Simulation of the conformation and dynamics of a double-helical model for DNA

We propose a partially flexible, double-helical model for describing the conformational and dynamic properties of DNA. In this model, each nucleotide is represented by one element (bead), and the known geometrical features of the double helix are incorporated in the equilibrium conformation. Each bead is connected to a few neighbor beads in both strands by means of stiff springs that maintain the connectivity but still allow for some extent of flexibility and internal motion. We have used Brownian dynamics simulation to sample the conformational space and monitor the overall and internal dynamics of short DNA pieces, with up to 20 basepairs. From Brownian trajectories, we calculate the dimensions of the helix and estimate its persistence length. We obtain translational diffusion coefficient and various rotational relaxation times, including both overall rotation and internal motion. Although we have not carried out a detailed parameterization of the model, the calculated properties agree rather well with experimental data available for those oligomers.     

Molecular dynamics studies of alanine racemase: a structural model for drug design

Alanine racemase (AlaR) is a bacterial enzyme that catalyzes the interconversion of L- and D-alanine, which is an essential constituent of the peptidoglycan layer of the bacterial cell wall and requires pyridoxal 5'-phosphate (PLP) as a cofactor. The enzyme is universal to bacteria, including mycobacteria, making it an attractive target for drug design. To investigate the effects of flexibility on the binding modes of the substrate and an inhibitor and to analyze how the active site is affected by the presence of the substrate versus inhibitor, a molecular dynamics simulation on the full AlaR dimer from Bacillus stearothermophilus (pdb code: 1SFT) with a D-alanine molecule in one active site and the noncovalent inhibitor, propionate, in the second site has been carried out. Within the time scale of the simulation, we show that the active site becomes more stabilized in the presence of substrate versus inhibitor. The results of this simulation are in agreement with the proposed mechanism of alanine racemase reaction in which the substrate carboxyl group directly participates in the catalysis by acting cooperatively with Tyr 265' and Lys 39. A structural water molecule in contact with both substrate and inhibitor (i.e., in both active sites) and bridging residues in both active sites was identified. It shows a remarkably low mobility and does not exchange with bulk water. This water molecule can be taken into account for the design of specific AlaR inhibitors by either utilizing it as a bridging group or displacing it with an inhibitor atom. The results presented here provide insights into the dynamics of the alanine racemase in the presence of substrate/inhibitor, which will be used for the rational design of novel inhibitors.     

Pulmonary surfactant protein B: a structural model and a functional analogue

Surfactant proteins B and C (SP-B and SP-C), together with phospholipids, are important constituents of pulmonary surfactant and of preparations used for treatment of respiratory distress syndrome (RDS). SP-B belongs to the saposin family of homologous proteins, which include other lipid-interacting proteins, like the membranolytic NK-lysin. SP-B, in contrast to other saposins, is hydrophobic and a disulfide-linked dimer, and its mechanism of action is not known. A model of the three-dimensional structure of one SP-B subunit was generated from the structure of monomeric NK-lysin determined by nuclear magnetic resonance, and the SP-B dimer was formed by joining two subunits via the intersubunit disulfide bond Cys48-Cys48'. After energy minimization, intersubunit hydrogen bonds/ion pairs were formed between the strictly conserved residues Glu51 and Arg52, which creates a central non-polar region located in between two clusters of positively charged residues. The structural features support a function of SP-B in cross-linking of lipid membranes. Mixtures of phospholipids, an SP-C analogue and polymyxin B (which cross-links lipid vesicles but is structurally unrelated to SP-B) exhibit in vitro surface activity which is indistinguishable from that of analogous mixtures containing SP-B instead of polymyxin B. This suggests an avenue for identification of SP-B analogues that can be used in synthetic surfactants for treatment of RDS.     

Yeast calmodulin: structural and functional differences compared with vertebrate calmodulin

Calmodulin of the baker's yeast (Saccharomyces cerevisiae) showed a similar affinity for Ca2+ to that of vertebrate calmodulin. The maximum binding number of Ca2+ to yeast calmodulin was, however, 3 mol/mol, which is lower than that of vertebrate calmodulin (4 mol/mol). The same maximum activity of porcine brain phosphodiesterase was attained when 100 times higher concentration of yeast calmodulin than that of vertebrate calmodulin was added. On the other hand, the maximum activation of chicken gizzard myosin light chain kinase was attained with 1,000 times higher concentration of yeast calmodulin than that of vertebrate calmodulin, and the maximum activity with yeast calmodulin was less than 1/5 of that with vertebrate calmodulin. Several amino acid substitutions observed in the yeast calmodulin, particularly at the alpha-helical rod connecting the two globular domains, may affect the interaction mode of various target enzymes with this calmodulin.     

Differences in structural dynamics of muscle and yeast actin accompany differences in functional interactions with myosin.

We have used spectroscopic probes ErIA and IAEDANS attached to Cys374 to compare the structural dynamics of yeast actin filaments with that of muscle actin, to understand the structural basis of the less productive interaction of yeast actin with myosin. Time-resolved phosphorescence anisotropy (TPA) of ErIA and steady-state fluorescence of IAEDANS were measured. TPA indicated more rapid rotational motion and more restricted angular amplitude in yeast actin. The fluorescence spectrum was less intense and more red-shifted in yeast actin, suggesting more exposure of the probe to solvent. These results indicate that the two actins differ substantially in the conformational dynamics of the C-terminal region. Binding of myosin S1 induced significantly different spectroscopic changes in TPA and fluorescence of muscle and yeast actin. As a result, the spectroscopic differences between the two actins were decreased by the addition of S1. These results suggest that yeast actin is less effective at activating myosin because of larger changes required in the structure of actin upon strong myosin binding. These results provide insight into the relationship between actomyosin dynamics and function, and they provide a useful framework for structure-function analysis of mutant yeast actin.     

GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks

In recent years, graph theoretical analyses of neuroimaging data have increased our understanding of the organization of large-scale structural and functional brain networks. However, tools for pipeline application of graph theory for analyzing topology of brain networks is still lacking. In this report, we describe the development of a graph-analysis toolbox (GAT) that facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI) that facilitates construction and analysis of brain networks, comparison of regional and global topological properties between networks, analysis of network hub and modules, and analysis of resilience of the networks to random failure and targeted attacks. Area under a curve (AUC) and functional data analyses (FDA), in conjunction with permutation testing, is employed for testing the differences in network topologies; analyses that are less sensitive to the thresholding process. We demonstrated the capabilities of GAT by investigating the differences in the organization of regional gray-matter correlation networks in survivors of acute lymphoblastic leukemia (ALL) and healthy matched Controls (CON). The results revealed an alteration in small-world characteristics of the brain networks in the ALL survivors; an observation that confirm our hypothesis suggesting widespread neurobiological injury in ALL survivors. Along with demonstration of the capabilities of the GAT, this is the first report of altered large-scale structural brain networks in ALL survivors.     

Peptidergic modulation of male sexual behavior in Lymnaea stagnalis: structural and functional characterization of -FVamide neuropeptides

In the simultaneous hermaphrodite snail Lymnaea stagnalis, copulation as a male is controlled by neurons that send axons to the male copulatory organs via a single penis nerve. Using direct mass spectrometry of a penis nerve sample, we show that one of the molecular ions has a mass corresponding to GAPRFVamide, previously identified from the buccal ganglia, and named Lymnaea inhibitory peptide (LIP). The identity of this peptide is confirmed by partial peptide purification from the penis nerve, followed by post source decay mass spectrometry. We cloned the LIP-encoding cDNA, which predicts a prohormone that gives rise to five copies of LIP (now re-named LIP A), two other -FVamide peptides (LIPs B and C), and five structurally unrelated peptides. The LIP gene is expressed in neurons of the right cerebral ventral lobe that send their axons into the penis nerve. We show that the LIP A peptide is present in these neurons and in the penis nerve, and confirmed the presence of LIP B and C in the penis nerve by post source decay mass spectrometry. Finally, we demonstrate that LIP A, B and C inhibit the contractions of the penis retractor muscle, thereby implicating their role in male copulation behavior.     

ACTH and brain membrane phosphorylation: a model for modulation by neuropeptides

It has been hypothesized that changes in the phosphorylation of synaptic membrane constituents (proteins and lipids) may affect transmission in certain types of synapses. In this paper some of the recent evidence that neuropeptides like ACTH may bring about their behavioral activity by influencing brain protein and lipid phosphorylation is reviewed. An ACTH-sensitive, cAMP-independent protein kinase was isolated from rat brain synaptosomal plasma membranes. This enzyme was partially characterized and it was observed that its activity greatly depended on the presence of calcium ions. One of its substrate proteins B-50 (MW 48,000; IEP 4.5) may play a key role in the turnover of a special class of membrane phospholipids i.e. the (poly)phosphoinositides. Evidence was obtained to suggest that the degree of phosphorylation of the B-50 protein determines the conversion of diphosphoinositol to triphosphoinositol. A model which links the protein phosphorylation to lipid phosphorylation and which points to a functional role for peptides in the regulation of the permeability of brain membranes for calcium ions will be discussed. As the structure-activity relationship for the peptide effects on grooming behavior closely resembles that on phosphorylation, it is assumed that this neurochemical event may indeed be of relevance to the biological activity of the peptide. As the ion permeability may be altered by the peptide it can be suggested that this may lead to modulation of transynaptic information processing in the brain.     

Temperature-induced structural changes of apo-lactoferrin and their functional implications: a molecular dynamics simulation study

Lactoferrin (Lf) is an iron-binding glycoprotein present in secretory fluids from human and bovine sources. Sequence alignment was employed to identify a region on the C-lobe of Lf capable of binding to bacterial cell surfaces, followed by all-atom explicit solvent molecular dynamics simulations to study the conformational changes of Lf after exposure to three processing temperatures: pasteurisation (72°C), spray drying (90°C) and ultra-high temperature (UHT) (127°C). Below 90°C, the simulations indicate relatively minor changes in overall protein structure. At UHT conditions (127°C), however, marked disruptions to protein structure were found as demonstrated by a substantial decrease in protein dimensions due to collapse in the inter-lobe region. There was also a marked increase in residue fluctuations in several regions of known functional importance, including antibacterial, iron-binding, and putative membrane binding regions, the latter of which is stabilised by a triplet of hydrophobic residues comprised of Leu446, Trp448 and Leu451 at low temperature, but which are disrupted under UHT conditions. A unique network analysis confirmed these results as demonstrated by large clusters of residues with increased dynamical correlation in the N-terminal lobe.     

Molecular dynamics simulation on structural conformation of conjugated polymer-functionalised films for optimal fluorescent performance

The sensitive structure-related fluorescent properties of p-phenyleneethynylene (PPE)-functionalised fluorescent films with side chains and without side chains in different chemical environments are studied by molecular dynamics simulations. The calculations demonstrate that the structural change plays a crucial role in the fluorescent performance of PPE films, in which a major contribution is from the conformation of side chains. The PPE molecules with sides chains immobilised on SiO₂ substrate prefer to aggregate together in a dry state, but are more likely to stay in a monomolecular state in THF solvent. To an optimal concentration of the solvent molecules, the side chains are even perpendicular to the backbones of the molecules. The aggregation and separation of the PPE molecules with side chains are found to be controlled by the contraction and extension of the side chains connected to PPE. The van der Waals' force between the side chains is mainly responsible for these changes, which leads to a spreading out of the side chains in the presence of THF. All the results from the simulation studies can successfully explain the experimental observations.     

Global dynamics of a selection model for the growth of a population with genotypic fertility differences

A population growth model is considered for a one locus two allele problem with selection based entirely on fertility differences. A local stability analysis is carried out for the critical points — which include possible polymorphic states — of the resulting nonlinear differential equations. The methods of dynamical systems theory are applied to obtain limiting genotypic proportions for every initial state. Thus the results are global and there are no periodic solutions.Research for this paper was partially supported by the National Science and Engineering Research Council of Canada Grant NSERC A-8130Research for this paper was partially supported by the National Science and Engineering Research Council of Canada Grant NSERC A-4823Research supported by NSF Grant MCS 7901069. A portion of the work was carried out while the author was a Visiting Professor at the University of Utah, Salt Lake City, Utah     

Recovery from heart failure: structural and functional analysis in a canine model

Chronic, rapid ventricular pacing produces congestive heart failure in the dog. Using echocardiography, the features of developing heart failure were analysed and the capacity of this model for recovery was assessed once pacing had been discontinued. Fifteen dogs were studied; nine were paced at 250 beats/min (bpm) to severe heart failure (5.0 +/- 1.8 weeks) and six served as sham controls. In the paced animals at severe heart failure, two-dimensional echocardiography demonstrated a significant increase in diastolic cross-sectional cardiac area (from 11 +/- 3 to 16 +/- 2 cm2, p less than 0.05), associated with a marked fall n area ejection fraction (54 +/- 8 to 21 +/- 8%, p less than 0.05), and significant left ventricular wall thinning (from 6.0 +/- 0.7 to 4.7 +/- 0.9 mm, p less than 0.05). In addition, significant increases in heart rate (77 +/- 7 to 126 +/- 13 bpm, sinus rhythm; p less than 0.05), respiratory rate (41 +/- 13 to 80 +/- 20 cycles/min, p less than 0.05), and body weight (21 +/- 1 to 24 +/- 3 kg, p less than 0.05) were noted. Serum sodium fell (146 +/- 3 to 140 +/- 8 mmol/L, p less than 0.05), while blood urea nitrogen (6 +/- 2 to 10 +/- 2 mmol/L, p less than 0.05) and creatinine (86 +/- 12 to 101 +/- 15 mmol/d, p less than 0.05) increased. Recovery was characterized by rapid improvement such that all measured parameters normalized by 1 week, except for cross-sectional cardiac area which remained dilated up to 4 weeks (14 +/- 3 cm2, p less than 0.05 versus control).(ABSTRACT TRUNCATED AT 250 WORDS)     

Effects of soman inhibition and of structural differences on cholinesterase molecular dynamics: a neutron scattering study

Incoherent elastic neutron scattering experiments on members of the cholinesterase family were carried out to investigate how molecular dynamics is affected by covalent inhibitor binding and by differences in primary and quaternary structure. Tetrameric native and soman-inhibited human butyrylcholinesterase (HuBChE) as well as native dimeric Drosophila melanogaster acetylcholinesterase (DmAChE) hydrated protein powders were examined. Atomic mean-square displacements (MSDs) were found to be identical for native HuBChE and for DmAChE in the whole temperature range examined, leading to the conclusion that differences in activity and substrate specificity are not reflected by a global modification of subnanosecond molecular dynamics. MSDs of native and soman-inhibited HuBChE were identical below the thermal denaturation temperature of the native enzyme, indicating a common mean free-energy surface. Denaturation of the native enzyme is reflected by a relative increase of MSDs consistent with entropic stabilization of the unfolded state. The results suggest that the stabilization of HuBChE phosphorylated by soman is due to an increase in free energy of the unfolded state due to a decrease in entropy.     

Assessment of structural and functional similarities and differences between caeca of the bluegill

Bluegill Lepomis macrochirus possess six to eight gastrointestinal caeca, >70% having seven. The terminal caeca toward abdominal edge (C6, C7) were always larger than the terminal caeca toward the vertebral column (C1, C2) and middle caeca (C3, C4, C5). The caeca varied in relative thickness of the histological layers and lumen space. The terminal caeca (C1, C2, C6, C7) have anatomical positional advantage over, and possess more contents, than the middle ones (C3, C4, C5) in both field and laboratory conditions. Hence, all caeca in bluegill may have the same function but their functional potentials are not the same. Two factors, size of caeca and anatomical position of caeca, apparently work synergistically to cause variation in their functional efficiency.     

Connexinopathies: a structural and functional glimpse

Mutations in human connexin (Cx) genes have been related to diseases, which we termed connexinopathies. Such hereditary disorders include nonsyndromic or syndromic deafness (Cx26, Cx30), Charcot Marie Tooth disease (Cx32), occulodentodigital dysplasia and cardiopathies (Cx43), and cataracts (Cx46, Cx50). Despite the clinical phenotypes of connexinopathies have been well documented, their pathogenic molecular determinants remain elusive. The purpose of this work is to identify common/uncommon patterns in channels function among Cx mutations linked to human diseases. To this end, we compiled and discussed the effect of mutations associated to Cx26, Cx32, Cx43, and Cx50 over gap junction channels and hemichannels, highlighting the function of the structural channel domains in which mutations are located and their possible role affecting oligomerization, gating and perm/selectivity processes.     

Connexinopathies: a structural and functional glimpse

Mutations in human connexin (Cx) genes have been related to diseases, which we termed connexinopathies. Such hereditary disorders include nonsyndromic or syndromic deafness (Cx26, Cx30), Charcot Marie Tooth disease (Cx32), occulodentodigital dysplasia and cardiopathies (Cx43), and cataracts (Cx46, Cx50). Despite the clinical phenotypes of connexinopathies have been well documented, their pathogenic molecular determinants remain elusive. The purpose of this work is to identify common/uncommon patterns in channels function among Cx mutations linked to human diseases. To this end, we compiled and discussed the effect of mutations associated to Cx26, Cx32, Cx43, and Cx50 over gap junction channels and hemichannels, highlighting the function of the structural channel domains in which mutations are located and their possible role affecting oligomerization, gating and perm/selectivity processes.