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At least 199 records · Page 11Linked to original sources
PubMed1998

Computer simulation study of synthetic 4-helix bundle that binds halothane.

1. The synthetic peptide H10A24 self-assembles in aqueous solution into a 4-helix bundle, which exhibits saturable binding of halothane. 2. Molecular dynamics simulation techniques have been used to study the vacuum structure of this bundle. 3. The simulation, initiated as four ideal parallel alpha-helices, resulted in a compact bundle, whose secondary structure remains predominantly alpha-helical. 4. The hydrophobic core has no apparent pocket large enough to accomodate halothane.

Algorithms↗
PubMed2000

Adsorptionlike collapse of diblock copolymers

A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive Monte Carlo simulations in two and three dimensions. In the former case, an identification with the statistical geometry of suitable percolation paths allows one to predict that the number of contacts between the blocks grows like N9/16. In the compact phase the blocks are mixed and, in two dimensions, also zipped, in such a way to form a spiral, double chain structure.

Journal Article↗
PubMed2000

Model for computer simulation of bone tissue.

The paper deals with the dependence of the torsional moment on the angle of the compact bone torsion in laboratory animals and humans. Based on the data for laboratory animals obtained by measurements, the data on dependence of the torsional moment and the angle of torsion were predicted for humans. The measurements were carried out in four groups of laboratory animals. One was the control group, and the other three groups were treated by various vitamin D3 metabolites. The same measurements were performed also in only one group of humans, due to the impossibility to treat humans with vitamin D3 metabolites. The functional relationship between the angle of torsion and the torsional moment for all the groups of animal bone tissue were determined by measurements, and results were used to predict the reaction of the human compact bone tissue if treated by vitamin D3 metabolites.

Animals↗
PubMed2023

A new horizon in the phosphorylated sites of AGA: the structural impact of C163S mutation in aspartylglucosaminuria through molecular dynamics simulation.

Aspartylglucosaminuria (AGU) is a lysosomal storage disorder caused by insufficient aspartylglucosaminidase (AGA) activity leading to chronic neurodegeneration. We utilized the PhosphoSitePlus tool to identify the AGA protein's phosphorylation sites. The phosphorylation was induced on the specific residue of the three-dimensional AGA protein, and the structural changes upon phosphorylation were studied via molecular dynamics simulation. Furthermore, the structural behaviour of C163S mutation and C163S mutation with adjacent phosphorylation was investigated. We have examined the structural impact of phosphorylated forms and C163S mutation in AGA. Molecular dynamics simulations (200 ns) exposed patterns of deviation, fluctuation, and change in compactness of Y178 phosphorylated AGA protein (Y178-p), T215 phosphorylated AGA protein (T215-p), T324 phosphorylated AGA protein (T324-p), C163S mutant AGA protein (C163S), and C163S mutation with Y178 phosphorylated AGA protein (C163S-Y178-p). Y178-p, T215-p, and C163S mutation demonstrated an increase in intramolecular hydrogen bonds, leading to greater compactness of the AGA forms. Principle component analysis (PCA) and Gibbs free energy of the phosphorylated/C163S mutation structures exhibit transition in motion/orientation than Wild type (WT). T215-p may be more dominant among these than the other studied phosphorylated forms. It might contribute to hydrolyzing L-asparagine functioning as an asparaginase, thereby regulating neurotransmitter activity. This study revealed structural insights into the phosphorylation of Y178, T215, and T324 in AGA protein. Additionally, it exposed the structural changes of the C163S mutation and C163S-Y178-p of AGA protein. This research will shed light on a better understanding of AGA's phosphorylated mechanism.Communicated by Ramaswamy H. Sarma.

Molecular Dynamics Simulation↗
PubMed2000

Stability of Si-interstitial defects: from point to extended defects

Trends in the growth of extended interstitial defects are extracted from extensive tight-binding and ab inito local density approximation simulations. With an increasing number of interstitials, the stable defect shape evolves from compact to chainlike to rodlike. The rodlike 311 defect, formed from (011) interstitial chains, is stabilized as it grows, elongating in the chain direction. Accurate parametrization of the defect-formation energy on the number of interstitials and interstitial chains, together with the anisotropy of the interstitial capture radius, enables macroscopic defect-growth simulations.

Journal Article↗
PubMed2002

Molecular dynamics simulations of calcium-free calmodulin in solution.

A 4-ns molecular dynamics simulation of calcium-free calmodulin in solution has been performed, using Ewald summation to treat electrostatic interactions. Our simulation results were mostly consistent with solution experimental studies, including NMR, fluorescence and x-ray scattering. The secondary structures within the N- and C-terminal domains were conserved in the simulation, with trajectory structures similar to the NMR-derived model structure 1CFD. However, the relative orientations of the domains, for which there are no NMR restraints, differed in details between the simulation and the 1CFD model. The most interesting information provided by the simulations is that the dynamics of calcium-free calmodulin in solution is dominated by slow rigid body reorientations of the domains. The interdomain distance fluctuated between 29 and 39 A, and interdomain orientation angle, defined as the pseudo-dihedral formed by the four calcium binding sites, varied between -2 degrees and 108 degrees. Similarly, the domain linker region also exhibited significant fluctuations, with its length varying in the 34-45 A range and its bend angle in the 10-100 degrees range. The simulations are in accord with fluorescence results suggesting that calcium-free calmodulin is more compact and more flexible than the calcium activated form. Surprisingly, quite similar solvent accessibilities of the hydrophobic patches were seen in the calcium-free trajectory described in this work and previously generated calcium-loaded calmodulin simulations. Thus, our simulations suggest a reexamination of the standard model of the structural change of calmodulin upon calcium binding, involving exposure of the hydrophobic patches to solvent.

Biophysical Phenomena↗
PubMed2002

Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data.

Unfolding transitions of an intrinsically unstable annexin domain and the unfolded state structure have been examined using multiple approximately 10-ns molecular dynamics simulations. Three main basins are observed in the configurational space: native-like state, compact partially unfolded or intermediate compact state, and the unfolded state. In the native-like state fluctuations are observed that are nonproductive for unfolding. During these fluctuations, after an initial loss of approximately 20% of the core residue native contacts, the core of the protein transiently completely refolds to the native state. The transition from the native-like basin to the partially unfolded compact state involves approximately 75% loss of native contacts but little change in the radius of gyration or core hydration properties. The intermediate state adopts for part of the time in one of the trajectories a novel highly compact salt-bridge stabilized structure that can be identified as a conformational trap. The intermediate-to-unfolded state transition is characterized by a large increase in the radius of gyration. After an initial relaxation the unfolded state recovers a native-like topology of the domain. The simulated unfolded state ensemble reproduces in detail experimental nuclear magnetic resonance data and leads to a convincing complete picture of the unfolded domain.

Amino Acid Sequence↗
PubMed1999

Factors that affect the folding ability of proteins.

The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the stability of the native state. We consider a number of estimates of the stability that can be determined without simulation, including the energy gap between the native state and the structurally dissimilar part of the spectrum (Z score) and, for sequences with fully compact native states, the gap in energy between the native and first excited fully compact states. These estimates are found to be more robust predictors of folding ability than a parameter sigma that requires simulation for its evaluation: sigma = 1 - Tf/Ttheta, where Tf is the temperature at which the fluctuation of an order parameter is at its maximum and Ttheta is the temperature at which the specific heat is at its maximum. We show that the interpretation of Ttheta as the collapse transition temperature is not correct in general and that the correlation between sigma and the folding ability arises from the fact that sigma is related to the energy gap (Z score).

Monte Carlo Method↗
PubMed2005

Monte Carlo simulation of protein folding in the presence of residue-specific binding sites.

Ensemble growth Monte Carlo (EGMC) and dynamic Monte Carlo (DMC) simulations are used to study sequential folding and thermodynamic stability of hydrophobic-polar (HP) chains that fold to a compact structure. Molecularly imprinted cavities are modeled as hard walls having sites that are attractive to specific polar residues on the chain. Using EGMC simulation, we find that the folded conformation can be stabilized using a small number of carefully selected residue-specific sites while a random selection of surface-bound residues may only slightly contribute toward stabilizing the folded conformation, and in some cases may hinder the folding of the chain. DMC simulations of the surface-bound chain confirm increased stability of the folded conformation over a free chain. However, a different trend of the equilibrium population of folded chains as a function of residue-external site interactions is predicted with the two simulation methods.

Algorithms↗
PubMed2003

Molecular dynamics simulation of the unfolding of the human prion protein domain under low pH and high temperature conditions.

Four 10-ns molecular dynamics (MD) simulations of the human prion protein domain (HuPrP 125-228) in explicit water solution have been performed. Each of the simulations mimicked a different environment of the protein: the neutral pH environment was simulated with all histidine residues neutral and bearing a ND proton and with other titratable side chains charged, the weakly acidic environment was simulated with all titratable side chains charged, the strongly acidic environment was simulated with all titratable side chains protonated. The protein in neutral pH environment was simulated at both ambient (298 K) and higher (350 K) temperatures. The native fold is stable in the neutral pH/ambient temperature simulation. Through out all other simulations, a quite stable core consisted of 10-20 residues around the disulfide bond retain their initial conformations. However, the secondary structures of the protein show changes of various degrees compared to the native fold, parts of the helices unfolded and the beta-sheets extended. Our simulations indicated that the heat-induced unfolding and acid-induced unfolding of HuPrP might follow different pathways: the initial stage of the acid-induced unfolding may include not only changes in secondary structures, but also changes in the tertiary structures. Under the strongly acidic condition, obvious tertiary structure changes take place after 10-ns simulation, the secondary structure elements and the loops becoming more parallel to each other, resulting in a compact state, which was stabilized by a large number of new, non-native side chain-side chain contacts. Such tertiary structure changes were not observed in the higher temperature simulation, and intuitively, they may favor the further extension of the beta-sheets and eventually the agglomeration of multiple protein molecules. The driving forces for this tertiary structure changes are discussed. Two additional 10-ns MD simulations, one with Asp202 protonated and the other with Glu196 protonated compared to the neutral pH simulation, were carried out. The results showed that the stability of the native fold is very subtle and can be strongly disturbed by eliminating a single negative charge at one of such key sites. Correlations of our results with previous experimental and theoretical studies are discussed.

Computer Simulation↗
PubMed1990

Bioadhesive lozenge for the improved delivery of cetylpyridinium chloride.

Conventional lozenges produce a high initial release of drug in the oral cavity, which rapidly declines to subtherapeutic levels, and requires multiple daily administration with associated problems of systemic toxicity and compliance. Various multilayer compacts containing cetylpyridinium chloride were evaluated in vitro using release into simulated saliva (buffer pH 6.6). The drug loading, the wax content of the active layer, and the composition of the bioadhesive layer were important variables affecting product performance. Following preliminary in vivo studies, the release of a three-layered device containing drug in a nonadhesive and flavored waxy exposed layer was studied in six humans using HPLC and was shown not to be affected by location within the mouth. In comparison with a proprietary lozenge formulation, the device produced more uniform and effective levels of drug (approximately 20 micrograms.mL-1), with adequate comfort, taste, and irritancy over a period of 3 h.

Adhesiveness↗
PubMed2002

Macrophages influence a competition of contact guidance and chemotaxis for fibroblast alignment in a fibrin gel coculture assay.

Rat dermal fibroblasts were dispersed initially in the outer shell of a fibrin gel sphere, while the inner core either was devoid of cells or contained peritoneal exudate cells (primarily macrophages), thereby mimicking the inflammatory phase of wound healing. The fibroblasts compacted floating fibrin microspheres over time. In the absence of macrophages, the initial distribution of fibroblasts (only in the shell) induced circumferential alignment of fibrin fibrils via compaction of the shell relative to the core. The aligned fibrils created a contact guidance field, which was manifested by strong circumferential alignment of the fibroblasts. However, in the presence of macrophages, the fibroblasts exhibited more radial alignment despite the simultaneous contact guidance field in the circumferential direction associated with compaction. This was attributed to a chemotactic gradient emanating from the core due to a putative factor(s) released by the macrophages. The presence of a radial chemotactic stimulus was supported by the finding of even greater radial alignment when fibrin microspheres were embedded in an agarose-fibrin gel that abolished compaction and consequently the contact guidance field. Our assay permits the simulation of tissue morphogenetic processes that involve cell guidance phenomena and tractional restructuring of the extracellular matrix.

Animals↗
PubMed1997

Non-native local interactions in protein folding and stability: introducing a helical tendency in the all beta-sheet alpha-spectrin SH3 domain.

The relative importance of secondary structure interactions versus tertiary interactions for stabilising and guiding the folding process is a matter for discussion. Phenomenological models of protein folding assign an important role to local contacts in protein folding and stability. On the other hand, simplistic lattice simulations find that secondary structure is mainly the product of protein compaction and that optimisation of folding speed seems to require small contributions of local contacts to the stability of the folded state. To examine the extent to which secondary structure propensities influence protein folding and stability, we have designed mutations that introduce a strong non-native helical propensity in the first 19 residues of the alpha-spectrin SH3 domain. The mutant proteins have the same three-dimensional structure as the wild-type, but they are less stable and have less co-operative folding transitions. There seems to be a relationship between the non-native helical propensity and the compaction of the denatured state. This suggests that in the denatured ensemble under native conditions there is a significant proportion of compact structures with non-native secondary structures. Our results demonstrate that non-local interactions can overcome strong non-native secondary structure propensities and, more important, that optimisation of folding speed and co-operativity requires the latter to be relatively small.

Amino Acid Sequence↗
PubMed1999

Structure of the anchor-domain of myristoylated and non-myristoylated HIV-1 Nef protein.

Negative factor (Nef) is a regulatory myristoylated protein of human immunodeficiency virus (HIV) that has a two-domain structure consisting of an anchor domain and a core domain separated by a specific cleavage site of the HIV proteases. For structural analysis, the HIV-1 Nef anchor domain (residues 2-57) was synthesized with a myristoylated and non-myristoylated N terminus. The structures of the two peptides were studied by1H NMR spectroscopy and a structural model was obtained by restrained molecular dynamic simulations. The non-myristoylated peptide does not have a unique, compactly folded structure but occurs in a relatively extended conformation. The only rather well-defined canonical secondary structure element is a short two-turn alpha-helix (H2) between Arg35 and Gly41. A tendency for another helical secondary structure element (H1) can be observed for the arginine-rich region (Arg17 to Arg22). Myristoylation of the N-terminal glycine residue leads to stabilization of both helices, H1 and H2. The first helix in the arginine-rich region is stabilized by the myristoylation and now contains residues Pro14 to Arg22. The second helix appears to be better defined and to contain more residues (Ala33 to Gly41) than in the absence of myristoylation. In addition, the hydrophobic N-terminal myristic acid residue interacts closely with the side-chain of Trp5 and thereby forms a loop with Gly2, Gly3 and Lys4 in the kink region. This interaction could possibly be disturbed by phosphorylation of a nearby serine residue, and modifiy the characteristic membrane interactions of the HIV-1 Nef anchor domain.

Amino Acid Sequence↗
PubMed2003

Structure and dynamics of the lantibiotic mutacin 1140.

Mutacin 1140 is a member of a family of ribosomally synthesized peptide bacteriocins called lantibiotics (lanthionine-containing antibiotics) and is produced by the Gram-positive bacterium Streptococcus mutans. Mutacin 1140 has been shown to be effective against a broad array of Gram-positive bacteria. Chromatography and mass spectroscopy data suggested that mutacin 1140 forms a small compact structure. Nuclear magnetic resonance (NMR) data and restrained molecular dynamics simulations showed that mutacin 1140 interconverts between multiple structures. Calculations of scalar (J) coupling constants showed the best agreement with experimental values when the entire population-weighted ensemble of structures was used, providing independent support for the ensemble. Representative structures from each major group in the ensemble had a common feature in which they are all kinked around the hinge region forming a horseshoe-like shape, and the regions of flexibility of the molecule were limited and well-defined. The structures determined in this study provide a starting point for modeling the mutacin 1140-membrane interactions and pore formation.

Amino Acid Sequence↗
PubMed2006

Decommissioning procedures for an 11 MeV self-shielded medical cyclotron after 16 years of working time.

The present article describes the decommissioning of a compact, self-shielded, 11 MeV medical cyclotron. A Monte Carlo simulation of the possible nuclear reactions was performed in order to plan the decommissioning activities. In the course of the cyclotron dismantling, cyclotron components, shields, and floor concrete samples were measured. Residual activities were analyzed with a Ge(Li) detector and compared with simulation data. Doses to staff involved in the decommissioning procedure were monitored by individual TL dosimeters. The simulations identified five radioactive nuclides in shields and floor concrete: 55Fe and 45Ca (beta emitters, total specific activity: 2.29 x 10(4) Bq kg) and 152Eu, 154Eu, 60Co (gamma emitters, total specific activity: 1.62 x 10(3) Bq kg-1). Gamma-ray spectrometry confirmed the presence of gamma emitters, corresponding to a total specific activity of 3.40 x 10(2) Bq kg-1. The presence of the radioisotope 124Sb in the lead contained in the shield structure, corresponding to a simulated specific activity of 9.38 x 10(3) Bq kg-1, was experimentally confirmed. The measured dose from external exposure of the involved staff was <20 muSv, in accordance with the expected range of values between 10 and 20 muSv. The measured dose from intake was negligible. Finally, the decommissioning of the 11 MeV cyclotron does not represent a risk for the involved staff, but due to the presence of long-lived radioisotopes, the cyclotron components are to be treated as low level radioactive waste and stored in an authorized storage area.

Computer Simulation↗
PubMed2001

Structural properties of self-attracting walks.

Self-attracting walks (SATW) with attractive interaction u>0 display a swelling-collapse transition at a critical u(c) for dimensions d>or=2, analogous to the Theta transition of polymers. We are interested in the structure of the clusters generated by SATW below u(c) (swollen walk), above u(c) (collapsed walk), and at u(c), which can be characterized by the fractal dimensions of the clusters d(f) and their interface d(I). Using scaling arguments and Monte Carlo simulations, we find that for u u(c), the clusters are compact, i.e., d(f)=d and d(I)=d-1. At u(c), the SATW is in a new universality class. The clusters are compact in both d=2 and d=3, but their interface is fractal: d(I)=1.50+/-0.01 and 2.73+/-0.03 in d=2 and d=3, respectively. In d=1, where the walk is collapsed for all u and no swelling-collapse transition exists, we derive analytical expressions for the average number of visited sites and the mean time to visit S sites.

Journal Article↗
PubMed1976

Quantification of bone mineralization using computed tomography.

Computed tomography was used to find a sensitive parameter for bone mineralization. A precision scanning instrument was constructed for determination of the mineral distribution in sections of the forearm. The quality of the reconstructed images allows separate quantification of compact and spongy bone even when gamma rays are used. Computer simulation and measured of models and macerated human bones showed that under clinical conditions it is possible to quantify spongy bone density within an accuracy of +/-2%.

Adolescent↗