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PubMed2004

Role of solvent in determining conformational preferences of alanine dipeptide in water.

Evidence from a variety of spectroscopic probes indicates that (phi, psi) values corresponding to the left-handed polyproline II helix (P(II)) are preferred for short alanine-based peptides in water. On the basis of results from theoretical studies, it is believed that the observed preference is dictated by favorable peptide-solvent interactions, which are realized through formation of optimal hydrogen-bonding water bridges between peptide donor and acceptor groups. In the present study, we address this issue explicitly by analyzing the hydration structure and thermodynamics of 16 low-energy conformers of the alanine dipeptide (N-acetylalanine-N'-methylamide) in liquid water. Monte Carlo simulations in the canonical ensemble were performed under ambient conditions with all-atom OPLS parameters for the alanine dipeptide and the TIP5P model for water. We find that the number of hydrogen-bonded water molecules connecting the peptide group donor and acceptor atoms has no effect on the solvation thermodynamics. Instead, the latter are determined by the work done to fully hydrate the peptide. This work is minimal for conformations that are characterized by a minimal overlap of the primary hydration shells around the peptide donor and acceptor atoms. As a result, peptide-solvent interactions favor "compact" conformations that do not include P(II)-like geometries. Our main conclusion is that the experimentally observed preference for P(II) does not arise due to favorable direct interactions between the peptide and water molecules. Instead, the latter act to unmask underlying conformational preferences that are a consequence of minimizing intrapeptide steric conflicts.

Dipeptides↗

PubMed2004

Prediction and identification using wavelet-based recurrent fuzzy neural networks.

This paper presents a wavelet-based recurrent fuzzy neural network (WRFNN) for prediction and identification of nonlinear dynamic systems. The proposed WRFNN model combines the traditional Takagi-Sugeno-Kang (TSK) fuzzy model and the wavelet neural networks (WNN). This paper adopts the nonorthogonal and compactly supported functions as wavelet neural network bases. Temporal relations embedded in the network are caused by adding some feedback connections representing the memory units into the second layer of the feedforward wavelet-based fuzzy neural networks (WFNN). An online learning algorithm, which consists of structure learning and parameter learning, is also presented. The structure learning depends on the degree measure to obtain the number of fuzzy rules and wavelet functions. Meanwhile, the parameter learning is based on the gradient descent method for adjusting the shape of the membership function and the connection weights of WNN. Finally, computer simulations have demonstrated that the proposed WRFNN model requires fewer adjustable parameters and obtains a smaller rms error than other methods.

Algorithms↗

PubMed2005

Fully truncated cone-beam reconstruction on Pi lines using prior CT.

C-arms are well suited for obtaining cone-beam projections intra-operatively. Due to the compact size of the detector used, the data are usually truncated within the field of view. As a result, direct application of a standard cone-beam reconstruction algorithm gives rise to undesirable artifacts and incorrect values in the reconstructed image volume. When prior information such as a pre-operative CT scan is available, fully truncated cone-beam projections can be used to recover the change within a small region of interest without such artifacts. A method for integrating prior CT is developed using the concept of pi-lines and tested on real flat-panel and simulated cone-beam data.

Algorithms↗

PubMed2005

Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens.

MOTIVATION: Differential detection on symptom-related pathogens (SRP) is critical for fast identification and accurate control against epidemic diseases. Conventional polymerase chain reaction (PCR) requires a large number of unique primers to amplify selected SRP target sequences. With multiple-use primers (mu-primers), multiple targets can be amplified and detected in one PCR experiment under standard reaction condition and reduced detection complexity. However, the time complexity of designing mu-primers with the best heuristic method available is too vast. We have formulated minimum-set mu-primer design problem as a set covering problem (SCP), and used modified compact genetic algorithm (MCGA) to solve this problem optimally and efficiently. We have also proposed new strategies of primer/probe design algorithm (PDA) on combining both minimum-set (MS) mu-primers and unique (UniQ) probes. Designed primer/probe set by PDA-MS/UniQ can amplify multiple genes simultaneously upon physical presence with minimum-set mu-primer amplification (MMA) before intended differential detection with probes-array hybridization (PAH) on the selected target set of SRP. RESULTS: The proposed PDA-MS/UniQ method pursues a much smaller number of primers set compared with conventional PCR. In the simulation experiment for amplifying 12 669 target sequences, the performance of our method with 68% reduction on required mu-primers number seems to be superior to the compared heuristic approaches in both computation efficiency and reduction percentage. Our integrated PDA-MS/UniQ method is applied to the differential detection on 9 plant viruses from 4 genera with MMA and PAH of 11 mu-primers instead of 18 unique ones in conventional PCR while amplifying overall 9 target sequences. The results of wet lab experiments with integrated MMA-PAH system have successfully validated the specificity and sensitivity of the primers/probes designed with our integrated PDA-MS/UniQ method.

Algorithms↗

PubMed1982

An investigation of the relationship between particle size and compression during capsule filling with an instrumented mG2 simulator.

An instrumented mG2 capsule filling machine simulator has been employed to study the effects of the amount of compression (compression ratio) on the capsule fill weight uniformity and measured compression and ejection stresses. Four size fractions of lactose were studied (mean particle sizes 15.6, 17.8, 37.5 and 155.2 micron). The range of compression over which satisfactory filling could be achieved was large for fine, cohesive powders but decreased with increasing particle size. The lower limit of filling ability was the ability to retain the powder and the amount of compression needed to achieve retention increased with increasing particle size. The upper limit on compression, was the compaction of the powder which prevented the piston acting to cause retention. Large particle sizes were able to undergo only a small change in volume before compaction occurred whilst fine, cohesive powders were considerably more compressible and hence could be filled satisfactorily at higher compression settings.

Capsules↗

PubMed2006

A compact bandpass filter with enhanced stopband characteristics by an asymmetric cross-shape defected ground structure.

In this paper, we present an effective technique to enhance stopband bandwidth for a bandpass filter by using an asymmetric, cross-shape defected ground structure (CSDGS). A single CSDGS can provide a higher attenuation rate near passband and broader stopband bandwidth. Moreover, with the asymmetric CSDGS, two different resonant frequencies can be excited and controlled independently, resulting in synthesizing a passband. The synthesized bandpass filter can be modeled by parallel LC resonant circuits in connection with T-networks. The bandwidth and insertion loss of this bandpass filter at 4.2 GHz is 28.6% and -1.44 dB, respectively, and 20 dB rejection in the stopband is up to four times the central frequency. All the synthesized bandpass filters have been measured and are in good agreement with simulated results.

Letter↗

PubMed2003

An elastic network model of HK97 capsid maturation.

The structure of the capsid of bacteriophage HK97 has been solved at various stages of maturity by crystallography and cryo-electron microscopy, and has been reported previously in the literature. Typically the capsid assembles through polymerization and maturation processes. Maturation is composed of proteolytic cleavages to the precursor capsid (called Prohead II), expansion triggered by DNA packaging (in which the largest conformational changes of the capsid appear), and covalent cross-links of neighboring subunits to create the mature capsid called Head II. We apply a coarse-grained elastic network interpolation (ENI) to generate a feasible pathway for conformational change from Prohead II to Head II. The icosahedral symmetry of the capsid structure offers a significant computational advantage because it is not necessary to consider the whole capsid structure but only an asymmetric unit consisting of one hexamer plus an additional subunit from an adjacent pentamer. We also analyze normal modes of the capsid structure using an elastic network model which is also subject to symmetry constraints. Using our model, we can visualize the smooth evolution of capsid expansion and revisit in more detail several interesting geometric changes recognized in early experimental works such as rigid body motion of two compact domains (A and P) with two refolding extensions (N-arm and E-loop) and track the approach of the two particular residues associated with isopeptide bonds that make hexagonal cross-links in Head II. The feasibility of the predicted pathway is also supported by the results of our normal mode analysis.

Bacteriophages↗

PubMed1994

Secondary structure formation in model polypeptide chains.

Model polypeptide chains were folded into 3-D compact conformations using distance geometry techniques. Interresidue distances were predicted from the hydrophobicity of the monomers and were refined by repeated projections into lower-dimensional spaces. Main-chain hydrogen bond networks were constructed and propagated through the structure by adjusting local conformations to comply with ideal distance constraints around hydrogen bonds. The resulting folds were compact globules with distinct hydrophobic cores and contained secondary structure elements like real protein molecules. Apart from similarity in appearance, several properties of the model chains were also very close to those of native folded polypeptides. The method in its present form can serve as a starting point for the development of a novel structure prediction algorithm.

Chemical Phenomena↗

PubMed2004

Free volume properties of a linear soft polymer: a computer simulation study.

Molecular dynamics simulation of a linear soft polymer has been performed and the free volume properties of the system have been analyzed in detail in terms of the Voronoi polyhedra of the monomers. It is found that there are only small density fluctuations present in the system. The local environment of the monomers is found to be rather spherical, even in comparison with liquids of atoms or small molecules. The monomers are found to be, on average, eight coordinated by their nearest geometric neighbors, including intra-chain and inter-chain ones. The packing of the monomers is found to be rather compact, in a configuration of 1900 monomers there are, on average, only three voids large enough to incorporate a spherical particle as large as a monomer, indicating that the density of the large vacancies in the system is considerably, i.e., by a few orders of magnitude lower than in molecular liquids corresponding to roughly the same reduced densities.

Journal Article↗

PubMed2006

Chirally directed formation of nanometer-scale proline clusters.

Ion mobility measurements, combined with molecular mechanics simulations, are used to study enantiopure and racemic proline clusters formed by electrospray ionization. Broad distributions of cluster sizes and charge states are observed, ranging from clusters containing only a few proline units to clusters that contain more than 100 proline units (i.e., protonated clusters of the form [xPro + nH](n+) with x = 1 to >100 and n = 1-7). As the sizes of clusters increase, there is direct evidence for nanometer scale, chirally induced organization into specific structures. For n = 4 and 5, enantiopure clusters of approximately 50 to 100 prolines assemble into structures that are more elongated than the most compact structure that is observed from the racemic proline clusters. A molecular analogue, cis-4-hydroxy-proline, displays significantly different behavior, indicating that in addition to the rigidity of the side chain ring, intermolecular interactions are important in the formation of chirally directed clusters. This is the first case in which assemblies of chirally selective elongated structures are observed in this size range of amino acid clusters. Relationships between enantiopurity, cluster shape, and overall energetics are discussed.

Mass Spectrometry↗

PubMed1993

Protein fold refinement: building models from idealized folds using motif constraints and multiple sequence data.

A general solution to the problem of directly incorporating data from multiple sequence alignments into the construction of molecular models was approached through the calculation of an estimated pairwise distance based on conserved hydrophobicity. A scaling method was developed that allowed the required bulk geometric properties of the estimated pair-wise distances (mean and mean squared) to mimic those expected in a globular protein. These properties were maintained independently of the composition, length, number or degree of conservation of the original sequences. Despite being a poor estimate for individual distances were found to be compatible with the native structure and could be weighted highly. While the estimated distances provided a general drive towards hydrophobic packing, more specific structure (including secondary structures and motifs) were induced by regularization towards an ideal form. These constraints were used to refine an outline starting structure (derived only from secondary structure axes) towards a compact form that was sufficiently protein-like for side chains to be added with almost no further adjustment of the alpha-carbon positions. This process allows rough folds based on abstract representations of protein architecture to be rapidly converted to a form where they can be analysed by the growing number of methods designed to assess molecular models.

Chemical Phenomena↗

PubMed2000

Invasion percolation with long-range correlations: first-order phase transition and nonuniversal scaling properties

We present the results of extensive Monte Carlo simulations of the invasion percolation model with trapping (TIP) with long-range correlations, a problem which is relevant to multiphase flow in field-scale porous media, such as oil reservoirs and groundwater aquifers, as well as flow in rock fractures. The correlations are generated by a fractional Brownian motion characterized by a Hurst exponent H. We employ a highly efficient algorithm for simulating TIP, and a novel method for identifying the backbone of TIP clusters. Both site and bond TIP are studied. Our study indicates that the backbone of bond TIP is loopless and completely different from that of site TIP. We obtain precise estimates for the fractal dimensions of the sample-spanning cluster (SSC), the minimal path, and the backbone of site and bond TIP, and analyze the size distribution of the trapped clusters, in order to identify all the possible universality classes of TIP with long-range correlations. For site TIP with H > 1/2 the SSC and its backbone are compact, indicating a first-order phase transition at the percolation threshold, while the minimal paths are essentially straigth lines. For H < 1/2 the SSC, its backbone, and the minimal paths are all fractal with fractal dimensions that depend on the Hurst exponent H. The fractal dimension of the loopless backbone for bond TIP is much less than that of site TIP for any H.

Journal Article↗

PubMed2006

Folding transition-state and denatured-state ensembles of FSD-1 from folding and unfolding simulations.

Characterization of the folding transition-state ensemble and the denatured-state ensemble is an important step toward a full elucidation of protein folding mechanisms. We report herein an investigation of the free-energy landscape of FSD-1 protein by a total of four sets of folding and unfolding molecular dynamics simulations with explicit solvent. The transition-state ensemble was initially identified from unfolding simulations at 500 K and was verified by simulations at 300 K starting from the ensemble structures. The denatured-state ensemble and the early-stage folding were studied by a combination of unfolding simulations at 500 K and folding simulations at 300 K starting from the extended conformation. A common feature of the transition-state ensemble was the substantial formation of the native secondary structures, including both the alpha-helix and beta-sheet, with partial exposure of the hydrophobic core in the solvent. Both the native and non-native secondary structures were observed in the denatured-state ensemble and early-stage folding, consistent with the smooth experimental melting curve. Interestingly, the contact orders of the transition-state ensemble structures were similar to that of the native structure and were notably lower than those of the compact structures found in early-stage folding, implying that chain and topological entropy might play significant roles in protein folding. Implications for FSD-1 folding mechanisms and the rate-limiting step are discussed. Analyses further revealed interesting non-native interactions in the denatured-state ensemble and early-stage folding and the possibility that destabilization of these interactions could help to enhance the stability and folding rate of the protein.

DNA-Binding Proteins↗

PubMed1999

The effect of conformation on the membrane permeation of coumarinic acid- and phenylpropionic acid-based cyclic prodrugs of opioid peptides.

In an earlier study using Caco-2 cells, an in vitro cell culture model of the intestinal mucosa, we have shown that the coumarinic-based (3 and 4) and the phenylpropionic acid-based (5 and 6) cyclic prodrugs were more able to permeate the cell monolayers than were the corresponding opioid peptides, [Leu5]-enkephalin (1, H-Tyr-Gly-Gly-Phe-Leu-OH) and DADLE (2, H-Tyr-D-Ala-Gly-Phe-D-Leu-OH). In an attempt to explain the increased permeation of the cyclic prodrugs, we have determined the possible conformations of these cyclic prodrugs in solution, using spectroscopic techniques (2D-NMR, CD) and molecular dynamics simulations. Spectroscopic as well as molecular dynamic studies indicate that cyclic prodrug 4 exhibits two major conformers (A and B) in solution. Conformer A exhibited a type I beta-turn at Tyr1-D-Ala2-Gly3-Phe4. The presence of a turn was supported by ROE cross-peaks between the NH of D-Ala2 and the NH of Gly3 and between the NH of Gly3 and the NH of Phe4. Conformer B of cyclic prodrug 4 consisted of type II beta-turns at the same positions. The type II turn was stabilized by hydrogen bonding, thus forming a more compact structure, whereas the type I turn did not exhibit similar intramolecular hydrogen bonding. Spectroscopic data for compounds 3, 5 and 6 are consistent with the conclusion that these cyclic prodrugs have solution structures similar to those observed with cyclic prodrug 4. The increased lipophilicity and well-defined secondary structures in cyclic prodrugs 3-6, but not in the linear peptides 1 and 2, could both contribute to the enhanced ability of these prodrugs to permeate membranes.

Cell Membrane Permeability↗

PubMed2006

Effect of feed length on settleability, substrate uptake and storage in a sequencing batch reactor treating an industrial wastewater.

The paper compares the performance of two Sequencing Batch Reactors (SBRs) treating the same industrial wastewater (composed of formic acid, ethylene glycol and methanol) operated at two different lengths of the feed. The two SBRs were operated in parallel under the same conditions of organic load (0.85 gCOD l(-1) d(-1)) and sludge age (about 10 d), the only difference being the length of the feed: less than 1 min vs. 5 h. In this way the conditions of a plug flow reactor and of a completely mixed reactor were simulated. The two systems were compared on sludge settleability (related to filaments abundance and floc morphology), substrate uptake rates and polyhydroxyalkanoates (PHAs) storage rates. The main difference between the two systems was in the settling properties of the sludge: both SVI and effluent solids were higher in the system with slow feed. With regard to filamentous microorganisms, even though both reactors were inoculated with the same sludge with high concentration of filaments, they were rapidly washed out from both systems. Microscopic observations showed that the reason for the different settling properties of the two sludges was in the floc structure, which was more compact in the system operated with fast feed. These data support the theory of the role of diffusion inside the flocs in determining the settling properties of the sludge. The maximum substrate uptake rates and PHA storage rates were similar in the two systems, showing that also the microorganisms grown at a constant and low substrate concentration were able to quickly increase their activity and to store PHAs when in the presence of a sudden change in substrate concentration.

Industrial Waste↗

PubMed2001

Calculation of ensembles of structures representing the unfolded state of an SH3 domain.

The N-terminal SH3 domain of drk (drkN SH3 domain) exists in equilibrium between a folded (F(exch)) and an unfolded (U(exch)) form under non-denaturing conditions. In order to further our previous descriptions of the U(exch) state, we have developed a protocol for calculating ensembles of structures, based on experimental spectroscopic data, which broadly represent the unfolded state. A large number of unfolding trajectories were generated, starting from the folded state structure of the protein, in order to provide a reasonable sampling of the conformational space accessible to this sequence. Unfolded state ensembles have been "calculated" using a newly developed program ENSEMBLE, which optimizes the population weights assigned to each structure based on experimental properties of the U(exch) state. Pseudo-energy terms for nuclear Overhauser effects, J-coupling constants, (13)C chemical shifts, translational diffusion coefficients and tryptophan ring burial based on NMR and fluorescence data have been implemented. The population weight assignment procedure was performed for different starting ensembles. Small numbers of structures (<60) dominate the final ensembles compared to the total number in the starting ensembles, suggesting that the drkN SH3 domain U(exch) state can be described by a limited number of lower-energy conformations. The calculated U(exch) state ensembles are much more compact than a "random coil" chain, with significant native-like residual structure observed. In particular, a sizable population of conformers having the n-src loop and distal beta-hairpin structures exist in the calculated U(exch) state ensembles, and Trp36 is involved in a large number of interactions, both native and non-native.

Animals↗

PubMed2006

Role of Mg2+ and Ca2+ in DNA bending: evidence from an ONIOM-based QM-MM study of a DNA fragment.

The binding of hydrated Mg2+ and Ca2+ ions with a DNA fragment containing two phosphate groups, three sugar units, and a G.C base pair is modeled in the anion and dianion states using a three-layer ONIOM approach. A monodentate binding mode was the most stable structure observed for both the ions in the anion model. However, the interactions of Mg2+ and Ca2+ with the dianion model of the DNA fragment gave rise to a large structural deformation at the base pair region, leading to the formation of "ring" structures. In both anion and dianion models, Mg2+-bound structures were considerably more stable than the corresponding Ca2+-bound structures. This feature and the formation of ring structures in the dianion models strongly supported the higher coordination power of the Mg2+ toward DNA systems for its compaction. The charge of the DNA fragment appeared to be crucial in deciding the binding strength as well as the binding mechanism of the metal ions. To the best of our knowledge, this is the first theoretical investigation of the interaction of a comparatively larger DNA model system with the biologically important Mg2+ and Ca2+ ions.

Base Pairing↗

PubMed2005

Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA.

DNA binding of Klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template DNA. The temperature dependence of the binding affinity exhibits distinct curvature, with tightest binding at 25-30 degrees C. Nonlinear temperature dependence indicates Klenow binds different primed-template constructs with large heat capacity (DeltaCp) values (-870 to -1220 cal/mole K) and thus exhibits large temperature dependent changes in enthalpy and entropy. Binding is entropy driven at lower temperatures and enthalpy driven at physiological temperatures. Large negative DeltaCp values have been proposed to be a 'signature' of site-specific DNA binding, but type I DNA polymerases do not exhibit significant DNA sequence specificity. We suggest that the binding of Klenow to a specific DNA structure, the primed-template junction, results in a correlated thermodynamic profile that mirrors what is commonly seen for DNA sequence-specific binding proteins. Klenow joins a small number of other DNA-sequence independent DNA binding proteins which exhibit unexpectedly large negative DeltaCp values. Spectroscopic measurements show small conformational rearrangements of both the DNA and Klenow upon binding, and small angle x-ray scattering shows a global induced fit conformational compaction of the protein upon binding. Calculations from both crystal structure and solution structural data indicate that Klenow DNA binding is an exception to the often observed correlation between DeltaCp and changes in accessible surface area. In the case of Klenow, surface area burial can account for only about half of the DeltaCp of binding.

Binding Sites↗