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PubMed2001

Hydration of the calcium ion. An EXAFS, large-angle x-ray scattering, and molecular dynamics simulation study.

The structure of the hydrated calcium(II) ion in aqueous solution has been studied by means of extended X-ray absorption fine structure spectroscopy (EXAFS), large-angle X-ray scattering (LAXS), and molecular dynamics (MD) methods. The EXAFS data displayed a broad and asymmetric distribution of the Ca-O bond distances with the centroid at 2.46(2) A. LAXS studies on four aqueous calcium halide solutions (1.5-2 mol dm(-)(3)) gave a mean Ca-O bond distance of 2.46(1) A. This is consistent with a hydration number of 8 determined from correlations between mean distances and coordination numbers from crystal structures. The LAXS studies showed a second coordination sphere with a mean Ca.O(II) distance of 4.58(5) A, and for the hydrated halide ions the distances Cl.O 3.25(1) A, Br.O 3.36(1) A, and I.O 3.61(1) A were obtained. Molecular dynamics simulations of CaCl(2)(aq) were performed using three different Ca(2+)-OH(2) pair potentials. The potential from the GROMOS program gave results in agreement with experiments, i.e., a coordination number of 8 and an average Ca-O distance of 2.46 A, and was used for further comparisons. Theoretical EXAFS oscillations were computed for individual MD snapshots and showed very large variations, though the simulated average spectrum from 2000 snapshots gave satisfactory agreement with the experimental EXAFS spectra. The effect of thermal motions of the coordinated atoms is inherent in the MD simulation method. Thermal disorder parameters evaluated from simulated spatial atom distribution functions of the oxygen atoms coordinated to the calcium ion were in close agreement with those from the current LAXS and EXAFS analyses. The combined results are consistent with a root-mean-square displacement from the mean Ca-O distance of 0.09(2) A in aqueous solution at 300 K.

Body Water↗
PubMed2006

Synthetic polymers and biomembranes. How do they interact? Atomistic molecular dynamics simulation study of PEO in contact with a DMPC lipid bilayer.

The understanding of interactions of poly(ethylene glycol) (PEG) or poly(ethylene oxide) (PEO) with biological interfaces has important technological application in industry and in medicine. In this paper, structural and dynamical properties of PEO at the dimyristoylphospatidylcholine (DMPC) bilayer/water interface have been investigated by molecular dynamics (MD) and steered molecular dynamics (SMD) simulations. The structural properties of a PEO chain in bulk water, at the water/vacuum interface, and in the presence of the membrane were compared with available experimental data. The presence of a barrier for the PEO penetration into the DMPC bilayer has been found. A qualitative estimation of the barrier provided a value equal to approximately 19 kJ/mol, that is, 7 times the value of kT at 310 K.

Dimyristoylphosphatidylcholine↗
PubMed1993

Molecular dynamics in refinement against fiber diffraction data.

The molecular dynamics (MD) method has been adapted for refinement of the structures of helical macromolecular aggregates aginst X-ray fiber diffraction data. To test the effectiveness of the method, refinements of the tobacco mosaic virus structure were carried out against a set of simulated fiber diffraction intensities using the MD method as well as the conventional restrained least-squares (RLS) method. The MD refinement converged to a very low R factor and produced a structure with generally satisfactory sterochemistry, while the RLS refinemnt was trapped at a local energy minimum with a larger R factor. Results suggest that the effective experimental radius of convergence of the MD method is significantly greater than that of the RLS method. Even when the initial structure is too far from the true structure to allow direct refinement, the MD method is able to find local minima that resemble the true structure sufficiently to allow improved phasing and thus lead to interpretable difference maps for model rebuilding.

Capsid↗
PubMed2003

Conformational analysis of endomorphin-2 by molecular dynamics methods.

Endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH(2)) is a highly potent and selective mu-opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N-terminal NH(2)) and charged (N-terminal NH(3) (+)) molecules. Based on the results of NMR investigations showing an equilibrium mixture of cis and trans Tyr(1)-Pro(2) peptide bonds for EM2 in solution, simulations were performed with restrained cis-Pro and trans-Pro peptide bonds, too. A separate SA study with unrestrained Pro peptide bonds was also conducted. Preferred conformational states are presented in Ramachandran plots. The g(+), g(-), and trans populations of the aromatic amino acid residue side chains were determined in chi(1) space. The distances between the N-terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic rings and the Pro(2) ring, were determined. The energy distribution of the structures obtained by SA was calculated. The preferred secondary structural elements were different kinds of beta-turns, an inverse gamma-turn located in the N-terminal region, and regular and inverse gamma-turns located in the C-terminal region. These turns were stabilized by intramolecular H-bonds and bifurcated H-bonds.

Amino Acid Sequence↗
PubMed2003

Molecular dynamics simulations of the transmembrane domain of the oncogenic ErbB2 receptor dimer in a DMPC bilayer.

Molecular dynamics simulations of an atomic model of the transmembrane domain of the oncogenic ErbB2 receptor dimer embedded in an explicit dimyristoylphosphatidylcholine (DMPC) bilayer were performed for more than 4 ns. The oncogenic Glu mutation in the membrane spanning segment plays a major role in tyrosine kinase activity and receptor dimerization, and is thought to be partly responsible for the structure of the transmembrane domain of the active receptor. MD results show that the interactions between the two transmembrane helices are characteristic of a left-handed packing as previously demonstrated from in vacuo simulations. Moreover, MD results reveal the absence of persistent hydrogen bonds between the Glu side chains in a membrane environment, which raise the question of the ability for Glu alone to stabilize the TM domain of the ErbB2 receptor. Interestingly the formation of the alpha-pi motif in the two ErbB2 transmembrane helices confirms the concept of intrinsic sequence-induced conformational flexibility. From a careful analysis of our MD results, we suggest that the left-handed helix-helix packing could be the key to correctly orient the intracellular domain of the activated receptor dimer. The prediction of such interactions from computer simulations represents a new step towards the understanding of signaling mechanisms.

Computer Simulation↗
PubMed2006

Subplate neurons regulate maturation of cortical inhibition and outcome of ocular dominance plasticity.

Synaptic plasticity during critical periods of development requires intact inhibitory circuitry. We report that subplate neurons are needed both for maturation of inhibition and for the proper sign of ocular dominance (OD) plasticity. Removal of subplate neurons prevents the developmental upregulation of genes involved in mature, fast GABAergic transmission in cortical layer 4, including GABA receptor subunits and KCC2, and thus prevents the switch to a hyperpolarizing effect of GABA. To understand the implications of these changes, a realistic circuit model was formulated. Simulations predicted that without subplate neurons, monocular deprivation (MD) paradoxically favors LGN axons representing the deprived (less active) eye, exactly what was then observed experimentally. Simulations also account for published results showing that OD plasticity requires mature inhibition. Thus, subplate neurons regulate molecular machinery required to establish an adult balance of excitation and inhibition in layer 4, and thereby influence the outcome of OD plasticity.

Animals↗
PubMed2003

Anatomy of a supergroup: does a criterion of normal perimetric performance generate a supernormal population?

PURPOSE: To interpret individual results from automated perimeters, a normative database must be developed. Typically, a set of criteria determines those subjects that may be included in the database. This study examined whether a criterion of normal performance on an established perimeter generates a subgroup with supernormal perimetric performance. METHODS: The right-eye perimetric results of 100 subjects were analyzed. Subjects had visual acuities of 6/12 or better, no history of eye disease, and normal slit lamp biomicroscopic and ophthalmoscopic examinations. Subjects performed test-retest visual field examinations on a Humphrey Field Analyzer (HFA) 24-2 test (Zeiss Humphrey Systems, Dublin, CA), and on a custom frequency-doubling (FD) perimeter with targets spaced in the same 24-2 pattern. RESULTS: Test-retest correlation (Spearman rank correlation coefficients, rs) for mean defect (MD) and pattern SD (PSD) were 0.65 and 0.40 (HFA), and 0.82 and 0.39 (FD perimeter). Three subjects with HFA MDs in the lower 5% had similarly low MDs on retest, whereas no subject was common between the test and retest for the lower 5% of HFA PSD. Correlation between the HFA and FD test results were 0.41 (MD) and 0.05 (PSD). Based on these correlations, the bias introduced into perimetric probability limits were determined, by using Monte Carlo simulations. CONCLUSIONS: Although a criterion of a normal MD may produce a subpopulation with supernormal perimetric performance, a criterion of a normal PSD is less likely to do so. Also, a criterion on one test type is less likely to create a supernormal group on a different test type. The bias introduced into perimetric probability limits is small.

Adult↗
PubMed2004

Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V.

Coagulation factor V (FV) is a large plasma glycoprotein with functions in both the pro- and anticoagulant pathways. In carriers of the so-called R2-FV haplotype, the FV D2194G mutation, in the C2 membrane-binding domain, is associated with low expression levels, suggesting a potential folding/stability problem. To analyze the molecular mechanisms potentially responsible for this in vitro phenotype, we used molecular dynamics (MD) and continuum electrostatic calculations. Implicit solvent simulations were performed on the x-ray structure of the wild-type C2 domain and on a model of the D2194G mutant. Because D2194 is located next to a disulfide bond (S-S bond), MD calculations were also performed on S-S bond depleted structures. D2194 is part of a salt-bridge network and investigations of the stabilizing/destabilizing role of these ionic interactions were carried out. Five mutant FV molecules were created and the expression levels measured with the aim of assessing the tolerance to amino acid changes in this region of molecule. Analysis of the MD trajectories indicated increased flexibility in some areas and energetic comparisons suggested overall destabilization of the structure due to the D2194G mutation. This substitution causes electrostatic destabilization of the domain by approximately 3 kcal/mol. Together these effects likely explain the lowered expression levels in R2-FV carriers.

Amino Acid Substitution↗
PubMed2006

Application of the new MMPI-2 Malingered Depression scale to individuals undergoing neuropsychological evaluation: relative lack of relationship to secondary gain and failure on validity indices.

The Malingered Depression (Md) scale for the MMPI-2 (Steffan, Clopton, & Morgan, 2003) was recently developed to detect attempts at malingering depressive symptomatology. The Steffan et al. cutoffs for the Md scale were derived through comparisons of undergraduate malingering simulators with depressed undergraduates. In order to explore the potential utility for neuropsychological practice, we examined the Md scale among 160 individuals with and without a context of secondary gain referred for neuropsychological evaluation. Md results were compared to other MMPI-2 validity indices and performance on effort testing. While Md was found to correlate highly with other validity indices from the MMPI-2, it was also correlated significantly with measures of depression, both in individuals with and without a secondary gain context. Md scores were not significantly different between secondary gain and no secondary gain groups, whereas FBS and L were significantly different. The effect of passing or failing validity indicators on rates of Md scores exceeding the Steffan et al. cutoffs was limited. Only among the few individuals exceeding a high threshold on the F scale or combinations of F, FBS, and effort indicators was it common to also surpass the Md cutoff. Overall, Md showed relatively little relationship to either secondary gain status or cognitive malingering in our sample. Given that such factors do not necessarily produce high scores on Md, the utility of the scale to clinical neuropsychologists appears low.

Adult↗
PubMed1993

Inversion of receptor binding preferences by mutagenesis: free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins.

The Escherichia coli L-arabinose-binding protein (ABP) participates as a specific receptor in the transport of L-arabinose, D-fucose, and D-galactose through the periplasmic space. The wild-type protein binds L-arabinose about 40 times more strongly than D-fucose. A mutation of the protein at position 108 (Met-->Leu) causes a specificity change. The Met108Leu ABP slightly prefers binding of D-fucose over L-arabinose. Molecular dynamics (MD) and thermodynamic integration (TI) computer simulations were performed to study the mechanism of sugar discrimination and specificity change based on the known high-resolution X-ray structures. The specificity change was evaluated by calculating the difference in free energy of L-arabinose versus D-fucose bound to wild-type and Met108Leu ABP. The calculated free energy differences are consistent with the experimentally observed specificity of wild-type and Met108Leu ABP. The simulations indicate that the specificity change of Met108Leu ABP is accomplished mainly by reduced Lennard-Jones interactions of residue 108 with L-arabinose and improved interactions with D-fucose. In addition to MD/TI calculations on sugar binding, finite difference Poisson-Boltzmann calculations were performed to identify the most stable ionization state of buried ionizable residues in ABP.

Arabinose↗
PubMed1998

Molecular dynamics simulation of interaction of histone-like protein of mycobacterium tuberculosis (Hlpmt) and histone of clostridium pasteurianum (DBHclopa) with 35 based paired GC rich U-bend DNA.

Three dimensional structure of the first ninety two residues of histone like protein from Mycobacterium tuberculosis (Hlpmt) and histone of Clostridium pasteurianum (DBHclopa) are obtained here, on the basis of amino acid sequences of the two proteins, making use of secondary structure prediction programs, sequence search and HOMOLOGY based modeling tools available on Internet. The proteins were docked to a 35 base paired GC rich U bend DNA (U35DNA). Structures of proteins Hlpmt and DBHclopa; U35DNA; and complexes: Hlpmt-U35DNA and DBHclopa-U35DNA were optimized by molecular mechanics (MM) and simulated for 260 pico seconds (ps) in vacuum by molecular dynamics (MD) technique using AMBER 4.0 package with Cornell et al force field. The proteins, when simulated alone, showed compaction. DBHclopa showed larger compaction compared with Hlpmt. U35DNA when simulated alone straightened out and assumed a B-form. In the complexes, Hlpmt showed same order of compaction as in absence of DNA, while DBHclopa showed reduced compaction. In the presence of Hlpmt two ends of helicoidal axis of U35DNA came closer, but slightly out of plane, indicative of its role in overwinding and packaging double stranded DNA. DBHclopa did not give rise to DNA overwinding. The results show architectural role of Hlpmt and DBHclopa in DNA packaging and its sequence dependence.

Amino Acid Sequence↗
PubMed2002

Dynamic structure of He-Ne mixtures by molecular dynamics simulation: from hydrodynamic to fast and slow sound modes.

Molecular dynamics (MD) results for the dynamic structure of a He(0.77)Ne(0.23) gas mixture at two densities (15.8 and 36.1 nm(-3)) show a clear crossover from hydrodynamic modes to distinct excitations for the two species. The higher density dispension curve neatly shows high- and low-frequency branches setting on with a rather localized transition. The lower density results agree very well with existing neutron scattering data and, in particular, display hydrodynamic behavior up to k approximately 2 nm(-1), in contrast with the conclusions of previous simulation studies. A smooth transition to fast sound is shown to take place for 2<k/nm(-1)<5, where the present MD data fill the existing gap in the experimental results.

Journal Article↗
PubMed2005

[Does HRCT-emphysema index represent the entire lung?].

PURPOSE: : Comparison of emphysema index derived of thin section MD-CT of the entire lung volume and HRCT, simulated by calculation of every twentieth image of the whole data-set. MATERIALS AND METHODS: Pulmonary emphysema was quantified by semiautomatic, segmentation of lung borders and assessment of lung volume and emphysema volume within these borders. The emphysema index (pixel index) was calculated. Statistical analysis was done by the sign-test and Bland-Altman-analysis. RESULTS: Median lung volume, emphysema volume and emphysema index are significantly higher in simulated HRCT. Median lung volume (emphysema volume) calculated by HRCT is 5118 ml (407 ml) and 5040 ml (367 ml) calculated by the entire MD-CT data-set, representing differences of 1 and 8 % related to the median lung and emphysema volumes. Emphysema index is 0.09 (HRCT) and 0.08 (MD-CT). CONCLUSION: HRCT overrates emphysema index compared to thin section MD-CT of the entire lung volume.

Adolescent↗
PubMed1999

Computer simulation of the interaction of non-steroidal anti-inflammatory drugs: indoprofen and NS398 with cyclooxygenase.

We have applied computer simulation technique to study interaction of two anti-inflammatory drugs (NSAIDs) indoprofen and NS398 with cyclooxygenase (COX-1 and COX-2) enzymes. We have also investigated conformational flexibility of the two drugs by systematic search and simulated annealing molecular dynamics (SAMD) methods. Both the drugs were docked in the cyclooxygenase channel using in house docking program IMF1. The complexes were energy minimised by molecular mechanics (MM) method. These were heated for 30 picoseconds (ps), equilibrated for 110 ps at 300K and subjected to 'production simulation' for 110 ps by molecular dynamics (MD) method using Sanderís module of AMBER 5.0 package and united atom force field mostly from PARM96.DAT. Integration was carried out with time step of 0.001 ps, distance dependent di-electric constant with scaling factor 2.0 for 1-4 interaction and cut-off distance for non-bonded pair-list equal to 8A. The non-bonded pair-list was upgraded after every 20 cycles. The coordinate output from MD trajectories is analysed using analysis package of AMBER 5.0, MOLMOL, P-CURVES 3.0 and in house packages: ANALMD, ANALP1. We have observed perturbative changes in COX-1 and COX-2 structures due to indoprofen and NS398. In case of indoprofen specific changes between COX-1 and COX-2 were noted in helix D, H6, S6 and helix H8 in the cyclooxygenase cavity. In case of NS398 these were in helix B in membrane binding domain, helix H6, S8 and S10 in cyclooxygenase cavity and helices H14-H16 in small lobe close to haem binding region. Implications of these results in enzyme selectivity by NSAIDs is discussed here.

Anti-Inflammatory Agents, Non-Steroidal↗
PubMed2003

Ab initio folding of helix bundle proteins using molecular dynamics simulations.

We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.

Computer Simulation↗
PubMed1998

Molecular dynamics simulations of the structure of aldose reductase complexed with the inhibitor tolrestat.

This study reports a molecular dynamics (MD) investigation on the structure of aldose reductase (ALR2) complexed with the potent inhibitor tolrestat. The simulations predict four different orientations of tolrestat into the ALR2 binding site; these orientations have in common a strong interaction of the anionic carboxylate with Tyr48, His110, Trp111 and NADP+, but completely differ for the orientation of the aromatic portion of the inhibitor. Interestingly, the orientation in which tolrestat gives the most attractive interaction energy with the enzyme is in full accord with the x-ray crystal structure of the complex that has been reported in the literature after this work was completed. In addition, the suggestion of more than one orientation of tolrestat during MD is in agreement with recent electrospray mass spectrometry experiments on the ALR2-tolrestat complex.

Aldehyde Reductase↗
PubMed2007

Increased culture recovery of Zygomycetes under physiologic temperature conditions.

Poor recovery of Zygomycetes hyphae from tissue specimens may result from failure of current culture methods to mimic physiologic conditions found in hyphae-laden infected tissue. We describe the use of an in vitro model simulating Zygomycetes growth under necrotic or hypoxic tissue conditions. We preconditioned hyphae of clinical Zygomycetes isolates in flasks under anaerobic conditions using Ana-Packs (Becton Dickinson Microbiology Systems, Sparks, MD) at 37 degrees C for 48 hours, thus simulating in vivo growth in an infracted hypoxic lesion, and compared the recovery of paired inocula at 37 degrees C and 25 degrees C. Incubation of stock culture isolates at 37 degrees C resulted in significantly better culture recovery (about 10-fold) when compared with incubation at 25 degrees C (P < .0001). In addition, we similarly evaluated 25, 291 consecutive clinical specimens. Among 41 specimens, the yield of Zygomycetes cultures incubated at 37 degrees C (23/41 [56%]) was significantly higher than that incubated at 25 degrees C (9/41 [22%]; P = .0001). Overall, we found that culture recovery was significantly (254%) enhanced at 37 degrees C.

Anaerobiosis↗
PubMed2006

Computational design of proteins stereochemically optimized in size, stability, and folding speed.

Artificial proteins potentially barrier-free in the folding kinetics are approached computationally under the guidance of protein-folding theories. The smallest and fastest folding globular protein triple-helix-bundle (THB) is so modified as to minimize or eliminate its presumed barriers in folding speed. As the barriers may reside in the ordering of either secondary or tertiary structure, the elements of both secondary and tertiary structure in the protein are targeted for prenucleation with suitable stereochemically constrained amino acid residues. The required elements of topology and sequence for the THB are optimized independently; first the topology is optimized with simulated annealing in polypeptides of highly simplified alphabet; next, the sequence in side chains is optimized using the standard inverse design methods. The resultant three best-adapted THBs, variable in topology and distinctive in sequences, are assessed by comparing them with a few benchmark proteins. The results of mainly molecular dynamics (MD) comparisons, undertaken in explicit water at different temperatures, show that the designed sequences are favorably placed against the chosen benchmarks as THB proteins potentially thermostable in the native folds. Folding simulation experiments with MD establish that the designed sequences are rapid in the folding of individual helices, but not in the evolution of tertiary structure; energetic cum topological frustrations remain but could be the artifacts of the starting conformations that were chosen in the THBs in the folding simulations. Overall, a practical high-throughput approach for de novo protein design has been developed that may have fruitful application for any type of tertiary structure.

Amino Acid Sequence↗