Fluorescence polarization studies of squid giant axons stained with N-methylanilinonaphthalenesulfonates

The polarized components of the extrinsic fluorescence of squid giant axons stained with 2,6-MANS or 1,8-MANS were studied. The polarization properties of the fluorescence changes associated with voltage-clamp pulses were found to be very different from those of the static fluorescence, supporting the notion that the optical changes involve highly oriented membrane adsorbed fluorophores. The theoretical expectations according to this hypothesis are discussed in detail. The experimental results are in good agreement with the theory assuming that possible probes reorientations are solely due to the action of the applied electric field upon the probes electric dipole. The quantitative analysis of the data for 2,6 MANS provides a fairly accurate determination of the orientation of the membrane bound 2,6-MANS molecules responsible for the fluorescence changes. Such orientation appears to be independent of the membrane face exposed to staining. The data for 1,8-MANS indicate a very different orientation of this isomer. The results suggest a profitable use of extrinsic fluorophores for studies of the structural organization of nerve membranes.     

Fluorescence polarization studies of squid giant axons stained with N-methylanilinonaphthalenesulfonates.

The polarized components of the extrinsic fluorescence of squid giant axons stained with 2,6-MANS or 1,8-MANS were studied. The polarization properties of the fluorescence changes associated with voltage-clamp pulses were found to be very different from those of the static fluorescence, supporting the notion that the optical changes involve highly oriented membrane adsorbed fluorophores. The theoretical expectations according to this hypothesis are discussed in detail. The experimental results are in good agreement with the theory assuming that possible probes reorientations are soley due to the action of the applied electric field upon the probes electric dipole. The quantitative analysis of the data for 2,6-MANS provides a fairly accurate determination of the orientation of the membrane bound 2,6-MANS molecules responsible for the fluorescence changes. Such orientation appears to be independent of the membrane face exposed to staining. The data for 1,8-MANS indicate a very different orientation of this isomer. The results suggest a profitable use of extrinsic fluorophores for studies of the structural organization of nerve membranes.     

Contractile Torque as a Steering Mechanism for Orientation of Adherent Cells

It is well established that adherent cells change their orientation in response to non-uniform substrate stretching. Most observations indicate that cells orient away from the direction of the maximal substrate strain, whereas in some cases cells also align with the direction of the maximal strain. Previous studies suggest that orientation and steering of the cell may be closely tied to cytoskeletal contractile stress but they could not explain the mechanisms that direct cell reorientation. This led us to develop a simple, mechanistic theoretical model that could predict a direction of cell orientation in response to mechanical nonuniformities of the substrate. The model leads to a simple physical mechanism -- namely the contractile torque -- that directs the cell toward a new orientation in response to anisotropic substrate stretching or substrate material anisotropy. A direction of the torque is determined by a dependence of the contractile stress on substrate strain. Model predictions are tested in the case of simple elongation of the substrate and found to be consistent with experimental data from the literature.     

Simultaneous control of hand displacements and rotations in orientation-matching experiments.

In reach-to-grasp movements, the interaction between the hand changes in position and those in orientation is poorly understood. A theoretical approach previously proposed (Torres EB and Zipser D. J Neurophysiol 88: 1-13, 2002) assumes that motion strategies are resolved in space independently from the temporal dynamics of the motion and predicts the coarticulation of the hand transport and rotation along the path. The model implies that this simultaneous control is independent of variations in speed and initial posture and required matching orientation. This paper presents experimental data from human subjects that confirm the model's predictions in the context of realistic, unconstrained, orientation-matching motions. Speed independence is quantified in the similarity of the postural and endpoint position-orientation paths obtained under three different speeds. Significant differences in hand and joint kinematics are shown in response to changes in initial posture and target orientation. The robustness of coarticulation under all three experimental conditions supports the idea of an intermediate stage that resolves the geometry of the motion independent of its temporal dynamics.     

Computational Modeling of Orientation Tuning Dynamics in Monkey Primary Visual Cortex

In the primate visual pathway, orientation tuning of neurons is first observed in the primary visual cortex. The LGN cells that comprise the thalamic input to V1 are not orientation tuned, but some V1 neurons are quite selective. Two main classes of theoretical models have been offered to explain orientation selectivity: feedforward models, in which inputs from spatially aligned LGN cells are summed together by one cortical neuron; and feedback models, in which an initial weak orientation bias due to convergent LGN input is sharpened and amplified by intracortical feedback. Recent data on the dynamics of orientation tuning, obtained by a cross-correlation technique, may help to distinguish between these classes of models. To test this possibility, we simulated the measurement of orientation tuning dynamics on various receptive field models, including a simple Hubel-Wiesel type feedforward model: a linear spatiotemporal filter followed by an integrate-and-fire spike generator. The computational study reveals that simple feedforward models may account for some aspects of the experimental data but fail to explain many salient features of orientation tuning dynamics in V1 cells. A simple feedback model of interacting cells is also considered. This model is successful in explaining the appearance of Mexican-hat orientation profiles, but other features of the data continue to be unexplained.     

Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings

The conformations of two synthetic trisaccharides of blood group A and B (alpha-L-Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-alpha-D-Galp and alpha-L-Fucp-(1-->2)-[alpha-D-Galp-(1-->3)]-alpha-D-Galp, respectively) and of a type A tetrasaccharide alditol, Fucp-(1-->2)-[alpha-D-GalpNAc-(1-->3)]-beta-D-Galp-(1-->3)-GalNAc-ol, were studied by NMR measurements of one-bond C-H residual dipolar couplings in partially oriented liquid crystal solutions. The conformations of the three oligosaccharides were analyzed by generating thousands of structures using a Monte-Carlo method. Two different strategies were applied to calculate theoretical dipolar couplings for these structures. In the first method, the orientation of the molecule was calculated from the optimal fit of the molecular model to the experimental data, while in the second method the orientation tensor was calculated directly from the moment of inertia of the molecular model. Both methods of analysis give similar results but with slightly better agreement with experiment for the former one. The analysis of the results implies a single unique conformation for both blood group epitopes in solution in disagreement with theoretical models suggesting the existence of two conformers in solution.     

Calculation of spectra of absorption and circular dichroism of Rhodopseudomonas acidophila light harvesting complexes based on roentgen structural data

Absorption and circular dichroism spectra of two forms of the peripheral light-harvesting complex from photosynthetic purple bacteria Rhodopseudomonas acidophila were calculated. Calculations were carried out on the basis of exciton theory for circular aggregates of bacteriochlorophyll molecules and X-ray data for these forms of the complex. It was shown that theoretical spectra fit well experimental ones at the same values of excitation energy, homogeneous and inhomogeneous broadening, and bandwidth for all bacteriochlorophyll molecules of complexes. To approximate the circular dichroism spectra of complexes, it was necessary to change the orientations and the values of the moments of transition of Qy molecules relative to their orientation determined on the basis of X-ray structure analysis data.     

Corner detection in curvilinear dot grouping

Corners, or discontinuities in orientation, are one of the most salient and useful properties of contours. But how sensitive are we in detecting them, and what does this sensitivity imply about the processes by which corners can be detected. In this paper we address both of these questions, starting with the observation that changing the samplign phase of a curve changes the geometry of its discrete trace, or the set of discrete (retinotopic) points onto which the curve projects. This motivates our stimuli — dotted curves —and our experimental design: if curves are represented by dots, the placement of the dots effects whether or not corners are perceived. Specifically, we present quantitative data on sensitivity to discontinuities as a function of dot phase, and address its theoretical explanation within a two-stage model of orientation selection. Curvature plays a key role in this model, and, finally, the model and experimental data are brought together by showing that a very coarse approximation to change in curvature (or differences in local curvature estimates) is sufficent to account for the psychophysical data on sensitivity to discontinuities.     

A combined STD-NMR/molecular modeling protocol for predicting the binding modes of the glycosidase inhibitors kifunensine and salacinol to Golgi alpha-mannosidase II

A combined STD-NMR/molecular modeling protocol to probe the binding modes of the glycosidase inhibitors kifunensine and salacinol to Drosophila melanogaster Golgi alpha-mannosidase II (dGMII) was tested. Saturation-transfer difference (STD) NMR experiments were carried out for the complexes of dGMII with these two inhibitors. The program AutoDock 3.0 was then used to optimize the interactions of the inhibitors with the residues in the active site of dGMII. Theoretical STD effects of the ligand protons in the complexes were calculated for the different binding modes with the recently developed CORCEMA-ST protocol. Comparison of experimental and theoretical effects then permitted selection of the likely binding modes of the ligands. The more rigid kifunensine was used initially to test the protocol. Excellent correlation between experimental and theoretical data was obtained for one of the binding modes that also corresponded to that observed in the crystal structure of the complex. The protocol was then extended to the more flexible salacinol. For the selected binding mode, good correlation of experimental and theoretical data for the five-membered ring was obtained; however, poor correlation for protons on the acyclic chain was obtained, suggesting flexibility in this portion of the molecule. Comparison of the selected binding mode with that from a crystal structure of salacinol with dGMII showed excellent superimposition of the five-membered ring but another orientation of the acyclic chain. The results suggest that reliable structural binding modes of a ligand to protein in aqueous solution can be provided with the combined use of STD-NMR spectroscopy, molecular modeling, and CORCEMA-ST calculations, although highly flexible portions of the ligand may be poorly defined.     

Large-scale modeling of the primary visual cortex: influence of cortical architecture upon neuronal response.

A large-scale computational model of a local patch of input layer 4 [Formula: see text] of the primary visual cortex (V1) of the macaque monkey, together with a coarse-grained reduction of the model, are used to understand potential effects of cortical architecture upon neuronal performance. Both the large-scale point neuron model and its asymptotic reduction are described. The work focuses upon orientation preference and selectivity, and upon the spatial distribution of neuronal responses across the cortical layer. Emphasis is given to the role of cortical architecture (the geometry of synaptic connectivity, of the ordered and disordered structure of input feature maps, and of their interplay) as mechanisms underlying cortical responses within the model. Specifically: (i) Distinct characteristics of model neuronal responses (firing rates and orientation selectivity) as they depend upon the neuron's location within the cortical layer relative to the pinwheel centers of the map of orientation preference; (ii) A time independent (DC) elevation in cortico-cortical conductances within the model, in contrast to a "push-pull" antagonism between excitation and inhibition; (iii) The use of asymptotic analysis to unveil mechanisms which underly these performances of the model; (iv) A discussion of emerging experimental data. The work illustrates that large-scale scientific computation--coupled together with analytical reduction, mathematical analysis, and experimental data, can provide significant understanding and intuition about the possible mechanisms of cortical response. It also illustrates that the idealization which is a necessary part of theoretical modeling can outline in sharp relief the consequences of differing alternative interpretations and mechanisms--with final arbiter being a body of experimental evidence whose measurements address the consequences of these analyses.     

Photoabsorption of green and red fluorescent protein chromophore anions in vacuo

Photoabsorption properties of green and red fluorescent protein chromophore anions in vacuo were investigated theoretically, based on the experimental results in gas phase [Phys. Rev. Lett. 2001, 87, 228102; Phys. Rev. Lett. 2003, 90, 118103]. Their calculated transition energies in absorption with TD-DFT and ZINDO methods are directly compared to the experimental reports in gas phase, and the calculations with ZINDO method can correctly reproduce the absorption spectra. The orientation and strength of their transition dipole moments were revealed with transition density. We also showed the orientation and result of their intramolecular charge transfer with transition difference density. The calculated results show that with the increase of the extended conjugated system, the orientation of transition dipole moments and the orientation of charge transfer can be reversed. They are the linear responds with the external electric fields. These theoretical results reveal the insight understanding of the photoinduced dynamics of green and red fluorescent protein chromophore anions and cations in vacuo.     

Theoretical conformational analysis of phospholipids bilayers

We present a computational approach describing the conformation of lipid molecules (1-2-dipalmitoyl-sn-glycero-3 phosphocholine (DPPC)) organized in bilayers. The classical semi-empirical method used in peptide conformational analysis has been extended successfully to lipids. The excellent agreement between our theoretical predictions and recent experimental data on the molecular organization of lipid bilayers suggests that the method could be a valuable tool in the lipid conformational analysis but also in the prediction of orientation and mode of insertion of amphiphilic molecules into the lipid bilayer.     

A maximum entropy analysis of protein orientations using fluorescence polarization data from multiple probes

Techniques have recently become available to label protein subunits with fluorescent probes at predetermined orientation relative to the protein coordinates. The known local orientation enables quantitative interpretation of fluorescence polarization experiments in terms of orientation and motions of the protein within a larger macromolecular assembly. Combining data obtained from probes placed at several distinct orientations relative to the protein structure reveals functionally relevant information about the axial and azimuthal orientation of the labeled protein segment relative to its surroundings. Here we present an analytical method to determine the protein orientational distribution from such data. The method produces the broadest distribution compatible with the data by maximizing its informational entropy. The key advantages of this approach are that no a priori assumptions are required about the shape of the distribution and that a unique, exact fit to the data is obtained. The relative orientations of the probes used for the experiments have great influence on information content of the maximum entropy distribution. Therefore, the choice of probe orientations is crucial. In particular, the probes must access independent aspects of the protein orientation, and two-fold rotational symmetries must be avoided. For a set of probes, a "figure of merit" is proposed, based on the independence among the probe orientations. With simulated fluorescence polarization data, we tested the capacity of maximum entropy analysis to recover specific protein orientational distributions and found that it is capable of recovering orientational distributions with one and two peaks. The similarity between the maximum entropy distribution and the test distribution improves gradually as the number of independent probe orientations increases. As a practical example, ME distributions were determined with experimental data from muscle fibers labeled with bifunctional rhodamine at known orientations with respect to the myosin regulatory light chain (RLC). These distributions show a complex relationship between the axial orientation of the RLC relative to the fiber axis and the azimuthal orientation of the RLC about its own axis. Maximum entropy analysis reveals limitations in available experimental data and supports the design of further probe angles to resolve details of the orientational distribution.     

Microstructural Modeling of Collagen Network Mechanics and Interactions with the Proteoglycan Gel in Articular Cartilage

Cartilage matrix mechanical function is largely determined by interactions between the collagen fibrillar network and the proteoglycan gel. Although the molecular physics of these matrix constituents have been characterized and modern imaging methods are capable of localized measurement of molecular densities and orientation distributions, theoretical tools for using this information for prediction of cartilage mechanical behavior are lacking. We introduce a means to model collagen network contributions to cartilage mechanics based upon accessible microstructural information (fibril density and orientation distributions) and which self-consistently follows changes in microstructural geometry with matrix deformations. The interplay between the molecular physics of the collagen network and the proteoglycan gel is scaled up to determine matrix material properties, with features such as collagen fibril pre-stress in free-swelling cartilage emerging naturally and without introduction of ad hoc parameters. Methods are developed for theoretical treatment of the collagen network as a continuum-like distribution of fibrils, such that mechanical analysis of the network may be simplified by consideration of the spherical harmonic components of functions of the fibril orientation, strain, and stress distributions. Expressions for the collagen network contributions to matrix stress and stiffness tensors are derived, illustrating that only spherical harmonic components of orders 0 and 2 contribute to the stress, while orders 0, 2, and 4 contribute to the stiffness. Depth- and compression-dependent equilibrium mechanical properties of cartilage matrix are modeled, and advantages of the approach are illustrated by exploration of orientation and strain distributions of collagen fibrils in compressed cartilage. Results highlight collagen-proteoglycan interactions, especially for very small physiological strains where experimental data are relatively sparse. These methods for determining matrix mechanical properties from measurable quantities at the microscale (composition, structure, and molecular physics) may be useful for investigating cartilage structure-function relationships relevant to load-bearing, injury, and repair.     

Orientation of Red Blood Cells and Rouleaux Disaggregation in Interference Laser Fields

The effect of interference laser fields on red blood cells (RBCs) was investigated both theoretically and experimentally. The optical trapping and orientation of individual RBC in interference fringes were observed. It was found that RBC rouleaux undergo disaggregation under the action of interference laser fields. To describe the effect of RBC orientation in interference fringes, we used the equation for torque exerted on a discoid dielectric particle in a gradient light field. The experimental results are in agreement with the predictions of the developed theoretical model.     

Membrane perturbation by the antimicrobial peptide PMAP-23: A fluorescence and molecular dynamics study

Several bioactive peptides exert their biological function by interacting with cellular membranes. Structural data on their location inside lipid bilayers are thus essential for a detailed understanding of their mechanism of action. We propose here a combined approach in which fluorescence spectroscopy and molecular dynamics (MD) simulations were applied to investigate the mechanism of membrane perturbation by the antimicrobial peptide PMAP-23. Fluorescence spectra, depth-dependent quenching experiments, and peptide-translocation assays were employed to determine the location of the peptide inside the membrane. MD simulations were performed starting from a random mixture of water, lipids and peptide, and following the spontaneous self-assembly of the bilayer. Both experimental and theoretical data indicated a peptide location just below the polar headgroups of the membrane, with an orientation essentially parallel to the bilayer plane. These findings, together with experimental results on peptide-induced leakage from large and giant vesicles, lipid flip-flop and peptide exchange between vesicles, support a mechanism of action consistent with the “carpet” model. Furthermore, the atomic detail provided by the simulations suggested the occurrence of an additional, more specific and novel mechanism of bilayer destabilization by PMAP-23, involving the unusual insertion of charged side chains into the hydrophobic core of the membrane.     

Electro-orientation of ellipsoidal erythrocytes. Theory and experiment.

The frequency-dependent orientation of human and llama erythrocytes suspended in isotonic solutions and subjected to linearly polarized electric fields is examined. Human erythrocytes may be represented as oblate spheroids (3.9:3.9:1.1 microns) with two distinguishable orientations, while the llama cells are approximated as ellipsoids with three distinct axes (4.0:2.0:1.1 microns). Under appropriate experimental conditions, both orientations of the human cells and all three orientations of the llama cells are observed. A theoretical cell model which accounts for the membrane as a thin confocal layer of ideal capacitance is used to predict the orientational spectra. The predicted spectra compare favorably in frequency range and orientational sequence with experimental data. Estimates for cell internal conductivity and permittivity are obtained by adjusting the values of these important parameters to achieve the closet fit of the theoretical curves to the data. By the use of this method, the internal conductivity of llama erythrocytes is estimated to be 0.26 S/m (+/- 20%), while the effective internal dielectric constant and conductivity of Euglena gracilis are estimated to be 120 (+/- 10%) and 0.43 S/m (+/- 20%), respectively.     

A generalized born implicit-membrane representation compared to experimental insertion free energies

An implicit-membrane representation based on the generalized Born theory of solvation has been developed. The method was parameterized against the water-to-cyclohexane insertion free energies of hydrophobic side-chain analogs. Subsequently, the membrane was compared with experimental data from translocon inserted polypeptides and validated by comparison with an independent dataset of six membrane-associated peptides and eight integral membrane proteins of known structure and orientation. Comparison of the insertion energy of alpha-helical model peptides with the experimental values from the biological hydrophobicity scale of Hessa et al. gave a correlation of 93% with a mean unsigned error of 0.64 kcal/mol, when charged residues were ignored. The membrane insertion energy was found to be dependent on residue position. This effect is particularly pronounced for charged and polar residues, which strongly prefer interfacial locations. All integral membrane proteins investigated orient and insert correctly into the implicit-membrane model. Remarkably, the membrane model correctly predicts a partially inserted configuration for the monotopic membrane protein cyclooxygenase, matching experimental and theoretical predictions. To test the applicability and usefulness of the implicit-membrane method, molecular simulations of influenza A M2 as well as the glycophorin A dimer were performed. Both systems remain structurally stable and integrated into the membrane.     

Lectin-sugar interaction. Calculated versus experimental binding energies.

Although a steadily increasing number of protein--ligand docking experiments have been performed successfully, there are only few studies concerning protein--sugar interactions. In this study, we investigate the interaction of wheat germ agglutinin (WGA) with N-acetylglucosamine and a number of its derivatives and predict the binding free energies using flexible docking techniques. To assess the quality of our predictions, we also determined those binding free energies experimentally in cell-binding studies. The predicted binding site, ligand orientation, and details of the binding mode are in perfect agreement with the known crystal structure of WGA with a sialoglycopeptide. Furthermore, we obtained an excellent linear correlation of our predicted binding free energies with both our own data and experimental data from the literature [Monsigny, M., Roche, A.C., Sene, C., Maget Dana, R. & Delmotte, F. (1980) Eur. J. Biochem. 104, 147-153.]. In both cases, predicted energies were within 1.0 kJ x mol(-1) of the experimental value. These results illustrate the usefulness of docking-based methods for the qualitative and quantitative prediction of protein--carbohydrate interactions. The insights gained from such theoretical studies may be used to complement the results from the still scarce crystal structures.