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PubMedDate not supplied

Tracking the motion of skeletal muscle with velocity-encoded MR imaging.

Phase-contrast magnetic resonance velocity-encoding techniques were used to track two-dimensional movement of skeletal muscle tissue. Axial and longitudinal planes in the forearms of five healthy volunteers were imaged during cyclic flexion and extension of the fingers, and the resulting data were used to plot the trajectories of the motion of pieces of muscle tissue. A phantom that produced complex two-dimensional trajectories validated the accuracy of the imaging and analysis techniques; after adjustments for phase errors, two-dimensional trajectories were tracked with an root-mean-square error of 0.1 cm. Preliminary results indicate that velocity-encoded image data can characterize motion trajectories and that refinements in data acquisition and analysis techniques may make it possible to correlate the movements of different regions within a muscle, characterize muscle contraction, and quantify longitudinal strain. This ability to track velocity vectors may provide a foundation for quantitative analysis of muscle motion.

Animals↗

PubMed2006

Low-temperature protein dynamics: a simulation analysis of interprotein vibrations and the boson peak at 150 k.

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about approximately 2-2.5 meV, originates from approximately 10(2) collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Cold Temperature↗

PubMed2003

Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysis.

Guanine:adenine (G:A) mismatches and in particular tandem G:A (tG:A) mismatches are frequently observed in biological RNA molecules and can serve as sites for tertiary interaction, metal binding and protein recognition. Depending on the surrounding sequence tG:A mismatches can adopt different basepairing topologies. In the sequence context (5'-) GGAC (tandem G:A in bold) a face-to-face (imino or Watson-Crick-like) pairing is preferred whereas in the CGAG context, G and A adopt a sheared arrangement. Systematic conformational searches with a generalized Born continuum model and molecular dynamics simulations including explicit water molecules and ions have been used to generate face-to-face and sheared tG:A mismatches in both CGAG and GGAC sequence contexts. Conformations from both approaches were evaluated using the same force field and a Poisson-Boltzmann continuum solvent model. Although the substate analysis predicted the sheared arrangement to be energetically preferred in both sequence contexts, a significantly greater preference of the sheared form was found for the CGAG context. In agreement with the experimental observation, the analysis of molecular dynamics trajectories indicated a preference of the sheared form in the case of the CGAG-context and a favorization of the face-to-face form in the case of the GGAC context. The computational studies allowed to identify energetic contributions that stabilize or destabilize the face-to-face and sheared tandem mismatch topologies. The calculated nonpolar solvation and Lennard-Jones packing interaction were found to stabilize the sheared topology independent of the sequence context. Electrostatic contributions are predicted to make the most significant contribution to the sequence context dependence on the structural preference of tG:A mismatches.

Adenine↗

PubMed1994

Contour representation of sway area in posturography and its application.

The representation of postural sway tendency in posturography is important to understand the features of body balance system and a variety of postural disorders. This study is concerned with the contour representation and analysis of postural sway trajectory in posturography. We propose two methodologies to derive the contour of postural sway based on the boundary points of sway area. An algorithm for finding the sway contour in each method was developed, and the experiments were performed to examine the computational efficiency between the methods proposed. Fourteen able-bodied men were asked to stand upright on a force platform to compare the numerical measures of sway shape with other quantitative sway measures used in previous research into balance. The results show that numerical measures of sway contour (area, perimeter, and complexity of sway shape) and radius length diagram can be used to describe the tendency of sway shape, whereas other quantitative sway measures represent the extent of sway amounts.

Algorithms↗

PubMed2006

Development of hand function and precision grip control in individuals with cerebral palsy: a 13-year follow-up study.

OBJECTIVE: Although children with cerebral palsy display large developmental differences in hand function from that of typically developing children by the age of 6 to 10 years, little is known about the developmental processes underlying hand function during subsequent development. In this study we investigated the development of manual dexterity in a timed motor task, the timing and amplitude of fingertip-force application during a precision grasping task, and the relationship between changes in these measures. We applied highly quantitative analytical approaches to determine if the fingertip-force application pattern and trial-to-trial variation of fingertip-force application change during development. METHODS: Twelve subjects with cerebral palsy (aged 6-8 years) participated in the first data-collection session conducted between 1989 and 1990. Ten of these subjects (5 with hemiplegia and 5 with diplegia, aged 19-21 years) returned between 2002 and 2003. Manual dexterity was measured by using timed tasks of the Jebsen-Taylor test of hand function. Subjects also lifted an object instrumented with force transducers while we measured the temporal coordination of fingertip coordination and the path ratio between the grip and vertical load-force trajectory (straightness). We used generalized procrustes analysis to determine if there were changes in shape of the force trajectory and intertrial variability. RESULTS: The Jebsen-Taylor test times decreased 45% from the first to the second data session. The overall time to complete the grip-lift task decreased 22%, mainly because of a faster transition from grasp to lift. The grip-force/load-force path ratios decreased from 1.7 to 1.35 (1 = straight line). Generalized procrustes analysis indicated a change in the shape and a decrease in variability in shape of the force-ratio path. CONCLUSIONS: Our results demonstrate that the efficiency in grasping had developed during a 13-year period for this small group of participants with cerebral palsy, which suggests that improvement in hand function occurs over a longer time frame than commonly would be expected.

Adult↗

PubMed2006

The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions.

The effect of the box shape on the dynamic behavior of proteins simulated under periodic boundary conditions is evaluated. In particular, the influence of simulation boxes defined by the near-densest lattice packing (NDLP) in conjunction with rotational constraints is compared to that of standard box types without these constraints. Three different proteins of varying size, shape, and secondary structure content were examined in the study. The statistical significance of differences in RMSD, radius of gyration, solvent-accessible surface, number of hydrogen bonds, and secondary structure content between proteins, box types, and the application or not of rotational constraints has been assessed. Furthermore, the differences in the collective modes for each protein between different boxes and the application or not of rotational constraints have been examined. In total 105 simulations were performed, and the results compared using a three-way multivariate analysis of variance (MANOVA) for properties derived from the trajectories and a three-way univariate analysis of variance (ANOVA) for collective modes. It is shown that application of roto-translational constraints does not have a statistically significant effect on the results obtained from the different simulations. However, the choice of simulation box was found to have a small (5-10%), but statistically significant effect on the behavior of two of the three proteins included in the study.

Protein Conformation↗

PubMed1998

Local instability and oscillations of trajectories in a diluted symmetric neural network.

Using a generalized version of the signal-to-noise analysis, we study local instabilities of trajectories for the parallel dynamics of an extremely diluted, symmetric, Hopfield neural network. In order to reach a better understanding of the structure of the attractors of this model, a revision of the asymmetric version is performed in the case of zero and non-zero temperatures. New unexpected dynamical behaviours are found. Moreover, despite accepted beliefs, both analytical and numerical deviations between the dynamical properties of the two models (symmetric and asymmetric) can be exhibited. We show that, in some range of parameters, the diluted symmetric network exhibits strong dynamical oscillations of the neuronal activity, similar to those observed in synchronized networks. Furthermore, a deeper knowledge of the structure near attractors is achieved from this stability/instability analysis thanks to explicit analytical formulae for a two-step parallel dynamics for a symmetric network.

Models, Theoretical↗

PubMed1997

Development of differential preganglionic projections to pre- and paravertebral sympathetic ganglia.

Sympathetic preganglionic axons project to spatially distinct targets in the periphery. A precise topographic pattern exists within the thoracic preganglionic cell column relative to the direction of axonal projections within the sympathetic chain. In this study, the time course and pattern of axonal outgrowth from different populations of preganglionic neurons in the chicken embryo is examined in detail to clarify the origin of the topography in this system. Projections to prevertebral targets are established by development of the splanchnic nerves by stage 25, well after the earliest somatic motor projections at stage 19 but at least two stages before the reported onset of paravertebral projections. Further, preganglionic axons that project rostrally into the sympathetic chain may do so earlier than those that project caudally in the chain. The separation of preganglionic axons into prevertebral, rostral paravertebral or caudal paravertebral directions occurs at a common site in the ventral mesenchyme, established by the initial ventromedial projection of the splanchnic nerves. Analysis of the axonal trajectories of rostrally and caudally projecting cells reveals that preganglionic axons are not selectively fasciculated before their point of separation at the sympathetic chain. The patterning of the preganglionic cell column is specified before the establishment of functional connections within the chain, indicating that target contact is not a determinant of the segmental pattern. We suggest that the differential outgrowth of preganglionic axons to peripheral targets is determined by the unique identities of underlying subpopulations of preganglionic axons.

Acetylcholinesterase↗

PubMed1996

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer.

The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundred systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 angstroms. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.

Biophysics↗

PubMed1999

Exploring protein interiors: the role of a buried histidine in the KH module fold.

The K-homology (KH) module is a novel RNA-binding motif. The structures of a representative KH motif from vigilin (vig-KH6) and of the first KH domain of fmr1 have been recently solved by nuclear magnetic resonance (NMR) and automated assignment-refinement techniques (ARIA). While a hydrophobic residue is found at position 21 in most of the KH modules, a buried His is conserved in all the 15 KH repeats of vigilin. This position must therefore have a key structural role in stabilizing the hydrophobic core. In the present work, we have addressed the following questions in order to obtain a detailed description of the role of His 21: i) what is the exact role of the histidine in the hydrophobic core of vig-KH6? ii) can we define the interactions that allow a conserved buried position to be occupied by a histidine both in vig-KH6 and in the whole vigilin KH sub-family? iii) how is the structure and stability of vig-KH6 influenced by the state of protonation of this histidine? To answer these questions, we have carried out an extensive refinement of the vig-KH6 structure using both an improved ARIA protocol starting from different initial structures and successively running restrained and unrestrained trajectories in water. An analysis of the stability of secondary structural elements, solvent accessibility, and hydrogen bonding patterns allows hypothesis on the structural role of residue His 21 and on the interactions that this residue forms with the environment. The importance of the protonation state of His 21 on the stability of the KH fold was addressed and validated by experimental results.

Carrier Proteins↗

PubMed1999

In vitro motility evaluation of aggregated cancer cells by means of automatic image processing.

BACKGROUND: Set up of an automatic image processing based method that enables the motility of in vitro aggregated cells to be evaluated for a number of hours. METHODS: Our biological model included the PC-3 human prostate cancer cell line growing as a monolayer on the bottom of Falcon plastic dishes containing conventional culture media. Our equipment consisted of an incubator, an inverted phase contrast microscope, a Charge Coupled Device (CCD) video camera, and a computer equipped with an image processing software developed in our laboratory. This computer-assisted microscope analysis of aggregated cells enables global cluster motility to be evaluated. This analysis also enables the trajectory of each cell to be isolated and parametrized within a given cluster or, indeed, the trajectories of individual cells outside a cluster. RESULTS: The results show that motility inside a PC-3 cluster is not restricted to slight motion due to cluster expansion, but rather consists of a marked cell movement within the cluster. CONCLUSIONS: The proposed equipment enables in vitro aggregated cell motility to be studied. This method can, therefore, be used in pharmacological studies in order to select anti-motility related compounds. The compounds selected by the equipment described could then be tested in vivo as potential anti-metastatic.

Algorithms↗

PubMed2026

Immune-Like Malignant Epithelial Programs Shape Tumor-Immune Interactions and Inform Prognostic Stratification in Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is characterized by marked cellular heterogeneity, yet how malignant epithelial states contribute to immune regulation and clinical outcomes remains incompletely defined. We integrated single-cell RNA-sequencing data to map the cellular landscape of LUAD and identify malignant epithelial cells based on inferred copy-number alterations. Epithelial states were further examined through trajectory inference, transcription factor analysis, and cell-cell communication profiling. Single-cell-derived genes were subsequently integrated with TCGA and independent GEO cohorts to construct and validate a machine learning-based prognostic signature. Malignant epithelial cells displayed distinct functional programs, including an immune-like state associated with genomic instability, immune-related transcriptional activity, tumor-immune communication, and patient outcomes. The resulting immune-like malignant epithelial cell signature (IMEC-Sig) consistently stratified survival across multiple cohorts. Low IMEC-Sig scores were accompanied by greater immune infiltration, higher immune checkpoint expression, and increased immunophenoscore, whereas high scores were linked to a comparatively immunosuppressive phenotype. Pan-cancer analyses further identified KRT8 as a gene associated with unfavorable prognosis, and functional experiments showed that KRT8 silencing suppressed proliferation, migration, invasion, and colony formation in LUAD cells. Together, these findings connect malignant epithelial heterogeneity with the immune context and clinical outcomes, support IMEC-Sig as a biologically informed prognostic tool, and nominate KRT8 as a potential therapeutic target in LUAD.

Humans↗

PubMed2003

Brownian dynamics simulation of helix-capping motifs.

Helix-capping motifs are believed to play an important role in stabilizing alpha-helices and defining helix start and stop signals. We performed microsecond scale Brownian dynamics simulations to study ten XAAD sequences, with X = (A,E,I,L,N,Q,S,T,V,Y), to examine their propensity to form helix capping motifs and correlate these results with those obtained from analyzing a structural database of proteins. For the widely studied capping box motif S**D, where the asterisk can be any amino acid residue, the simulations suggested that one of the two hydrogen bonds proposed earlier as a stabilizing factor might not be as important. On the other hand, side-chain interactions between the capping residue and the third residue downstream on the polypeptide chain might also play a role in stabilizing this motif. These results are consistent with explicit-solvent molecular dynamics simulations of two capping box motifs found in the proteins BPTI and alpha-dendrotoxin. Principal component analysis of the SAAD trajectory showed that the first three principal components, after those corresponding to translational-rotational motion were removed, accounted for more than half of the conformational fluctuations. The first component separated the conformational space into two parts with the all-helical conformation and the capping box motif lying largely in one part. The second component, on the other hand, could be used to describe conformational transitions between the all-helical form and the capping box motif.

Amino Acid Motifs↗

PubMed2004

Characterization of the conformational behavior of peptide Contryphan Vn: a theoretical study.

In this work we report the study of a peptide, the Contryphan Vn produced by Conus ventricosus, a vermivorous cone snail living in the temperate Mediterranean sea. This cyclic peptide of nine residues is a ring closed by a Cys-Cys (Cys: cysteine) disulfide bond containing two proline (Pro) residues and two tryptophans (Trp), one of them being a D-Trp. We present a statistical mechanical characterization of the peptide, simulated in water for about 200 ns with classical molecular dynamics (MD). In recent years there has been a growing interest in the study of the mechanics and dynamics of biological molecules, and in particular for proteins and peptides, about the relationship between collective motions and the active conformations which exert the biological function. To this aim we used the essential dynamics analysis on the MD trajectory and extracted, from the total fluctuations of the molecule, the dominant dynamical modes responsible of the principal conformational transitions. The Contryphan Vn small size allowed us to investigate in details the all-atoms dynamics and the corresponding thermodynamics in conformational space defined by the most significant intramolecular motions.

Animals↗

PubMed1984

Rheological properties of living cytoplasm: a preliminary investigation of squid axoplasm (Loligo pealei).

A magnetic sphere viscoelastometer has been developed to perform rheological experiments in living axoplasm of Loligo pealei. The technique includes the use of a calibrated magnetic sphere viscoelastometer on surgically implanted ferro-magnetic spheres in intact squid giant axons. The axoplasm was discerned to be "living" by the biological criterion of tubulovesicular organelle motility, which was observed before and after experimentation. From these in vivo experiments, new structural characteristics of the axoplasm have been identified. First, analysis of magnetic sphere trajectories has shown the axoplasm to be a complex viscoelastic fluid. Directional experimentation showed that this material is structurally anisotropic, with a greater elastic modulus in the direction parallel to the axon long axis. Second, both magnetic sphere and in vivo capillary experiments suggested that the axoplasm is tenaciously anchored to the axolemma. Third, it was found that axoplasm could be modelled as a linear viscoelastic material in the low shear rate range of 0.0001 to 0.004 s-1. The simplest mechanical model incorporating the discovered properties of the material in this range is Burger's model.

Animals↗

PubMed2005

Isobaric-isothermal monte carlo simulations from first principles: application to liquid water at ambient conditions.

A series of first-principles Monte Carlo simulations in the isobaric-isothermal ensemble were carried out for liquid water at ambient conditions (T=298 K and p=1 atm). The Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and norm-conserving Goedecker-Teter-Hutter (GTH) pseudopotentials were employed with the CP2 K simulation package to examine systems consisting of 64 water molecules. The fluctuations in the system volume encountered in simulations in the isobaric-isothermal ensemble require a reconsideration of the suitability of the typical charge-density cutoff and the regular grid-generation method previously used for the computation of the electrostatic energy in first-principles simulations in the microcanonical or canonical ensembles. In particular, it is noted that a much higher cutoff is needed and that the most computationally efficient method of creating grids can result in poor simulations. Analysis of the simulation trajectories using a very large charge-density cutoff at 1200 Ry and four different grid-generation methods point to a significantly underestimated liquid density of about 0.8 g cm-3 resulting in a somewhat understructured liquid (with a value of about 2.7 for the height of the first peak in the oxygen-oxygen radial distribution function) for BLYP-GTH water at ambient conditions. In addition, a simulation using a charge-density cutoff at 280 Ry yields a higher density of 0.9 g cm-3, showing the sensitivity of the simulation outcome to this parameter.

Journal Article↗

PubMed1993

Controlling the regiospecificity and coupling of cytochrome P450cam: T185F mutant increases coupling and abolishes 3-hydroxynorcamphor product.

Cytochrome P450cam (P450CIA1) catalyzes the hydroxylation of camphor and several substrate analogues such as norcamphor and 1-methyl-norcamphor. Hydroxylation was found experimentally at the 3, 5, and 6 positions of norcamphor, but only at the 5 and 6 positions of 1-methyl-norcamphor. In the catalytic cycle, the hydroxylation of substrate is coupled to the consumption of NADH. For camphor, the degree of coupling is 100%, but for both norcamphor and 1-methyl-norcamphor, the efficiency is dramatically lowered to 12% and 50%, respectively. Based on an examination of the active site of P450cam, it appeared that mutating position 185 might dramatically alter the product specificity and coupling of hydroxylation of norcamphor by P450cam. Analysis of molecular dynamics trajectories of norcamphor bound to the T185F mutant of cytochrome P450cam predicted that hydroxylation at the 3 position should be abolished and that the coupling should be dramatically increased. This mutant was constructed and the product profile and coupling experimentally determined. The coupling was doubled, and hydroxylation at the 3 position was essentially abolished. Both of these results are in agreement with the prediction.

Binding Sites↗

PubMed2005

Molecular dynamics study of water penetration in staphylococcal nuclease.

The ionization properties of Lys and Glu residues buried in the hydrophobic core of staphylococcal nuclease (SN) suggest that the interior of this protein behaves as a highly polarizable medium with an apparent dielectric constant near 10. This has been rationalized previously in terms of localized conformational relaxation concomitant with the ionization of the internal residue, and with contributions by internal water molecules. Paradoxically, the crystal structure of the SN V66E variant shows internal water molecules and the structure of the V66K variant does not. To assess the structural and dynamical character of interior water molecules in SN, a series of 10-ns-long molecular dynamics (MD) simulations was performed with wild-type SN, and with the V66E and V66K variants with Glu66 and Lys66 in the neutral form. Internal water molecules were identified based on their coordination state and characterized in terms of their residence times, average location, dipole moment fluctuations, hydrogen bonding interactions, and interaction energies. The locations of the water molecules that have residence times of several nanoseconds and display small mean-square displacements agree well with the locations of crystallographically observed water molecules. Additional, relatively disordered water molecules that are not observed crystallographically were found in internal hydrophobic locations. All of the interior water molecules that were analyzed in detail displayed a distribution of interaction energies with higher mean value and narrower width than a bulk water molecule. This underscores the importance of protein dynamics for hydration of the protein interior. Further analysis of the MD trajectories revealed that the fluctuations in the protein structure (especially the loop elements) can strongly influence protein hydration by changing the patterns or strengths of hydrogen bonding interactions between water molecules and the protein. To investigate the dynamical response of the protein to burial of charged groups in the protein interior, MD simulations were performed with Glu66 and Lys66 in the charged state. Overall, the MD simulations suggest that a conformational change rather than internal water molecules is the dominant determinant of the high apparent polarizability of the protein interior.

Algorithms↗