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PubMed2025

Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituents.

Epigenetic modifications of histone tails are key mechanisms of genome regulation. In particular, tri-methylation of lysines (K) 9 and K27 of the histone H3 tail is important for genome silencing. In this work, we explore, using all-atom molecular dynamics simulations, the effect of these two epigenetic marks on the structure and interactions of the H3 tail in several contexts: isolated tails, nucleosomes, chromatosomes, and stacked nucleosomes. Overall, we find that although the isolated tails do not show significant conformational changes upon methylation, a more flexible and extended H3 tail compared to the native tail results in the nucleosome systems, with K9 methylation effects more pronounced. This change could facilitate the interaction of the tail with protein readers like heterochromatin protein 1 or Polycomb group. We also observe that both methylations increase the interactions of the H3 tail with the linker DNA in the context of the chromatosome, producing a chromatosome with tighter linker DNA, which could favor chromatin compaction. For stacked nucleosomes mimicking i±2 zigzag interactions, methylation of either K9 or K27 reduces the interactions of one of the H3 tails with its parental nucleosome and increases its interactions with the nonparental nucleosome, which could also help compact the chromatin fiber. In the three nucleosome-containing systems, we observe an asymmetry between the two tails, especially in the chromatosome, where one tail extends to interact with the linker DNA. This asymmetry modulates the effect that methylation has on each tail. Thus, overall, methylations of K9 and K27 have a subtle but notable impact on the H3 tail structure and its interactions within the chromatin fiber. These results help explain how this epigenetic modification compacts chromatin fibers and promotes longer-range interactions; these changes also guide how to approximate these effects in coarse-grained chromatin models.

Histones↗

PubMed1990

Determination of the conformation of Lewis blood group oligosaccharides by simulation of two-dimensional nuclear Overhauser data.

Through control of both the nmr probe temperature and of the solvent viscosity, phase-sensitive two-dimensional 1H nuclear Overhauser data (NOESY) at 300 and 500 MHz are obtained with excellent signal-to-noise ratios for Lewis blood group penta- and hexasaccharides isolated from human milk. Relatively long mixing times are required to produce measurable NOE intensities in these oligosaccharides, which makes a full relaxation matrix analysis necessary. By measurements of selective T1 for a few isolated 1H resonances, it was possible to generate a simulation of the complete NOESY spectrum at arbitrary mixing time for comparison with the experimental data. From an exhaustive search of the conformational space, it was found that only a small range of glycosidic dihedral angles of the nonreducing terminal Lewis blood group determinant fragments of the milk oligosaccharides LNF-2 and LND-1 produce simulated spectra agreeing within experimental error to the data. Conformational energy calculations reveal that each of these conformations is also one of minimum energy. It is concluded that the Lewis(a) and Lewis(b) oligosaccharides adopt relatively compact rigid structures in solution, as shown by the observation of cross peaks between protons in nonadjacent residues. Like the blood group A and H oligosaccharides, there exists only a small dependence of the conformation for Lewis(a) and Lewis(b) oligosaccharides on solvent. The apparent lack of dependence of conformation of these oligosaccharides on DMSO in D2O suggests that modification of solvent viscosity with mixtures of DMSO:D2O may provide a useful general strategy of NOESY studies of oligosaccharides.

Carbohydrate Conformation↗

PubMed1994

Solution structure of PMP-D2, a 35-residue peptide isolated from the insect Locusta migratoria.

The three-dimensional solution structure of PMP-D2, a 35 amino acid peptide isolated from the insect Locusta migratoria, has been determined from two-dimensional 1H NMR spectroscopy data. The structure calculations were performed from 222 NOE-derived interproton distances and 11 dihedral angles calculated from the JHN-H alpha coupling constants, using either a combination of distance geometry and restrained simulated annealing or by restrained simulated annealing alone. PMP-D2 contains three disulfide bridges that have been assigned from NMR data and structure calculations and independently confirmed using chemical and enzymatic methods. The core region of PMP-D2 adopts a compact globular fold, stabilized by hydrophobic interactions, which consists of a short three-stranded antiparallel beta-sheet involving residues 8-11, 15-19, and 25-29. Back-calculation of the NOESY spectra was used to validate the final structures. Analysis of the CD spectra of PMP-D2 under various conditions of ionic strength and in the presence of organic solvents demonstrates the high stability of this molecule. PMP-D2 was recently shown to inhibit Ca2+ currents. This activity is discussed based on the comparison of PMP-D2 three-dimensional structure with the recently established three-dimensional structure of the Ca2+ channel blocker omega-conotoxin GVIA.

Amino Acid Sequence↗

PubMed1995

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation.

Type I collagen is a rod-like protein which self-assembles in a regular array to form elongated fibrils. The process of fibril formation, termed fibrillogenesis, is driven by the increase in entropy associated with loss of water from the bound monomers. A model based on diffusion limited aggregation (DLA) was used to investigate some of the mechanisms involved in this process. The aggregates created in the model displayed several features in common with collagen fibrils including an elongated morphology and a preference for tip growth. Analysis of these aggregates revealed a linear relationship between mass and distance from the tip, consistent with experimental observations. Intrafibrillar fluidity was introduced into the model by using a surface diffusion term. This led to the formation of aggregates with more compact morphologies. These results strongly implicate the role of diffusion limited growth in collagen fibril formation.

Collagen↗

PubMed1989

A hexagonal orthogonal-oriented pyramid as a model of image representation in visual cortex.

Retinal ganglion cells represent the visual image with a spatial code, in which each cell conveys information about a small region in the image. In contrast, cells of primary visual cortex employ a hybrid space-frequency code in which each cell conveys information about a region that is local in space, spatial frequency, and orientation. Despite the presumable importance of this transformation, we lack any comprehensive notion of how it occurs. Here we describe a mathematical model for this transformation. The hexagonal orthogonal-oriented quadrature pyramid (HOP) transform, which operates on a hexagonal input lattice, employs basis functions that are orthogonal, self-similar, and localized in space, spatial frequency, orientation, and phase. The basis functions, which are generated from seven basic types through a recursive process, form an image code of the pyramid type. The seven basis functions, six bandpass and one low-pass, occupy a point and a hexagon of six nearest neighbors on a hexagonal sample lattice. The six bandpass basis functions consist of three with even symmetry, and three with odd symmetry. The three even kernels are rotations of 0, 60, and 120 degrees of a common kernel; likewise for the three odd kernels. At the lowest level, the inputs are image samples. At each higher level, the input lattice is provided by the low-pass coefficients computed at the previous level. At each level, the output is subsampled in such a way as to yield a new hexagonal lattice with a spacing square root 7 larger than the previous level, so that the number of coefficients is reduced by a factor of seven at each level. In the biological model, the input lattice is the retinal ganglion cell array. The resulting scheme provides a compact, efficient code of the image and generates receptive fields that resemble those of the primary visual cortex.

Computer Simulation↗

PubMed1992

Structure and dynamics of des-pentapeptide-insulin in solution: the molten-globule hypothesis.

Structures of insulin in different crystal forms exhibit significant local and nonlocal differences, including correlated displacement of elements of secondary structure. Here we describe the solution structure and dynamics of a monomeric insulin analogue, des-pentapeptide-(B26-B30)-insulin (DPI), as determined by two-dimensional NMR spectroscopy and distance geometry/restrained molecular dynamics (DG/RMD). Although the solution structure of DPI exhibits a general similarity to its crystal structure, individual DG/RMD structures in the NMR ensemble differ by rigid-body displacements of alpha-helices that span the range of different crystal forms. These results suggest that DPI exists as a partially folded state formed by coalescence of distinct alpha-helix-associated microdomains. The physical reality of this model is investigated by comparison of the observed two-dimensional nuclear Overhauser enhancement (NOE) spectroscopy (NOESY) spectrum with that predicted from crystal and DG/RMD structures. The observed NOESY spectrum contains fewer tertiary contacts than predicted by any single simulation, but it matches their shared features; such "ensemble correspondence" is likely to reflect the effect of protein dynamics on observed NOE intensities. We propose (i) that the folded state of DPI is analogous to that of a compact protein-folding intermediate rather than a conventional native state and (ii) that the molten state is the biologically active species. This proposal (the molten-globule hypothesis) leads to testable thermodynamic predictions and has general implications for protein design.

Calorimetry↗

PubMed1994

[Technique and applications of stereolithographic cranial models].

3-D-modelling of the skull is useful referring to improve diagnostics, for surgical planning and simulation of surgical procedure. Stereolithography is a constructive process producing a model by building it up layer by layer with plastic using an "ultraviolet" laser to catalyse the polymerization of a liquid plastic solution. This fast prototyping derives from using a new interface between a CT-Scanner and a SLA. By avoiding the tool path problems inherent in conventional computerdriven CNC milling machines we succeeded in producing closed cavities and even intraosseous course of vessels and nerves. The compact and smooth surface makes manual postprocessing unnecessary. By using a new software (interpolation +/- 0.25 mm) we could improve the accuracy. At our studies we found a maximum aberration of at least 0.25 mm.

Adolescent↗

PubMed1985

Systems model for pupil size effect. II. Feedback model.

The human pupillary control system has been the subject of interest to biologists and engineers as an example of a sensorimotor reflex which can be embedded in a control system paradigm. We present a nonlinear feedback model whose compact structure allows us to hypothesize possible physiological mechanisms which generate the proper behavior of the pupil system. The important pupil responses, including pupil size effect, asymmetry, and response the high-frequency stimuli, are defined. This model was simulated on a digital computer and comparisons to the paradigm experimental responses were performed, demonstrating a fit to each of the observed conditions. Improvements on previous models are discussed.

Feedback↗

PubMed1994

Improvements to the quality of MRI cluster analysis.

Cluster analysis techniques are gaining widespread use for segmentation of MRI data, especially for volume measurement and 3-D display purposes. This paper describes four improvements to such techniques: (1) The use of intensity simulations to model cluster plots; (2) Correction of image nonuniformity; (3) Anisotropic smoothing of data; and (4) Automatic isolation of tissues of interest. Simulation of cluster plots allows an informed choice of pulse sequence(s) and acquisition parameters to be made. Correction of image nonuniformity and anisotropic smoothing reduce the spread of signal intensity from a single tissue thus producing significantly more compact clusters, whilst the isolation of tissues of interest prevents overlap of clusters from the tissues of interest with those not under consideration. These techniques may be used to improve the results of cluster analysis or traded off, for example to allow lower signal-to-noise images, shorter repetition time images, or fewer images to be used for segmentation.

Cluster Analysis↗

PubMed1994

Solution structure of a peptide fragment of human alpha-lactalbumin in trifluoroethanol: a model for local structure in the molten globule.

BACKGROUND: At low pH, human alpha-lactalbumin forms a partly folded molten globule state that contains a non-native clustering of the side chains of Tyr103, Trp104 and His107. In order to understand the conformation of this region of the protein in the molten globule state, we investigated the structure of a peptide corresponding to residues 101-110 of human alpha-lactalbumin in trifluoroethanol. RESULTS: We determined the structure of the 101-110 peptide from an NMR data set of 145 nuclear Overhauser effects and nine 3JHN alpha coupling constants, using an ensemble calculation approach to take into account the possibilities of conformational averaging of the data. The backbone of residues 3-10 in the peptide adopts a series of turns, that involving residues 5-8 being the best defined, while the side chains of residues 1, 3, 4, 5, 6 and 7 form a hydrophobic cluster. CONCLUSIONS: The peptide conformation differs from that previously determined for residues 101-110 in crystal structures of native alpha-lactalbumin determined at both high and low pH, particularly in the relative orientations of the side chains. The series of turns seen in the peptide could, however, be related to the alpha-helical structure seen for residues 104-111 in crystals at high pH, and may be important in the molten globule state for bringing the peptide chain into a compact conformation where favourable interactions between the side chains can occur.

Amino Acid Sequence↗

PubMed1994

Deep heating using a movable applicator phased array hyperthermia system. A preclinical feasibility study.

A preclinical evaluation of the 'movable applicator phased array hyperthermia system' was performed. The system employs four coherent applicators enabling power steering by amplitude and phase control. This concept has already been used in other systems, but the combination with a compact applicator design and easy movement of applicators has not been used before. The paper contains a description of the system and a verification of its performance using quality assurance tests with scanned E-field measurements. A clinical simulation was performed in pig to address the clinical feasibility of the system. The target volume was the left kidney. Two heating sessions, with and without occluded blood-flow to the kidney, were performed. In the low-flow experiments a temperature of 48 degrees C and 46 degrees C was obtained in the upper and lower pole of the kidney respectively. For the high-flow experiment the temperature in the upper pole was 48 degrees C.

Animals↗

PubMed1994

Probing the microenvironments of tryptophan residues in the monomeric crystallins of the bovine lens.

Tryptophan microenvironments have been examined in bovine beta s-, gamma II-, gamma IIIa-, gamma IIIb-, gamma IVa- and gamma IVb-crystallins by fluorescence methods. The proteins could be divided into two groups on the basis of the accessibilities of their tryptophan residues. The first group, comprising beta s, gamma II and gamma IIIb, appeared to have a compact structure with none of the tryptophans accessible to KI and only moderately so to acrylamide. By contrast in gamma IIIa, gamma IVa and gamma Vb, all tryptophans were readily accessible to acrylamide and 70% of the fluorescence could be quenched with KI. Spectral analysis, before and after quenching, time-resolved spectroscopy and simulations of the quenching curves suggested that gamma IIIa, gamma IVa and gamma IVb contain two classes of tryptophan residues. One class (tau 0 = 0.52 ns, fa = 0.3, lambda max = 324 nm) which was completely inaccessible to KI and relatively inaccessible to acrylamide (Ksv = 0.25 M-1), was assigned to the topologically equivalent residues in positions 42 and 131. The other class (tau 0 = 2.1-3.4 ns, fa = 0.7, lambda max = 330 nm) was accessible to both quenchers (Ksv = 5.00-5.15 M-1 and 2.47-2.60 M-1, for acrylamide and KI, respectively) and corresponded to the tryptophan residues in positions 68 and 157. The same classes may be present in the other low molecular weight proteins (tau 0 = 0.47-0.55 and 1.55-1.74) but the lower emission and low accessibilities to quenchers prevented their distinction and suggested that these proteins had more compact structures.

Acrylamide↗

PubMed1992

Molecular dynamics simulations of a monofucosylated biantennary glycan of the N-acetyllactosamine type: the human lactotransferrin glycan.

Molecular dynamics simulations were carried out to explore the conformational flexibility of the antennae of N-linked glycans. They were performed over 200 ps in vacuo on the complete disialylated monofucosylated biantennary glycan of the N-acetyllactosaminic type. Starting from a bird-conformation, the 3-D-structure evolved through 9 successive transitional states to a new, compact and energetically favorable conformation which had never been previously described. In this conformation, both antennae are organized in two coplanar loops rolled in a contrary direction and oriented perpendicularly to the plane of the di-N-acetyl chitobiose residue leading to a 'lobster conformation'. All the glycosidic linkages of the disialylated monofucosylated biantennary glycan, except the Fuc(alpha 1-6)GlcNAc(beta 1-), were modified by a phase transition. Particularly, the Man(beta 1-4) GlcNAc(beta 1-) linkage, which was previously described by NMR and X-ray diffraction as a rigid one, was involved in numerous conformational changes during 83 ps, even before the first transition phase. The freedom of mobility of the torsional angles of the Man(alpha 1-6)Man(beta 1-) linkage was limited, under these simulation conditions, to the angle psi which took three values: 30 degrees, 90 degrees and 180 degrees. Moreover, from 150 ps up to the end of the simulation, the value of the torsional angle omega of the NeuAc(alpha 2-6)Gal(beta 1-) linkage of the alpha-1,6-antenna continuously swung between 60 degrees and -60 degrees. Finally, we observed that the values of the torsional angles of the three linkages: NeuAc(alpha 2-6)Gal(beta 1-), Gal(beta 1-4)GlcNAc(beta 1-) and GlcNAc(beta 1-2)Man(beta 1-) of each of the two antennae were different, demonstrating their asymmetric conformation.

Amino Sugars↗

PubMed1994

Ingress of water into zeolite 4A powder plugs.

One dimensional profiles of the concentration of water absorbed from vapour diffusing into compacted type 4A zeolite powder have been obtained by broadline NMR imaging. After an induction period of approximately 6 h, a region of full hydration advances linearly with time into the zeolite plug. This behaviour is typical of Case II diffusion. A simple numerical simulation gives good agreement with the experimental results.

Diffusion↗

PubMedDate not supplied

A compact laser beam guidance system for interventional CT.

OBJECTIVE: We propose a simple, compact, and accurate light guidance system for interventional CT. MATERIALS AND METHODS: The system using intersecting laser beams is mounted on the CT gantry and ensures precise needle guidance even when the gantry is tilted. The device does not require additional software/hardware. RESULTS: Phantom simulations and clinical experiments have demonstrated an accuracy of +/- 1 degrees and +/- 1 mm. CONCLUSION: The laser guidance system for CT makes the intervention safer, faster, and more accurate.

Biopsy, Needle↗

PubMed1992

Supercoiled DNA energetics and dynamics by computer simulation.

A new formulation is presented for investigating supercoiled DNA configurations by deterministic techniques. Thus far, the computational difficulties involved in applying deterministic methods to supercoiled DNA studies have generally limited computer simulations to stochastic approaches. While stochastic methods, such as simulated annealing and Metropolis-Monte Carlo sampling, are successful at generating a large number of configurations and estimating thermodynamic properties of topoisomer ensembles, deterministic methods offer an accurate characterization of the minima and a systematic following of their dynamics. To make this feasible, we model circular duplex DNA compactly by a B-spline ribbon-like model in terms of a small number of control vertices. We associate an elastic deformation energy composed of bending and twisting integrals and represent intrachain contact by a 6-12 Lennard Jones potential. The latter is parameterized to yield an energy minimum at the observed DNA-helix diameter inclusive of a hydration shell. A penalty term to ensure fixed contour length is also included. First and second partial derivatives of the energy function have been derived by using various mathematical simplifications. First derivatives are essential for Newton-type minimization as well as molecular dynamics, and partial second-derivative information can significantly accelerate minimization convergence through preconditioning. Here we apply a new large-scale truncated-Newton algorithm for minimization and a Langevin/implicit-Euler scheme for molecular dynamics. Our truncated-Newton method exploits the separability of potential energy functions into terms of differing complexity. It relies on a preconditioned conjugate gradient method that is efficient for large-scale problems to solve approximately for the search direction at every step. Our dynamics algorithm is numerically stable over large time steps. It also introduces a frequency-discriminating mechanism so that vibrational modes with frequencies greater than a chosen cutoff frequency are essentially frozen by the method. With these tools, we rapidly identify corresponding circular and interwound energy minima for small DNA rings for a series of imposed linking-number differences. These structures are consistent with available electron microscopy data. The energetic exchange of stability between the circle and the figure-8, in very good agreement with analytical results, is also detailed. Molecular dynamics trajectories at 100 femtosecond time steps then reveal the rapid folding of the unstable circular state into supercoiled forms. Significant bending and twisting motions of the interwound structures are also observed. Such information may be useful for understanding transition states along the folding pathway and the role of enzymes that regulate supercoiling.(ABSTRACT TRUNCATED AT 400 WORDS)

Algorithms↗

PubMed1986

Validation of a compact system for measuring gas exchange.

Measuring gas exchange in critically ill patients can provide valuable information on their nutritional status and energy expenditure. Several semiautomated machines are available for measuring oxygen consumption (VO2) and carbon dioxide production (VCO2). This study evaluated, under controlled laboratory conditions, a Gould 9000 IV prototype designed for use with mechanically ventilated patients. Various VO2 and VCO2 values were simulated at different combinations of frequency, tidal volume, minute ventilation, and inspired oxygen fraction (FIO2). Variations in frequency, tidal volume, and minute ventilation had no significant effect on the measured VO2 and VCO2, but FIO2 had a dramatic effect on the accuracy of VO2. Errors in measured VO2 were 2.6%, 3.5%, 5.9%, and 16.9% at FIO2 values of 0.22, 0.40, 0.60, and 0.80, respectively. Addition of a dead space to the spirometer dump port (to prevent room-air contamination) corrected a larger error initially found. The accuracy of VCO2 was +/- 2.6%.

Carbon Dioxide↗

PubMed2025

Phylogenetic Methods Meet Deep Learning.

Deep learning (DL) has been widely used in various scientific fields, but its integration into phylogenetics has been slower, primarily due to the complex nature of phylogenetic data. The studies that apply DL to sequencing data often limit analyses to four-taxon trees. Many of these studies serve as "proof of principle" and perform similarly to traditional phylogeny reconstruction methods. New ways of using training data, such as encoding with compact bijective ladderized vectors or transformers, enable the handling of much larger trees and genomic data sets. This short perspective focuses on the application of DL in phylogenetics, introducing prevalent DL architectures. We highlight potential problems in the field by discussing the risks of using simulation-based training data and emphasize the importance of reproducibility and robustness in computational estimates. Finally, we explore promising research areas, including the combination of phylogenetics and population genetics in DL, the analysis of neighbor dependencies, and the potential to significantly reduce computational cost compared to traditional methods. This perspective illustrates the potential of DL in complementing traditional phylogeny reconstruction methods and aiding the advancement of phylogenetic analysis, especially in performing computationally demanding tasks such as model selection or estimating branch support values.

Humans↗