Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force.

The force required to rupture the streptavidin-biotin complex was calculated here by computer simulations. The computed force agrees well with that obtained by recent single molecule atomic force microscope experiments. These simulations suggest a detailed multiple-pathway rupture mechanism involving five major unbinding steps. Binding forces and specificity are attributed to a hydrogen bond network between the biotin ligand and residues within the binding pocket of streptavidin. During rupture, additional water bridges substantially enhance the stability of the complex and even dominate the binding interactions. In contrast, steric restraints do not appear to contribute to the binding forces, although conformational motions were observed.

Polarization effects stabilize bacteriorhodopsin's chromophore binding pocket: a molecular dynamics study.

Hybrid methods, which combine a quantum mechanical description of a chromophore by density functional theory (DFT) with a molecular mechanics (MM) model of the surrounding protein binding pocket, can enable highly accurate computations of the chromophore's in situ vibrational spectra. As a prerequisite, one needs a MM model of the chromophore-protein complex, which allows a correct sampling of its room-temperature equilibrium fluctuations by molecular dynamics (MD) simulation. Here, we show for the case of bacteriorhodopsin (BR) that MM-MD descriptions with standard nonpolarizable force fields entail a collapse of the chromophore binding pocket. As demonstrated by us, this collapse can be avoided by employing a polarized MM force field derived by DFT/MM hybrid computations. The corresponding MD simulations, which are complemented by a novel Hamiltonian replica exchange approach, then reveal a structural heterogeneity within the binding pocket of the retinal chromophore, which mainly pertains to the structure of the lysine chain covalently connecting the retinal chromophore with the protein backbone.

The infrared spectra of the retinal chromophore in bacteriorhodopsin calculated by a DFT/MM approach.

In the preceding paper (DOI 10.1021/jp902428x), we have derived the polarized force field "PBR" for bacteriorhodopsin (BR) using hybrid methods which combine density functional theory (DFT) with molecular mechanics (MM) models. This polarized force field has enabled extended molecular dynamics (MD) simulations of BR's chromophore binding pocket which closely preserve the experimentally well-known structure. Here, we employ the PBR-MD trajectories obtained for the conformational substates prevalent at physiological temperatures as material for the DFT/MM computation of the chromophore's vibrational spectra. By comparison with DFT results on the structure and vibrational spectra of an isolated chromophore, we identify the structural and spectral changes induced by the protein environment. Comparisons with the wealth of experimental data available in the literature on the chromophore's vibrational spectra yield estimates on the accuracy of the DFT/MM descriptions. We discuss why highly accurate DFT/MM descriptions are expected to become a decisive tool for solving the long-standing enigma of how the light-driven proton pump BR actually works.

Generalized radial basis function networks for classification and novelty detection: self-organization of optimal Bayesian decision.

By adding reverse connections from the output layer to the central layer it is shown how a generalized radial basis functions (GRBF) network can self-organize to form a Bayesian classifier, which is also capable of novelty detection. For this purpose, three stochastic sequential learning rules are introduced from biological considerations which pertain to the centers, the shapes, and the widths of the receptive fields of the neurons and allow ajoint optimization of all network parameters. The rules are shown to generate maximum-likelihood estimates of the class-conditional probability density functions of labeled data in terms of multivariate normal mixtures. Upon combination with a hierarchy of deterministic annealing procedures, which implement a multiple-scale approach, the learning process can avoid the convergence problems hampering conventional expectation-maximization algorithms. Using an example from the field of speech recognition, the stages of the learning process and the capabilities of the self-organizing GRBF classifier are illustrated.

Asymptotic level density in topological feature maps.

The Kohonen algorithm entails a topology conserving mapping of an input pattern space X subsetR(n) characterized by an a priori probability distribution P(x), xinX, onto a discrete lattice of neurons r with virtual positions w(r)inX. Extending results obtained by Ritter (1991) the authors show in the one-dimensional case for an arbitrary monotonously decreasing neighborhood function h(|r-r'|) that the point density D(W(r)) of the virtual net is a polynomial function of the probability density P(x) with D(w(r))~P(alpha)(w(r)). Here the distortion exponent is given by alpha=(1+12R)/3(1+6R) and is determined by the normalized second moment R of the neighborhood function. A Gaussian neighborhood interaction is discussed and the analytical results are checked by means of computer simulations.

The "Hot-Solvent/Cold-Solute" Problem Revisited.

The temperature steers the equilibrium and nonequilibrium conformational dynamics of macromolecules in solution. Therefore, corresponding molecular dynamics simulations require a strategy for temperature control which should guarantee that the experimental statistical ensemble is also sampled in silico. Several algorithms for temperature control have been proposed. All these thermostats interfere with the macromolecule's "natural" dynamics as given by the Newtonian mechanics. Furthermore, using a single thermostat for an inhomogeneous solute-solvent system can lead to stationary temperature gradients. To avoid this "hot solvent/cold solute" problem, two separate thermostats are frequently applied, one to the solute and one to the solvent. However, such a separate temperature control will perturb the dynamics of the macromolecule much more strongly than a global one and, therefore, can introduce large artifacts into its conformational dynamics. Based on the concept that an explicit solvent environment represents an ideal thermostat concerning the magnitude and time correlation of temperature fluctuations of the solute, we propose a temperature control strategy that, on the one hand, provides a homogeneous temperature distribution throughout the system together with the correct statistical ensemble for the solute molecule while, on the other hand, minimally perturbing its dynamics.

Evidence for a 13,14-cis cycle in bacteriorhodopsin.

We discuss to what extent the vibrational spectra of bacteriorhodopsin that have been observed and assigned by Smith et al. (1, 2) by means of resonance Raman and by Gerwert and Siebert (EMBO (Eur. Mol. Biol. Organ.) J. In press) by means of infrared absorption experiments are in agreement with a photo-cycle of bacteriorhodopsin that involves the sequence BR, IO(all-trans) --> K(13,14-cis) --> L(13,14-cis) --> M(13-cis) --> N(13-cis) --> O(all-trans). Our discussion is based on a quantumchemical modified neglect of diatomic overlap [MNDO] calculation of the vibrational spectra of the relevant isomers of the protonated retinal Schiff base. In particular, we investigated in these calculations the effects of different charge environments on the frequencies of the relevant C-C single bond stretching vibrations of these isomers.

Structural investigation of bacteriorhodopsin and some of its photoproducts by polarized Fourier transform infrared spectroscopic methods-difference spectroscopy and photoselection.

The direction of selected IR-transition moments of the retinal chromophore of bacteriorhodopsin (BR) and functional active amino acid residues are determined for light- and dark-adapted BR and for the intermediates K and L of the photocycle. Torsions around single bonds of the chromophore are found to be present in all the investigated BR states. The number of twisted single bonds and the magnitude of these torsions decreases in the order K, L, light-adapted BR, dark-adapted BR. In the last, only the C(14)-C(15) single bond is twisted. The orientation of molecular planes and chemical bonds of such protein side chains, which are perturbed during the transition of light-adapted BR to the respective intermediates, are deduced and the results compared with the current three dimensional model of BR. Trp 86 and Trp 185 are found to form a rigid part of the protein, whereas Asp 96 and Asp 115 perform molecular rearrangements upon formation of the L-intermediate.

A model for the lateral diffusion of "stiff" chains in a lipid bilayer.

We present random walk models for the diffusive motion of lipid probe molecules in a lipid bilayer and calculate the diffusion constants for probes spanning the entire bilayer and for probes extending through one lipid layer only. The "stiffness" of such molecules can explain the observed value of 2/3 for the ratio of these diffusion constants.

The effect of protonation and electrical interactions on the stereochemistry of retinal schiff bases.

Based on quantumchemical MNDOC calculations it is shown that the ground-state properties of a retinal Schiff base depend sensitively on its protonation state and charge environment. This is exemplified for the equilibrium geometry, for the distribution of partial charges and, in particular, for the thermal isomerization barriers around the pi-bonds. It is demonstrated that a protein, by protonating the retinal Schiff base and by providing one or two negative ions in its environment, can reduce double-bond isomerization barriers from 50 kcal/mol for the unprotonated compound to approximately 5 kcal/mol and can increase single bond barriers from 5 kcal/mol to approximately 20 kcal/mol. Thereby, the specific location of the ions relative to the polyene chain of the protonated retinal Schiff base determines the barrier heights. The results explain the ground-state isomerization reactions of retinal observed in bacteriorhodopsin and in squid retinochrome.

Self-organization of associative memory and pattern classification: recurrent signal processing on topological feature maps.

We extend the neural concepts of topological feature maps towards self-organization of auto-associative memory and hierarchical pattern classification. As is well-known, topological maps for statistical data sets store information on the associated probability densities. To extract that information we introduce a recurrent dynamics of signal processing. We show that the dynamics converts a topological map into an auto-associative memory for real-valued feature vectors which is capable to perform a cluster analysis. The neural network scheme thus developed represents a generalization of non-linear matrix-type associative memories. The results naturally lead to the concept of a feature atlas and an associated scheme of self-organized, hierarchical pattern classification.

Substituents at the c(13) position of retinal and their influence on the function of bacteriorhodopsin.

Retinal analogues in which the 13-methyl group is replaced by H, C(2)H(5), CF(3), and OCH(3) residues are studied by means of quantumchemical modified neglect of diatomic overlap-correlated version (MNDOC) calculations. The analogues are suitable to test the stereochemical mechanism of proton pumping in bacteriorhodopsin. The results explain the proton-pumping activities of bacterio-opsin reconstituted with these analogues and elucidate the decisive role of retinal's ground-state intramolecular properties in the pump cycle of bacteriorhodopsin.

An associative memory that can form hypotheses: a phase-coded neural network.

Nonlinear associative memories as realized, e.g., by Hopfield nets are characterized by attractor-type dynamics. When fed with a starting pattern, they converge to exactly one of the stored patterns which is supposed to be most similar. These systems cannot render hypotheses of classification, i.e., render several possible answers to a given classification problem. Inspired by von der Malsburg's correlation theory of brain function, we extend conventional neural network architectures by introducing additional dynamical variables. Assuming an oscillatory time structure of neural firing, i.e., the existence of neural clocks, we assign a so-called phase to each formal neuron. The phases explicitly describe detailed correlations of neural activities neglected in conventional neural network architectures. Implementing this extension into a simple self-organizing network based on a feature map, we present an associative memory that actually is capable of forming hypotheses of classification.

[Bone histomorphometric study in involuted fractured osteoporosis treated with 1-ethane-1-hydroxybiphosphonate (etidronate) during one year]. / Etude histomorphométrique osseuse dans l'ostéoporose fracturaire d'involution traitée par l'éthane-1, hydroxy-1, 1 bisphosphonate (étidronate) pendant un an.

The efficacy of the biphosphonate etidronate has recently been demonstrated versus the vertebral fracture rate in fractured involuted osteoporosis in the literature. However, it would appear that the increase in bone mass (measured from the calcium density) may alone account for these results. The authors undertook a histomorphometrie study in 20 patients with a group mean age of 55 years presenting recent vertebral fracture in the context of osteoporosis, in order to assess the cell changes which may affect bone quality. This factor remains the only one which can account for the reduced number of fractures. The patients received treatment with phosphorus (1,500 mg/d) for 3 days followed by etidronate (400 mg/d) for 14 days every 90 days. A permanent daily intake of 50 mg of calcium and 400 IU of vitamin D was also administered. Each patient underwent bone biopsy of the iliac wing before and after one year of treatment (4 cycles). No change in the bone mass or architectural parameters was observed. However, general slowing of the bone remodeling was found, affecting the natality and activity of the osteoforming and osteoresorbing cells. However, this remodeling which is traditionally uncoupled in osteoporosis was once more coupled. This results in a slowing of bone loss, ageing of the bone present and no change in the architecture. Thus, the diphosphonates appear to have a beneficial effect on the quality of bone rather than on its quantity. This represents a novel approach to the treatment of osteoporosis.