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PubMedDate not supplied

What determines growth direction in fungal hyphae?

We used high-resolution video microscopy and image analysis to map the trajectory of the Spitzenkörper in growing hyphae of Neurospora crassa and to correlate it with growth directionality. The Spitzenkörper followed a tortuous trajectory produced by a dominant forward motion accompanied by frequent, transverse oscillations. In hyphae with a fixed growth direction, the regression line of the Spitzenkörper trajectory corresponded to the longitudinal axis of the hypha. A permanent change in growth direction, i.e., the establishment of a new growth axis, was correlated with a sustained shift in Spitzenkörper trajectory away from the existing cell axis. In meandering hyphae, changes in growth directionality occurred somewhat erratically but there was a strong compensatory tendency reversing directional shifts and maintaining an overall fixed direction of growth. Although external factors greatly affect hyphal growth direction (tropisms), they are probably not the primary determinants of growth directionality. Inhibitors of microtubules, but not of actin microfilaments, caused hyphae to lose their growth directionality-providing support for the idea that Spitzenkörper trajectory is determined internally by a growing scaffolding of cytoplasmic microtubules. The meandering morphology of N. crassa hyphae was duplicated by computer simulation in support of the idea that hyphal morphogenesis is controlled by the position of the Spitzenkörper functioning as a vesicle supply center.

Computer Simulation↗

PubMed2000

Analysis of correlated motion in antibody combining sites from molecular dynamics simulations.

The crystal structures of the NC6.8-antisweet taste ligand complex and the uncomplexed antibody structures display significant differences in the conformations of residues in the combining site. A molecular dynamics method was employed to understand the flexibility and correlated motion of key combining site residues in the uncomplexed antibody. The simulations reveal that residues that show conformational differences between the complex and uncomplexed structures display strong dynamical correlations. Extensive analysis of the dynamics trajectory using time correlation methods is presented.

Acetates↗

PubMed1994

Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam.

Recent studies by Wackett and co-workers have shown that cytochrome P450cam is capable of reductively dehalogenating hexachloroethane at a significant rate, but that no appreciable dehalogenation of 1,1,1-trichloroethane is observed. A growing body of evidence indicates that differences in intrinsic reactivity can not completely explain this observation. We therefore explored the possible role of differences in preferred binding orientation and in active-site mobility. A detailed analysis of molecular dynamics trajectories with each of these substrates bound at the active site of P450cam is presented. While the dynamics and overall time-average structure calculated for the protein are similar in the two trajectories, the two substrates behave quite differently. The smaller substrate, 1,1,1-trichloroethane, is significantly more mobile than hexachloroethane and has a preferred orientation in which the substituted carbon is generally far from the heme iron. In contrast, for hexachloroethane, one of the chlorine atoms is nearly always in van der Waals contact with the heme iron, which should favor the initial electron transfer step.

Binding Sites↗

PubMed1995

Reprogramming of muscle activation patterns at the wrist in compensation for elbow reaction torques during planar two-joint arm movements.

The relationship between wrist kinematics, dynamics and the pattern of muscle activation were examined during a two-joint planar movement in which the two joints moved in opposite directions, i.e. elbow flexion/wrist extension and elbow extension/wrist flexion. Elbow movements (ranging from 10 to 70 deg) and wrist movements (ranging from 10 to 50 deg) were performed during a visual, step-tracking task in which subjects were required to attend to the initial and final angles at each joint. As the elbow amplitude increased, wrist movement duration increased and the wrist movement trajectories became quite variable. Analysis of the torques acting at the wrist joint showed that elbow movements produced reaction torques acting in the same direction as the intended wrist movement. Distinct patterns of muscle activation were observed at the wrist joint that were dependent on the relative magnitude of the elbow reaction torque in relation to the net wrist torque. When the magnitude of the elbow reaction torque was quite small, the wrist agonist was activated first. As the magnitude of the elbow reaction torque increased, activity in the wrist agonist decreased significantly. In conditions where the elbow reaction torque was much larger than the net wrist torque, the wrist muscle torque reversed direction to oppose the intended movement. This reversal of wrist muscle torque was directly associated with a change in the pattern of muscle activation where the wrist antagonist was activated prior to the wrist agonist. Our findings indicate that motion of the elbow joint is an important consideration in planning wrist movement. Specifically, the selection of muscle activation patterns at the wrist is dependent on the relative magnitude and direction of the elbow reaction torque in relation to the direction of wrist motion.

Animals↗

PubMed2002

Molecular dynamics and IR spectroscopy in investigation of phase transitions in molecular crystal 4,4'-bis(11-hydroxy-1-undecyloxy)biphenyl.

Molecular dynamics (MD) simulations combined with temperature-dependent IR spectroscopic measurements were used to study phase transitions in molecular crystals of the mesogenic diol 4,4'-bis(11-hydroxy-1-undecyloxy)biphenyl. DSC measurements revealed four phase transitions in this molecular crystal at approximately 327.1 K, 389.8 K, 419.1 K and 431.9 K. Analysis of the dynamic trajectories at temperatures of 300 K, 360 K, 400 K and 480 K revealed changes in conformation of the mesogenic diol molecules and consequently changes in crystal packing and crystal structure in the temperature range 300-480 K and enabled us to understand the mechanism of the phase transitions.

Biphenyl Compounds↗

PubMed2004

Characterization of molecular structures and properties of polyurethanes using molecular dynamics simulations.

Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the diisocyanates and diols, in particular changes in the mesogen, were investigated. Introduction of mesogenic segments into the polymers suppresses the ordering. Stiff end substituents (phenyl and alkoxy groups) of the mesogens stabilize the mesophases to such an extent that the negative influence of long polymer chains is compensated and the liquid-crystalline properties are recovered. All-atom molecular dynamics simulations in the Cerius2 modeling environment were carried out to characterize the structures of the polymers. Analysis of the dynamic trajectories at 20, 100, 120 and 170 degrees C revealed changes in conformation of macromolecules, which correlate with DSC measurements.

Calorimetry↗

PubMed1989

Differential growth resulting in the specification of different types of cellular architecture in root meristems.

Symplastic growth of plant organs may be described by a continuous growth tensor field. In tensorial analysis of meristems, the trajectories of periclinal and anticlinal cell walls represent trajectories of the principal directions of growth (PDGs); this follows from the maintenance of mutual orthogonality between periclinal and anticlinal wall trajectories during growth. Periclinal and anticlinal cell divisions are also oriented in the principal planes of growth. The growth tensor for the root apex is specified in such a way that the principal directions of the tensor fit the pattern of periclinal and anticlinal walls in the apex, and that the grid formed by material particles aligned along PDG trajectories preserve this alignment during growth. Two growth tensors are formulated--one giving a maximum and the other giving a minimum of the volumetric relative elemental growth rate at the region of the initial cell(s). Temporal sequences of deformation of a grid formed by lines coinciding with the principal directions of growth are shown. The formation of cellular patterns in root apices is simulated. Two types of patterns are obtained: one with an apical cell and merophytes, and another with files of cells converging towards a quiescent centre.

Biophysical Phenomena↗

PubMed1993

The forces acting on the human calcaneus.

The forces acting on the human calcaneus are analysed for a static standing posture. An optimization procedure is invoked to solve the statically indeterminate set of forces which could arise from muscles, ligaments and reactions between the calcaneus and other bones and also the ground. Two alternative objective functions are investigated; that which returns no active muscle force is considered the more realistic, since electromyographic studies show that in static standing only minor muscle activity occurs to counteract body sway. This set of forces is then applied to the bone for finite element stress analysis to produce stress trajectories, which are then validated against both the trabecular configuration of the cancellous bone of the calcaneus and also the distribution of the orientations of the hydroxyapatite crystal major and minor axes.

Biomechanical Phenomena↗

PubMed1992

Computer graphics presentations and analysis of hydrogen bonds from molecular dynamics simulation.

To obtain better insights into the dynamic nature of hydrogen bonding, computer graphics representations were introduced as an aid for the analysis of molecular dynamics trajectories. A schematic representation of hydrogen bonding patterns is generated to reflect the frequency and the type of hydrogen bonding occurring during the simulation period. Various trajectory plots for monitoring geometrical parameters and for analyzing three-center hydrogen bonding were also generated. The methods proposed are applicable to a variety of biopolymers. In this study, hydrogen bonding in the d(G)6.d(C)6 system was examined. For the nucleic acid fragments examined, three-center hydrogen bonds can be classified as in-plane and major or minor groove types. The in-plane three-center hydrogen bond represents a stable state in which both bonds simultaneously satisfy the relaxed hydrogen bonding criteria for a measurable period. On the other hand, groove three-center hydrogen bonds behave as a transient intermediate state in a flip-flop hydrogen bonding system.

Computer Graphics↗

PubMed1987

Organization of arm movements. Motion is segmented.

A kinematic analysis of human arm trajectories which underlie the production of learned, continuous movements (such as drawing of 'figure 8s' and stars) in free space is presented. The objective of this investigation was to see if a set of rules, which had been identified previously and which are appropriate for generating circular or elliptical motion of the wrist in an arbitrary plane, also hold true for arbitrary, learned trajectories provided one additional assumption is made: that apparently continuous complex movements are composed of unit segments. The results presented in this paper are consistent with this hypothesis. Furthermore, as predicted by the hypothesis, the wrist trajectory deviates little from planar motion in each segment while the plane of motion can change abruptly from one segment to the next.

Arm↗

PubMed2004

Structural and kinetic characterization of myoglobins from eurythermal and stenothermal fish species.

Teleost myoglobin (Mb) proteins from four fish species inhabiting different temperature environments were used to investigate the relationship between protein function and thermal stability. Mb was isolated from yellowfin tuna (homeothermal warm), mackerel (eurythermal warm), and the Antarctic teleost Notothenia coriiceps (stenothermal cold). Zebrafish (stenothermal tropical) myoglobin was expressed from cloned cDNA. These proteins differed in oxygen affinity, as measured by O2 dissociation rates and P50 values, and thermal stability as measured by autooxidation rates. Mackerel Mb had the highest P50 value at 25 degrees C (3.7 mmHg), corresponding to the lowest O2 affinity, followed by zebrafish (1.0 mmHg), yellowfin tuna (1.0 mmHg), and N. coriiceps (0.6 mmHg). Oxygen dissociation rates and Arrhenius plots were similar between all teleost species in this study, with the exception of mackerel myoglobin, which was two-fold faster at all temperatures tested. Myoglobin from the Antarctic teleost had the highest autooxidation rate (0.44 h(-1)), followed by mackerel (0.26 h(-1)), zebrafish (0.22 h(-1)), and yellowfin tuna (0.088 h(-1)). Primary structural analysis revealed residue differences distributed throughout the polypeptide sequences, making it difficult to identify, which, if any, residues contribute to structural flexibility. However, analysis of molecular dynamics trajectories indicates that Mb from the eurythermal mackerel is predicted to be the most flexible protein within the D loop and FG turn. At the same time, it has the lowest O2 affinity and the highest O2 dissociation rates when compared to myoglobins from teleosts that appear to be less flexible in our dynamics simulations.

Adaptation, Physiological↗

PubMed2004

The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences.

The papillomavirus E2 transcription and replication factors bind to the DNA consensus ACCGN(4)CGGT sequence (E2-BS), through both direct and indirect readout mechanisms. The two symmetric half-sites ACCG.CGGT are highly conserved in the genomes and are hydrogen bound with E2. Although E2 does not contact the N4 spacer, the affinities are modulated by the base composition of this DNA part. Nevertheless, the origin of either the global recognition mechanism or the spacer effect remains unclear, particularly in the case of the bovine papillomavirus type 1 E2 (BPV-1-E2) system, used as model to study the papillomaviruses. We present, herein, studies carried out on oligomers differently recognized by the BPV-1-E2 protein and based on molecular dynamic simulations including counterions and water. The sequences contain the conserved half-sites but three different spacers (CCAT, ACGT and AAAC), resulting in very high, high and low affinity targets for BPV-1-E2. In order to estimate how much the free DNAs resemble the bound conformations, comparisons are made with two DNAs extracted from E2-BS-BPV-1 crystallographic complexes, representative of high and moderate affinity structures. The analysis of 15 ns trajectories reveals that the ACCG/CGGT half-sites, whatever the spacer, have the same behavior and adopt average stable base-pair parameters very close to those of the bound conformations. In contrast, the three different free spacers strongly differ in their BI <--> BII backbone dynamics. The low affinity AAAC spacer exhibits stable BI backbone conformations, the high affinity ACGT spacer is characterized by a dramatic instability of the CpG phosphate groups, and the CpA and GpG backbones in the very high affinity CCAT.ATGG spacer are trapped in BII conformations. All resemble more of the moderate affinity complex DNA than the high affinity one. Nevertheless, the particular behavior of the CCAT and ACGT backbones allows the emergence of BII-rich spacers, a configuration reproducing both local and global helical features of the bound DNA conformation of the high affinity complex and favoring the minor groove curvature required in the complex. In particular, the CCAT-containing site spends almost half of the time in this form that well mimics the bound one. Thus, we propose that the E2 protein could take advantage of the invariant favorable structures of the half-sites to form a pre-complex, but would require a specific spacer intrinsic malleability to lock the interaction. Finally, the backbone conformational states, by their ability to translate information coded in the sequence into structural properties, provide insight into the mechanisms that contribute to fine binding site selection and specific nucleic acid ligand recognition.

Base Sequence↗

PubMed2005

Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding.

There is a change from three-state to two-state kinetics of folding across the homeodomain superfamily of proteins as the mechanism slides from framework to nucleation-condensation. The tendency for framework folding in this family correlates with inherent helical propensity. The cellular myeloblastis protein (c-Myb) falls in the mechanistic transition region. An earlier, preliminary report of protein engineering experiments and molecular dynamics simulations (MD) showed that the folding mechanism for this protein has aspects of both the nucleation-condensation and framework models. In the more in-depth analysis of the MD trajectories presented here, we find that folding may be attributed to both of these mechanisms in different regions of the protein. The folding of the loop, middle helix, and turn is best described by nucleation-condensation, whereas folding of the N and C-terminal helices may be described by the framework model. Experimentally, c-Myb folds by apparent two-state kinetics, but the MD simulations predict that the kinetics hide a high-energy intermediate. We stabilized this hypothetical folding intermediate by deleting a residue (P174) in the loop between its second and third helices, and the mutant intermediate is long-lived in the simulations. Equilibrium and kinetic experiments demonstrate that folding of the DeltaP174 mutant is indeed three-state. The presence and shape of the intermediate observed in the simulations were confirmed by small angle X-ray scattering experiments.

Computer Simulation↗

PubMed2006

Method for studying behavioural activity patterns during long-term recordings using a force-plate actometer.

The motor activity (MA) patterns of rodents are commonly detected in the laboratory using infrared photo-beams or running wheels. In chronobiological studies, the MA rhythm is considered as a behavioural output of the circadian pacemaker. This paper describes a method to obtain long-term records of MA in rodents, with a 1mm spatial resolution and a 1s temporal resolution. The device comprised a square platform laid on top of three force transducers, allowed the calculation of the coordinates of the centre of force exerted by a freely moving rodent, and continuously monitored its displacements. A specific computer program processed the trajectories, providing an exhaustive analysis of motion. To test this method, motor behavioural activity was studied in rats exposed to conditions that favoured rhythmicity: light-dark cycles of both 24 h (LD) and 22 h (T22), and constant darkness (DD). In addition, arrhythmicity patterns were studied under constant light (LL) conditions, and in animals with permanent lesions of the hypothalamic suprachiasmatic nucleus (SCNx). A single description of the general MA distribution at 24 h was obtained using infrared photo-beams. By contrast, under LD conditions, a 24-h rhythm with ultradian components was seen in the total distance travelled, whereas that detected in the number of slow motions showed less ultradian components. In addition, a regional preference in the nesting place was detected under both LD and DD conditions. In one SCNx animal and another exposed to LL conditions, both showing arrhythmicity in photo-beam-detected MA, a 24 h rhythm was observed in regional preference; other LL animal presented a 24 h rhythm in the number of slow motions. This method has capabilities lacking in commonly used techniques. The potential uses of this approach, principally in cronobiological studies, are discussed.

Animals↗

PubMed2005

Quest, chaos and restitution: living with chronic fatigue syndrome/myalgic encephalomyelitis.

Chronic illness is disruptive, threatening people's sense of identity and taken for granted assumptions. Transformations in values, expectations and life priorities are likely to be experienced and in order to regain a coherent sense of self, people must interpret their experiences. People with difficult to diagnose illnesses can find themselves living with greater uncertainty and stigma. This paper explores how people with chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) describe and interpret their illness experience by applying Arthur Frank's narrative typologies to analyse interviews with 17 British people with CFS/ME. The analysis proposes that a trajectory of narrative typologies is experienced, starting with a restitution narrative, moving to a chaos narrative and, for most, back to a restitution narrative and on to a quest narrative. The presentation of narrative types put forward by people living with CFS/ME differ to those presented by people who are HIV positive and have been treated for breast cancer.

Adolescent↗

PubMed2003

Molecular dynamics simulation of protein folding by essential dynamics sampling: folding landscape of horse heart cytochrome c.

A new method for simulating the folding process of a protein is reported. The method is based on the essential dynamics sampling technique. In essential dynamics sampling, a usual molecular dynamics simulation is performed, but only those steps, not increasing the distance from a target structure, are accepted. The distance is calculated in a configurational subspace defined by a set of generalized coordinates obtained by an essential dynamics analysis of an equilibrated trajectory. The method was applied to the folding process of horse heart cytochrome c, a protein with approximately 3000 degrees of freedom. Starting from structures, with a root-mean-square deviation of approximately 20 A from the crystal structure, the correct folding was obtained, by utilizing only 106 generalized degrees of freedom, chosen among those accounting for the backbone carbon atoms motions, hence not containing any information on the side chains. The folding pathways found are in agreement with experimental data on the same molecule.

Algorithms↗

PubMed2003

Molecular dynamics simulations of lignin peroxidase in solution.

The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.

Benzyl Alcohols↗

PubMed2004

Theoretical and experimental study of the D2194G mutation in the C2 domain of coagulation factor V.

Coagulation factor V (FV) is a large plasma glycoprotein with functions in both the pro- and anticoagulant pathways. In carriers of the so-called R2-FV haplotype, the FV D2194G mutation, in the C2 membrane-binding domain, is associated with low expression levels, suggesting a potential folding/stability problem. To analyze the molecular mechanisms potentially responsible for this in vitro phenotype, we used molecular dynamics (MD) and continuum electrostatic calculations. Implicit solvent simulations were performed on the x-ray structure of the wild-type C2 domain and on a model of the D2194G mutant. Because D2194 is located next to a disulfide bond (S-S bond), MD calculations were also performed on S-S bond depleted structures. D2194 is part of a salt-bridge network and investigations of the stabilizing/destabilizing role of these ionic interactions were carried out. Five mutant FV molecules were created and the expression levels measured with the aim of assessing the tolerance to amino acid changes in this region of molecule. Analysis of the MD trajectories indicated increased flexibility in some areas and energetic comparisons suggested overall destabilization of the structure due to the D2194G mutation. This substitution causes electrostatic destabilization of the domain by approximately 3 kcal/mol. Together these effects likely explain the lowered expression levels in R2-FV carriers.

Amino Acid Substitution↗