF1) of Lazaridis and Karplus; (4) generalized Born/Analytical Continuum Solvent; and (5) finite-difference Poisson-Boltzmann energy functions. We show that distinction of native-like membrane protein loops may be achieved using effective energies with the assumption of a homogenous environment; thus, the absence of the adjacent lipid bilayer does not affect the scoring ability. In particular, the Analytical Continuum Solvent and finite-difference Poisson-Boltzmann energy functions are seen to be the most powerful scoring functions. Interestingly, the use of the uncharged states of ionizable sidechains is shown to aid prediction, particularly for the simplest energy functions.

Algorithms↗