A model for the dynamic properties of integrating fibers: Target localization in a three-dimensional space—II. Computer simulation

• 1.1. The stimulation sequence provoked by a luminous point moving in front of a column of ommatidia was simulated for the eye of Squilla mantis.
• 2.2. The output from the ommatidia is transferred to one tangential, integrating fiber as graded potentials. These potentials follow a gaussian-shaped angular sensitivity function for each ommatidium.
• 3.3. The tangential fiber sums the inputs as they arrive and generates a spike if the sum is above threshold at one instant of time and at one point of the fiber.
• 4.4. The histograms of instantaneous frequencies of spike discharge resemble the input-pattern histograms.
• 5.5. The discharge pattern changes with distance and speed of the moving spot as well for the simulations as in electrophysiological recordings, and is adapted to the size of the animal.
• 6.6. The shape of the histograms (i.e. the pattern of spike discharge) is assumed to transmit the information on the position, speed and size of a moving target.

     

A physical model of nerve axon—I. Ionic distribution,potential profile,and resting potential

A theory which is based on a set of assumptions different from those of the sodium theory is developed. Here the mobile ions are considered to be distributed at Donnan equilibrium and the axoplasm is regarded as an analog of a cation-exchanger. Following the spirit of the Debye-Hückel theory, some important features of the ionic distribution and electrical potential of the nerve fiber have been calculated. The results appear to be in better agreement with the experimental observations than the Goldman-Hodgkin-Katz equation. A summary of this work has been reported in the 1974 March meeting of the American Physical Society and the 1976 annual meeting of the Biophysical Society.     

Static and dynamic properties of mid-size liquid n- alkanes,C12∼C400: a molecular dynamics simulation study

ABSTRACT

In this paper, we have extended our previous study of the static and dynamic properties (self-diffusion coefficient D_self and friction coefficient ζ) of liquid n-alkane systems up C₄₀₀ at several temperatures (～2300?K) using molecular dynamics (MD) simulations in the canonical ensembles. For the small n-alkanes with n?≤?120 (n: the chain length), the chains are clearly ?R² _ee?/6?R² _g? ≥ 1 (1.06 ～ 1.44), which leads to the conclusion that the liquid n-alkanes are far away from the ideal chain regime. But for the n-alkanes of n?≥?160, the chains are ?R² _ee?/6?R² _g? ≈ 1, indicating that they are Gaussian. It is found that the long chains of these n-alkanes at high temperatures show abnormalities in density and friction coefficient. We observed a clear transition in the power law dependence of n-alkane self-diffusion coefficient on the molecular weight (M) of n-alkane, D_self ～ M^?γ, occurs in the range C₁₂₀～C₁₆₀ at temperatures of 318, and 618?K, corresponding to a crossover from the ‘oligomer’ to the ‘Rouse’ regime. The entanglement lengths (N_e) are calculated by the Z1 code and discussed shortly.     

A coarse-grain MD (molecular dynamic) simulation of PCL–PEG and PLA–PEG aggregation as a computational model for prediction of the drug-loading efficacy of doxorubicin

Abstract

Formulating a hydrophobic drug that is water-soluble is a pharmaceutical challenge. One way is to incorporate the drug in an amphiphilic micelle composed from an aggregation of block copolymers. Design of a good nano-micelle requires many trial-and-error attempts. In this article, we developed a computational model based on a coarse-grained molecular dynamic (MD) simulation and correlated outputs with previous studies. A good correlation shows that this model reliably simulates poly-lactic acid–poly-ethylene glycol (PLA–PEG) and poly-caprolactone (PCL)–PEG aggregation in water with and without the presence of doxorubicin.

Communicated by Ramaswamy H. Sarma     

I. Cellular and molecular biology of sodium channel beta-subunits: therapeutic implications for pain? I. Cellular and molecular biology of sodium channel beta-subunits: therapeutic implications for pain?

Voltage-gated sodium channel alpha-subunits have been shown to be key mediators of the pathophysiology of pain. The present review considers the role of sodium channel auxiliary beta-subunits in channel modulation, channel protein expression levels, and interactions with extracellular matrix and cytoskeletal signaling molecules. Although beta-subunits have not yet been directly implicated in pain mechanisms, their intimate association with and ability to regulate alpha-subunits predicts that they may be a viable target for therapeutic intervention in the future. It is proposed that multifunctional sodium channel beta-subunits provide a critical link between extracellular and intracellular signaling molecules and thus have the ability to fine tune channel activity and electrical excitability.     

A stereochemical model for phospholipids: I. Conformational energy refinement and molecular packing of l-α-Dipalmitoyl lecithin (DPL)

The preferred conformations of L-α-dipalmitoyl-lecithin (DPL) have been refined using a steepest descent procedure throughout non-bonded potential energy calculations. The results indicate that energy differences between the conformers is very low and the energy parameters are quite constant around the minimum, suggesting a large degree of flexibility of this molecule.The molecular packing energy calculations have been performed by separating the two hydrocarbon chains from the polar head groups of the molecule. From the energy parameters for the packing of the aliphatic chains it results that for distances between adjacent chains up to 4·4 Å the intermolecular forces allow the maximum degree of freedom. This suggests that hydrocarbon chains do not play the main role in the packing process of DPL molecule. Therefore the energy parameters of the polar segment have been calculated, assuming that the C₂ asymmetric carbon atom represents the points of the hexagonal lattice and the rotation centre for each molecule. For the internal symmetry of this segment of the molecule two non-equivalent conformers have been selected over all sets of allowed conformations (the GGG and GGG¹ for the α₂, α₃ and α₅ torsion angles). The energy packing calculation has been carried out for two independent sets of data, with and without the electrostatic contributions. In the first case a unique topological situation is allowed with the P-N dipole lying parallel to the lattice plane. In the second case different situations including that with the P-N dipole lying orthogonal to the plane are allowed. These data are discussed in relation to different physical conditions.     

A potential new radiopharmaceutical for parathyroid imaging: Radiolabeled parathyroid-specific monoclonal antibody—I. Evaluation of 125I-labeled antibody in a nude mouse model system

Radioiodinated BB5-G1, a parathyroid-specific monoclonal antibody, and its F(ab′)₂ and Fab fragments were characterized using a nude mouse model system. Blood clearance studies indicated that the most slowly clearing species was the ¹²⁵I-BB5-G1 intact antibody, while the most rapidly clearing one was the ¹²⁵I-Fab fragment. ¹²⁵I-F(ab′)₂ retained its capacity to localize in the human parathyroid tissue implants with the uptake at 24 h being similar to that observed with the intact antibody. Poor localization was observed with the Fab fragment. These results suggest that BB5-G1 or its F(ab′)₂ fragment may be useful for parathyroid imaging.     

Dynamical systems under constant organization I. Topological analysis of a family of non-linear differential equations —A model for catalytic hypercycles

The paper presents a qualitative analysis of the following systems ofn differential equations: \(\dot x_i = x_i x_j - x_i \sum\nolimits_r^n { = 1} x_r x_s {\mathbf{ }}(j = i - 1 + n\delta _{i1} {\mathbf{ }}and{\mathbf{ }}s = r - 1 + n\delta _{r1} )\) , which show cyclic symmetry. These dynamical systems are of particular interest in the theory of selforganization and biological evolution as well as for application to other fields.     

Determination of thiamin diphosphate in whole blood samples by high-performance liquid chromatography—A method suitable for pediatric diagnostics

An improved and easy to use method for the determination of thiamin diphosphate (TDP) in 100 μl of whole blood was developed. The small sample volume makes it possible to assess the nutritional status of vitamin B₁ in infants and even in preterm infants. Sample preparation comprises the extraction of TDP from whole blood by hemolysis, protein precipitation with trichloroacetic acid, and subsequent centrifugation. Potassium ferricyanide is used for pre-column derivatization of TDP to its fluorescent thiochrome derivative. Chromatographic separation was carried out using a reversed-phase column and an isocratic elution which consisted of a phosphate buffer and acetonitrile. TDP was detected fluorimetrically and quantified by external standardization. Method validation showed a high precision, almost complete recovery, and a high sensitivity. The lower limit of detection and the lower limit of quantification were 0.2 ng/ml and 4 ng/ml, respectively. Linearity was demonstrated over the expected concentration range of 4–400 ng/ml. In conclusion, we present a convenient HPLC method for the determination of TDP which is precise, sensitive and suitable for pediatric diagnostics.     

Membrane potential difference of isolated plant vacuoles: positive or negative? I. Evidence for membrane binding of cationic probes

The binding of membrane potential cationic probes was studied on phospholipidic liposomes by equilibrium dialysis and microelectrophoresis. Surface binding of lipophilic cations (benzyltributylammonium or tetraphenylphosphonium) appears to be the major accumulation mechanism in liposomes and simulates the existence of a negative transmembrane potential (E_m), in absence of any transmembrane ionic gradient. Furthermore, this apparent negative potential has a classical response with regard to common E_m effectors, namely a depolarization induced by KCl or FCCP (carbonylcyanide p-trifluoromethoxyphenylhydrazone). The relevance of these results to the study of transtonoplast potential difference on isolated vacuoles was investigated. Tetraphenylphosphonium was shown to bind to the tonoplast, the essential features of binding and interaction with E_m effectors being similar in vacuoles and liposomes. Therefore the assumption of negligible binding of cationic probe to vacuoles, classically admitted in determinations of vacuolar E_m using lipophilic cations, is untenable.     

Identification of potential inhibitors for HCV NS3 genotype 4a by combining protein–ligand interaction fingerprint, 3D pharmacophore,docking, and dynamic simulation

HCV NS3 protease domain has been one of the most attractive targets for developing new drugs for HCV infection and many drugs were successfully developed, but all of them were designed for targeting HCV genotype 1 infection. HCV genotype 4a dominant in Egypt has paid less attention. Here, we describe our protocol of virtual screening in identification of novel potential potent inhibitors for HCV NS3 of genotype 4a using homology modeling, PLIF (protein–ligand interaction fingerprint), docking, pharmacophore, and dynamic simulation. A high-quality 3D model of HCV NS3 protease of genotype 4a was constructed using crystal structure of HCV NS3 protease of genotype 1b (PDB ID: 4u01) as a template. PLIF was generated using five crystal structures of HCV NS3 (PDB ID: 4u01, 3kee, 4ktc, 4i33, and 5epn) which revealed the most important residues and their interactions with the co-crystalized ligands. A 3D pharmacophore model consisting of six features was developed from the generated PLIF data and then used as a screening filter for 11,244 compounds. Only 423 compounds passed the pharmacophore filter and entered the docking-based virtual screening stage. The highest ranked five hits from docking result (compound (C1–C5)) were selected for further analysis. They exhibited stronger interaction and higher binding affinity than HCV NS3 protease ligands. Dynamic simulation of the protein–best lead complex was performed to validate and augment the virtual screening results and it showed that these compounds have a strong binding affinity and could be very effective in treating HCV genotype 4a infections.     

Biological modeling of complex chemotaxis behaviors for C. elegans under speed regulation—a dynamic neural networks approach

In this paper, the modeling of several complex chemotaxis behaviors of C. elegans is explored, which include food attraction, toxin avoidance, and locomotion speed regulation. We first model the chemotaxis behaviors of food attraction and toxin avoidance separately. Then, an integrated chemotaxis behavioral model is proposed, which performs the two chemotaxis behaviors simultaneously. The novelty and the uniqueness of the proposed chemotaxis behavioral models are characterized by several attributes. First, all the chemotaxis behavioral model sare on biological basis, namely, the proposed chemotaxis behavior models are constructed by extracting the neural wire diagram from sensory neurons to motor neurons, where sensory neurons are specific for chemotaxis behaviors. Second, the chemotaxis behavioral models are able to perform turning and speed regulation. Third, chemotaxis behaviors are characterized by a set of switching logic functions that decide the orientation and speed. All models are implemented using dynamic neural networks (DNN) and trained using the real time recurrent learning (RTRL) algorithm. By incorporating a speed regulation mechanism, C. elegans can stop spontaneously when approaching food source or leaving away from toxin. The testing results and the comparison with experiment results verify that the proposed chemotaxis behavioral models can well mimic the chemotaxis behaviors of C. elegans in different environments.     

Photosystem I charge separation in the absence of centers A and B. I. Optical characterization of center ‘A2’ and evidence for its association with a 64-kDa peptide

The flash-induced absorption transient at 698 nm in a Photosystem I subchloroplast particle showed the following characteristics after addition of 0.25–2.0% lithium dodecyl sulfate (LDS). (i) The 30-ms transient corresponding to the P-700⁺ P-430⁻ backreaction was replaced by a 1.2-ms transient. (ii) The amplitude of the transient did not change immediately after LDS addition, but decayed with a half-life of 10 min at pH 8.5. (iii) Methyl viologen had no effect on the magnitude or kinetics of the transient, indicating that it cannot accept an electron from this component. (iv) The difference spectrum of the transient from 400 nm to 500 nm was characteristic of an iron-sulfur protein. (v) The transient followed first-order Arrhenius behavior between 298 K and 225 K with an activation energy of 13.3 kJ/mol; between 225 K and 77 K, the 85-ms half-time remained temperature-invariant. These properties suggest that the LDS-induced absorption transient corresponds to the P-700⁺ A⁻₂ change recombination seen in the absence of a reduced electron-acceptor system. In the presence of LDS, the reaction-center complex was dissociated, allowing removal of the smaller peptides from the 64-kDa P-700-containing protein. With prolonged incubation, the iron-sulfur clusters were destroyed through conversion of the labile sulfide to zero-valence sulfur. About 35% of the zero-valence sulfur was found associated with the 64-kDa protein under conditions that allowed separation of the small peptides. We interpret the long lifetime of the P-700⁺ A⁻₂ transient after LDS addition and the association of zero-valence sulfur with a 64-kDa protein to indicate that A₂ is closely associated with, and perhaps integral with, the P-700-containing protein.     

Homology model,molecular dynamics simulation and novel pyrazole analogs design of Candida albicans CYP450 lanosterol 14 α-demethylase,a target enzyme for antifungal therapy

Candida albicans infections and their resistance to clinically approved azole drugs are major concerns for human. The azole antifungal drugs inhibit the ergosterol synthesis by targeting lanosterol 14α-demethylase of cytochrome P450 family. The lack of high-resolution structural information of fungal pathogens has been a barrier for the design of modified azole drugs. Thus, a preliminary theoretical molecular dynamic study is carried out to develop and validate a simple homologous model using crystallographic structure of the lanosterol 14α-demethylase of Mycobacterium tuberculosis (PDB ID-1EA1) in which the active site residues are substituted with that of C. albicans (taxid 5476). Further, novel designed pyrazole analogs (SGS1-16) docked on chimeric 1EA1 and revealed that SGS-16 show good binding affinity through non-bonding interaction with the heme, which is different from the leading azole antifungals. The ADME-T results showed these analogs can be further explored in design of more safe and effective antifungal agents.     

A study of staining for electron microscopy using collagen as a model system—VII. The effect of formaldehyde fixation

Exposure to formaldehyde brings about small but readily detectable changes in the staining behaviour of collagen fibrils. These changes can be interpreted in chemical terms by comparing fibril staining patterns with artificial patterns computer-generated from sequence data. Positive staining with phosphotung-state (where heavy metal is confined to anions), shows that most of the lysyl and hydroxylysyl side-chains lose their charge character as a result of formaldehyde treatment and cease to take up staining ions. The charge character of arginyl (and probably histidyl) residues is unaltered and these residues continue to react with stain. Acidic residues are also unaffected. These results accord with biochemical evidence that the initial reaction between proteins and formaldehyde leading to subsequent cross-linking involves modification of ε-amino (and α-amino) groups. They show too that the secondary condensation producing the actual cross-link does not alter the charge character of the second group, at least when it is on an arginyl (or histidyl) side-chain.Formaldehyde-induced changes in stain deposition can also be detected after negative staining, although they are slight compared with those brought about by glutaraldehyde. Unlike glutaraldehyde, formaldehyde introduces no bulky polymeric adducts into the fibril structure, and the conspicuous stain-excluding bands seen in negative staining patterns following glutaraldehyde fixation are absent after exposure to formaldehyde. For this reason, where chemical fixation is used to stabilize macromolecules and supramolecular aggregates prior to negative staining and high resolution electron optical imaging, formaldehyde would seem to be preferable to glutaraldehyde. Data from fibril staining patterns and from thermal stability measurements (made on collagen gels) show that formaldehyde fixation does not preclude a subsequent reaction with glutaraldehyde.As with other fixatives, there is reduced accessibility to stain after formaldehyde treatment. Accessibility is least in the overlap zone where the denser packing of collagen molecules provides greater opportunities for intermolecular cross-linking. Gel electrophoresis confirms that formaldehyde-induced cross-links in fibrils are predominantly intermolecular.     

A study of staining for electron microscopy using collagen as a model system—VIII. Simulation of the negative staining pattern

Simulated negative staining patterns of collagen fibrils were prepared for visual display by a graphical procedure in which amino acid side-chains along the staggered molecules were weighted according to their stain-excluding capacity. The simulated patterns were then compared directly with electron-optical images of collagen fibrils negatively stained with sodium phosphotungstate or lithium tungstate. These visual comparisons confirm previous observations that satisfactory matching occurs when side-chains are weighted according to their ‘bulkiness’ (average cross-sectional area or ‘plumpness’). Optimal matching at the edges of the overlap zones occurred when a hairpin-like conformation was assumed for the N-terminal telopeptides and a condensed conformation for the hydrophobic part of the C-terminal telopeptides. The negative staining pattern is known to include some element of positive staining; visual matching suggests that this additional uptake of positive staining ions occurs predominantly in the more accessible gap zone in a fibril D-period. A slight mismatching between observed and simulated patterns can be understood if the gap zone suffers greater axial shrinkage than the overlap zone when specimens are prepared for electron microscopy.