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PubMed2006

The role of water coordination in binary mixtures. A study of two model amphiphilic molecules in aqueous solutions by molecular dynamics and NMR.

Two binary aqueous mixtures which contain the small amphiphilic molecules TMAO (trimethylamine-N-oxide) and TBA (tert-butyl alcohol) have been investigated by molecular dynamics simulations and NMR chemical shift and self-diffusion measurements. TMAO is an osmolyte, while TBA is a monohydrate alcohol. Both possess bulky hydrophobic groups and polar heads, namely, NO in TMAO and OH in TBA. The hydrophilic/hydrophobic content of these isosteric molecules strongly modulates the structure and dynamics of the hydration shell, which is thought to be responsible for the effects observed on proteins and phospholipids. Simulation results, especially on hydrogen-bond networking, spatial correlations, and self-diffusivity, are consistent with NMR data and agree well with previous numerical studies on similar solutions. The methods employed allow the elucidation of the microscopic features of the solutions. For TBA solutions, the hydration shell is found to have a low density and a large spatial spread, and thus, above the molar fraction of 0.03, reduction of hydrophobic hydration drives self-aggregation of the solute. This effect does not take place in TMAO solutions, where the hydration shell is more compact and stable, maintaining its structure over a wider range of solute concentrations.

Computer Simulation↗

PubMed1994

The origins of protein secondary structure. Effects of packing density and hydrogen bonding studied by a fast conformational search.

Globular proteins fold to create compact structures rich in alpha-helices and beta-sheets. While studies of cubic lattice models of simplified polypeptide chains have concluded that secondary structure is a necessary consequence of chain compactness, different conclusions have been reached from studies of off-lattice models of simplified chains. In an attempt to resolve this controversy, we study an all-atom off-lattice model of a protein subject to a variety of simplified energy functions. A Monte Carlo simulated annealing algorithm is used to search conformational space quickly. The algorithm uses pivot-type moves in which a residue is selected at random and the values of its main-chain dihedral angles are changed. The energy function used to accept or reject moves is taken to be either a term proportional to the volume occupied by a structure (to mimic the hydrophobic effect), a term proportional to the energy of main-chain hydrogen bonding, or a combination of these two terms. Secondary structure content is evaluated using several different definitions. For all the definitions used, compactness alone produces a 10% increase in secondary structure content. However, this is a small fraction of the secondary structure observed in native protein structures. Structures produced by minimizing the hydrogen bond energy have extensive secondary structure but are not densely packed. Structures having both the high density of native structures and extensive secondary structure are produced by minimizing combinations of the volume and hydrogen bond energy terms. Our results emphasize the close relationship between secondary structure and the geometry of main-chain hydrogen bonding. The results are consistent with a description of protein folding in which the hydrophobic effect favors dense packing while hydrogen bonding determines the specific local geometry which generates secondary structure. To make an analogy with lattice studies of packing density and secondary structure, it seems that hydrophobicity provides the packing density while hydrogen bonding provides the lattice.

Algorithms↗

PubMed1998

Conformation of native, reduced and [5-55]Ala bovine pancreatic trypsin inhibitor in the gas phase.

Collision cross sections have been measured for gas phase ions of native oxidized bovine pancreatic trypsin inhibitor (BPTI), native reduced BPTI and a mutant form of BPTI containing a single disulphide bond between residues 5 and 55 ([5-55]Ala BPTI). Cross sections for [5-55]Ala BPTI and reduced BPTI were 9% and 17% greater respectively than those for native BPTI. Cross sections for native BPTI were smaller than previous estimates from the crystal structure but in reasonable agreement with values calculated from the radius of gyration determined by x-ray scattering from solution BPTI. The increase in cross section for reduced BPTI over native BPTI is similar to that seen in molecular dynamics simulations. The results show that the disulphide bonds of BPTI contribute to the folding of the gas phase ions, but that even in the absence of disulphide bonds the protein ions maintain compact structures. Comparisons to relative areas calculated from hydrodynamic radii of BPTI in solution suggest that when disulphide linkages are removed, BPTI in the gas phase unfolds less than BPTI in solution.

Amino Acid Substitution↗

PubMed1999

Solution structure and orientation of the transmembrane anchor domain of the HIV-1-encoded virus protein U by high-resolution and solid-state NMR spectroscopy.

The structure of the membrane anchor domain (VpuMA) of the HIV-1-specific accessory protein Vpu has been investigated in solution and in lipid bilayers by homonuclear two-dimensional and solid-state nuclear magnetic resonance spectroscopy, respectively. Simulated annealing calculations, using the nuclear Overhauser enhancement data for the soluble synthetic peptide Vpu1-39 (positions Met-1-Asp-39) in an aqueous 2,2,2-trifluoroethanol (TFE) solution, afford a compact well-defined U-shaped structure comprised of an initial turn (residues 1-6) followed by a linker (7-9) and a short helix on the N-terminal side (10-16) and a further longer helix on the C-terminal side (22-36). The side chains of the two aromatic residues (Trp-22 and Tyr-29) in the longer helix are directed toward the center of the molecule around which the hydrophobic core of the folded VpuMA is positioned. As the observed solution structure is inconsistent with the formation of ion-conductive membrane pores defined previously for VpuMA in planar lipid bilayers, the isolated VpuMA domain as peptide Vpu1-27 was investigated in oriented phospholipid bilayers by proton-decoupled 15N cross polarization solid-state NMR spectroscopy. The line widths and chemical shift data of three selectively 15N-labeled peptides are consistent with a transmembrane alignment of a helical polypeptide. Chemical shift tensor calculations imply that the data sets are compatible with a model in which the nascent helices of the folded solution structure reassemble to form a more regular linear alpha-helix that lies parallel to the bilayer normal with a tilt angle of </=30 degrees. The arrangement of the membrane-associated structures described previously for the cytoplasmic domain and for the anchor domain of Vpu identified in this work is discussed.

Amino Acid Sequence↗

PubMed2006

Patch-distribution effect on diffusion-limited process in dilute suspension of partially active spheres.

The normalized overall rate constant, kp/kf for diffusion-limited processes in a dilute suspension of spheres, partially covered with active patches of varying distribution states, is studied with sped-up Brownian dynamic simulations. A dimensionless separation index Is is defined to quantify the characteristics of patch distribution on the sphere surfaces, with values of 0 and 1 corresponding to the states of the most compact and loosest patch distributions, respectively. Remarkably, the normalized overall rate constant is found to strongly correlate with the dimensionless separation index at fixed patch coverage fcover exhibiting a positive, linear relationship. In addition, the slope of the kp/kf vs Is line, a measure of sensitivity of kp/kf to variation in the separation state of the distributed patches, is found to depend on patch coverage and patch size. This sensitivity exhibits a maximum value with respect to an increase in patch coverage, and the magnitude of the maximum sensitivity decreases with increasing patch size. The patch coverage, at which the maximum sensitivity occurs, increases with increasing patch size.

Journal Article↗

PubMed2005

A comparison of spreader penetration depth and load required during lateral condensation in teeth prepared using various root canal preparation techniques.

AIM: To compare the influence of various root canal preparation techniques on spreader penetration depth and load required during lateral condensation with gutta-percha and sealer. METHODOLOGY: Eighty extracted human teeth with single and straight canals were used. Twenty teeth were instrumented using one of four root canal preparation techniques. The four preparation techniques were: step-back technique without Gates-Glidden drills, step-back technique with Gates-Glidden drills, crown-down pressureless technique and hybrid technique (step-down/step-back). After root canal preparation had been completed a simulated periodontal ligament was fabricated from a uniform layer of silicone impression material. The roots were then mounted in an acrylic resin to simulate the physical condition found in tooth socket. A standardized stainless steel hand spreader of the same size as the master apical file was mounted in an Instron testing machine and lateral compaction with gutta-percha and sealer was performed. The load value was recorded from the Instron testing machine. The spreader penetration depths were measured with an endodontic ruler. The data obtained were analysed statistically using anova and Student's t-tests. RESULTS: No significant difference in initial spreader load needed to condense the master cone was found amongst the four canal preparation techniques (P > 0.05). The step-back technique with Gates-Glidden drills and the hybrid technique demonstrated the least difference between the initial spreader penetration and the working length (mean 1.925 and 2.25 mm, respectively). The step-back technique without Gates-Glidden drills and the crown-down pressureless technique had the greatest difference between initial spreader penetration and the working length (mean 4.425 and 4.75 mm, respectively). CONCLUSION: The flare created by canal preparation affected spreader penetration depth, but had no effect on the spreader load.

Dental Pulp Cavity↗

PubMed2001

Quantitative evaluation of nonrepetitive phase-encoding orders for first-pass, 3D contrast-enhanced MR angiography.

In this work, a detailed quantitative comparison was made of many alternative phase-encoding strategies for first-pass 3D MR angiography where each phase encode is only sampled once during the transient passage of contrast agent. A series of standard sequential and centric phase-encoding orders including elliptical centric were tested, as well as a new order called elliptical sequential. The characteristics of the different phase-encoding orders were tested using a computer simulation followed by experimental verification using a variable flip angle scheme. The characteristics to be considered included: arterial intensity, arterial-to-venous contrast, degree of artifact, and the blurring of the point-spread function. By making use of a wide range of start times and a rapidly varying contrast curve, the quantitative results clearly indicate the widely varying merits of each phase-encoding order. In general, when an optimal start time is used techniques that sample the low k-space views most compactly will produce the best results; however, the same methods are more problematic when the bolus arrival time deviates substantially from that expected.

Computer Simulation↗

PubMed1998

Simulated annealing for alpha-helical protein folding: searches in vicinity of the "molten globule" state.

A new model for simulation of protein folding of alpha-helical proteins with known secondary structure is proposed. We are dealing here with the analysis of alpha-helix packings rather than with a detailed atom structure of a whole protein. Starting from a random compact packing of the helices the search is focused on a vicinity of "molten globule" states of a protein. In contrast to the majority of the known approaches for estimation of a protein free energy we introduce a simplified potential of interactions with solvent and consider conformational energy of the loops in addition to mean-force potential. The model was applied to several globular alpha-helical proteins and demonstrated high prediction accuracy in comparison with other known models.

Computer Simulation↗

PubMed2001

Computer generation and quantitative morphometric analysis of virtual neurons.

An important goal in computational neuroanatomy is the complete and accurate simulation of neuronal morphology. We are developing computational tools to model three-dimensional dendritic structures based on sets of stochastic rules. This paper reports an extensive, quantitative anatomical characterization of simulated motoneurons and Purkinje cells. We used several local and global algorithms implemented in the L-Neuron and ArborVitae programs to generate sets of virtual neurons. Parameters statistics for all algorithms were measured from experimental data, thus providing a compact and consistent description of these morphological classes. We compared the emergent anatomical features of each group of virtual neurons with those of the experimental database in order to gain insights on the plausibility of the model assumptions, potential improvements to the algorithms, and non-trivial relations among morphological parameters. Algorithms mainly based on local constraints (e.g., branch diameter) were successful in reproducing many morphological properties of both motoneurons and Purkinje cells (e.g. total length, asymmetry, number of bifurcations). The addition of global constraints (e.g., trophic factors) improved the angle-dependent emergent characteristics (average Euclidean distance from the soma to the dendritic terminations, dendritic spread). Virtual neurons systematically displayed greater anatomical variability than real cells, suggesting the need for additional constraints in the models. For several emergent anatomical properties, a specific algorithm reproduced the experimental statistics better than the others did. However, relative performances were often reversed for different anatomical properties and/or morphological classes. Thus, combining the strengths of alternative generative models could lead to comprehensive algorithms for the complete and accurate simulation of dendritic morphology.

Algorithms↗

PubMed1996

Conformational and receptor-binding properties of the insect neuropeptide proctolin and its analogues.

Proctolin (Arg-Tyr-Leu-Pro-Thr) was the first insect neuropeptide to be chemically characterised. It plays an essential role in insect neurophysiology and is involved in muscular contraction and neuromodulation. Elements of secondary structure in solution have been studied by comparing data obtained from NMR and molecular dynamics simulations. Different secondary structural requirements are associated with agonist and antagonist activities. A favoured conformation of proctolin has an inverse gamma-turn, comprising an intramolecular hydrogen bond near the C-terminal end between Thr NH and Leu CO. Antagonists have a more compact structure resembling a 'paperclip' loop, containing an intramolecular hydrogen bond between Tyr NH and Pro CO, possibly stabilised by a salt bridge between the N- and C-terminal groups. A cyclic analogue retains antagonist activity and resembles a beta-bulge loop, also comprising intramolecular hydrogen bonds between Tyr NH and Pro CO and Thr CO. These models may offer feasible starting points for designing novel compounds with proctolinergic activity.

Animals↗

PubMed1997

Monte Carlo simulation of protein folding with orientation-dependent monomer-monomer interactions.

We present the results of lattice Monte Carlo simulations of protein folding in the framework of a model taking into account (i) the dependence of the energy of interaction of amino-acid residues on their orientation and (ii) the rigidity of the polypeptide chain with respect to the formation of kinks. If the chain is flexible, the final protein structures are predicted to be compact. Increasing the energy cost of creation of kinks is found to favor the formation of flat structures mimicking an ideal antiparallel beta sheet. For compact structures, the kinetics of folding exhibit the standard two-phase regime (a rapid collapse to one of the metastable stable, followed by slow reconfiguration of the chain to the native structure). For flat structures, the transition to the native state is often gradual.

Algorithms↗

PubMed1985

Efficiency of lod scores for representing multiple locus linkage data.

The problem of compact, fully efficient representation of multilocus data has not yet been solved. Lod scores can be used to map multilocus data, but because of certain statistical problems, this method loses some information. However, simulation studies show that for distances less than 10 or 20 cMo, where there is little danger of huge overestimates of distance, the lod score method yields estimators just as good as maximum likelihood (ML). Since short distances are the most important, the lod method is quite efficient. Its main drawback is misrepresentation of the likelihood under wrong gene orders. This problem can be ameliorated with a single multipoint calculation under each order. Thus, representation of multipoint data with lod scores can be very practical.

Biometry↗

PubMed2007

Stability of fused versus nonfused THA femoral impaction grafts.

Impaction grafting for THA involves compacting morselized cancellous bone (MCB) into a cavitary defect to build up bone stock. Ideally, the MCB subsequently remodels into a new contiguous cancellous lattice. A recent laboratory model of MCB fusion allows simulating an impaction graft construct in this ideal eventual clinical state. The purpose of the present study was to determine the relative stability of femoral impaction graft constructs in which the MCB has fused versus that for MCB in the freshly impacted nonfused condition. Cemented femoral impaction graft constructs were created in composite femurs. For fused constructs, the MCB was mixed with an amine epoxy that causes the MCB to set up into a contiguous structure biomechanically comparable to intact cancellous bone in compression. The constructs were loaded with 500,000 physiologic gait cycles. Three-dimensional motion was measured between the femur and the stem. The fused femoral impaction grafts were much more stable than the nonfused grafts at the proximal stem location, but MCB fusion had only a modest effect on distal stem stability. These results indicate that most of the opportunity to reduce femoral stem micromotion and migration lies proximal, and that steps to enhance impaction graft remodeling and fusion are most effectively focused proximally.

Arthroplasty, Replacement, Hip↗

PubMed1993

Lattice neural network minimization. Application of neural network optimization for locating the global-minimum conformations of proteins.

A way of formulating the protein-folding problem in neural network optimization terms is presented in this paper. This is accomplished by representing the conformation of a protein as an array of the amino acid sequence versus position on a three-dimensional face-centered cubic lattice with an energy function defined in terms of the array variables. The method is called lattice neural network minimization (LNNM). Using the neural network minimization method, the energy function is minimized to locate the global minimum energy for the conformation of the protein. The energy function consisted of site exclusion and bond connectivity penalty terms and a pairwise contact energy potential. The contact energy potential used in the procedure is the united-residue potential of Miyazawa, Jernigan and Covell. The LNNM method found the global minimum for a seven-residue peptide in all of the 15 runs carried out. The time for each run was approximately 30 seconds on one processor of an IBM 3090 computer. For a nine-residue peptide, the global minimum was found in 7 out of 15 runs (47%) in approximately 50 seconds per run. For this peptide, LNNM found the global minimum or the second lowest minimum in 10 of the runs. In the same total CPU times (approximately 750 seconds), a Monte Carlo simulated annealing method found the global minimum or the second lowest minimum in only two runs, demonstrating the superiority of LNNM over the standard Monte Carlo simulated annealing method for this nine-residue peptide. Starting from a uniform array for the protein crambin (46 residues) on the lattice, the energy of the crambin array was minimized and a compact low-energy structure was found in approximately 25 minutes of CPU time. Its energy was much lower than that of the native protein, suggesting that there are inadequacies in the Miyazawa-Jernigan-Covell potential. The LNNM method was applied to the prediction of what was previously called nucleation but more properly called chain-folding initiation sites (CFIS) of a protein. LNNM correctly predicted the CFIS for the two proteins examined, RNase S and T4 lysozyme. The LNNM method was also applied to another chain optimization problem, minimization of the root-mean-square distance error (r.m.s.d.) (a measure similar to r.m.s. deviation) in fitting X-ray structures to a lattice, with good results.

Models, Chemical↗

PubMed2006

A new hydrogel for the extended and complete prednisolone release in the GI tract.

The issue of incomplete release of poorly soluble drugs from sustained-release oral formulations is addressed using prednisolone (PDS) as the model drug and a novel highly swelling hydrogel as the rate-controlling material. The hydrogel was formed by heating N-carboxymethylchitosan (CMC) to 80 degrees C for 24 h. Swelling, alkalimetry, FTIR, DSC, and solid-state NMR studies showed that the treatment produced physical crosslinking, i.e., polymer chain entanglement. A controlled-release system was prepared by coating an inert compacted support of ethylcellulose (50 mg; diameter, 6 mm) with a CMC layer containing dispersed PDS powder (10-50 microm). The system was heated to crosslink the CMC coating, then drug release to simulated GI fluids was studied in vitro. The drug release pattern and term were modulated via the layer mass (LM) (10 or 14 mg cm(-2)) and/or the drug-polymer wt ratio (D/P) (1:5 or 2:5). The rate parameter, K, and the time exponent, n, of the Peppas equation were: K=26.6+/-0.3 h(-n), n = 0.78+/-0.02 (LM, 10 mg cm(-2); D/P, 1:5); K = 24.7+/-0.7 h(-n), n = 0.56+/-0.02 (LM, 14 mg cm(-2); D/P, 1:5); K = 20.7+/-0.3 h(-n), n = 0.76+/-0.01 (LM, 10 mg cm(-2); D/P, 2:5). Hydrogel swelling was faster than drug release. This was controlled, in a first stage, by drug dissolution-diffusion in the swollen gel, and subsequently, by diffusion. The drug release rate was unaffected by the GI pH variations, and slightly affected by the environmental hydrodynamics. The system promises an extended and complete release of poorly soluble drugs in the GI tract.

Chitosan↗

PubMed1999

Calculation of a Gap restoration in the membrane skeleton of the red blood cell: possible role for myosin II in local repair.

Human red blood cells contain all of the elements involved in the formation of nonmuscle actomyosin II complexes (V. M. Fowler. 1986. J. Cell. Biochem. 31:1-9; 1996. Curr. Opin. Cell Biol. 8:86-96). No clear function has yet been attributed to these complexes. Using a mathematical model for the structure of the red blood cell spectrin skeleton (M. J. Saxton. 1992. J. Theor. Biol. 155:517-536), we have explored a possible role for myosin II bipolar minifilaments in the restoration of the membrane skeleton, which may be locally damaged by major mechanical or chemical stress. We propose that the establishment of stable links between distant antiparallel actin protofilaments after a local myosin II activation may initiate the repair of the disrupted area. We show that it is possible to define conditions in which the calculated number of myosin II minifilaments bound to actin protofilaments is consistent with the estimated number of myosin II minifilaments present in the red blood cells. A clear restoration effect can be observed when more than 50% of the spectrin polymers of a defined area are disrupted. It corresponds to a significant increase in the spectrin density in the protein free region of the membrane. This may be involved in a more complex repair process of the red blood cell membrane, which includes the vesiculation of the bilayer and the compaction of the disassembled spectrin network.

Actins↗

PubMed2001

Influence of crystal structure on the tableting properties of sulfamerazine polymorphs.

PURPOSE: To understand the influence of polymorphic structure on the tableting properties of sulfamerazine. METHODS: Bulk powders of sulfamerazine polymorph I and of two batches. II(A) and II(B) of different particle size, of polymorph II were crystallized. The powders were compressed to form tablets whose porosity and tensile strength were measured. The relationships between tensile strength, porosity and compaction pressure were analyzed by the method developed by Joiris. E., et al. Pharm. Res. 15:1122-1130 (1998). RESULTS: The sensitivity of tensile strength to compaction pressure, known as the tabletability, follows the order. I >> II(A) > II(B) and the porosity at the same compaction pressure, which measures the compressibility, follows the order, I << II(A) < II(B). Therefore. the superior tabletability of I over II(A) or II(B) is attributed to its greater compressibility. Molecular simulation reveals slip planes in crystals of I but not in II. Slip planes provide I crystals greater plasticity and therefore greater compressibility and tabletability. Larger crystal size of II(B) than of II(A) leads to fewer contact points between crystals in the tablets and results in a slightly lower tabletability. CONCLUSIONS: Slip planes confer greater plasticity to crystals of I than II and therefore greater tabletability.

Anti-Infective Agents↗

PubMed2002

Unwinding globules under tension and polymer collapse.

Polymer collapse is known to be mediated by the formation of pearls. These intermediate structures behave as small globules under tension. The globule size is studied by molecular dynamic simulations as a function of the strength of an external stretching force applied to its ends, for different values of the chain length. A very strong first-order-like transition from a compact globule state to a stretched one is observed. A model of this transition in terms of a globule-chain system is presented. The critical force, above which the globule unwinds, is shown to satisfy a power law scaling like N(1/3) in the number of monomers.

Models, Chemical↗