Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51Linked to original sources
PubMed2005

Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise.

Residual dipolar couplings (RDCs) provide excellent probes for the exploration of dynamics in biomolecules on biologically relevant time-scales. Applying geometric motional models in combination with high-resolution structures to fit experimental RDCs allows the extraction of local dynamic amplitudes of peptide planes in proteins using only a limited number of data points. Here we compare the behaviour of three simple and intuitive dynamic modes: the Gaussian axial fluctuation model (1D-GAF), the two-site jump model, and a model supposing axially symmetric motion about a mean orientation. The requirement of a structural model makes this kind of methodology potentially very sensitive to structural imprecision. Numerical simulations of RDC dynamic averaging under different regimes show that the anisotropic motional models are more geometrically stringent than the axially symmetric model making it more difficult to alias structural noise as artificial dynamic amplitudes. Indeed, it appears that the model extracts accurate motional amplitudes even in the presence of significant structural error. We also show that a two-site jump model, also assuming the (alpha)C(i-1)-(alpha)C(i) as rotation axis, can only be distinguished from the previously developed GAF model beyond amplitude/jumps of around 40 degrees. The importance of appropriate estimation of the molecular alignment tensor for determination of local motional amplitudes is also illustrated here. We demonstrate a systematic scaling of extracted dynamic amplitudes if a static structure is assumed when determining the alignment tensor from dynamically averaged RDCs. As an example an artificial increase of 0.14 (0.85 compared to the expected 0.71) is observed in the extracted S2 if a pervasive 20 degrees GAF motion is present that is ignored in the tensor determination. Finally we apply a combined approach using the most appropriate motional model, to complete the analysis of dynamic motions from protein G.

Amino Acids↗
PubMed2004

Multibody dynamic simulation of knee contact mechanics.

Multibody dynamic musculoskeletal models capable of predicting muscle forces and joint contact pressures simultaneously would be valuable for studying clinical issues related to knee joint degeneration and restoration. Current three-dimensional multibody knee models are either quasi-static with deformable contact or dynamic with rigid contact. This study proposes a computationally efficient methodology for combining multibody dynamic simulation methods with a deformable contact knee model. The methodology requires preparation of the articular surface geometry, development of efficient methods to calculate distances between contact surfaces, implementation of an efficient contact solver that accounts for the unique characteristics of human joints, and specification of an application programming interface for integration with any multibody dynamic simulation environment. The current implementation accommodates natural or artificial tibiofemoral joint models, small or large strain contact models, and linear or nonlinear material models. Applications are presented for static analysis (via dynamic simulation) of a natural knee model created from MRI and CT data and dynamic simulation of an artificial knee model produced from manufacturer's CAD data. Small and large strain natural knee static analyses required 1 min of CPU time and predicted similar contact conditions except for peak pressure, which was higher for the large strain model. Linear and nonlinear artificial knee dynamic simulations required 10 min of CPU time and predicted similar contact force and torque but different contact pressures, which were lower for the nonlinear model due to increased contact area. This methodology provides an important step toward the realization of dynamic musculoskeletal models that can predict in vivo knee joint motion and loading simultaneously.

Computer Simulation↗
PubMed1998

Seat interface pressures of individuals with paraplegia: influence of dynamic wheelchair locomotion compared with static seated measurements.

OBJECTIVE: To provide a comparison of the seat interface pressures between static seating and dynamic seating during wheelchair locomotion of individuals with paraplegia. DESIGN: Repeated measures multivariate analysis of variance (MANOVA) comparing two conditions: static seat and dynamic seat interface pressures. SETTING: University campus and clinic. PARTICIPANTS: Fifteen participants, each of whom propelled a manual wheelchair for at least 5 hours per week over the previous 6 months and functioned with a spinal cord injury/ disability level of T1 or below. MAIN OUTCOME MEASURES: Peak pressure (PP) and pressure time integral (PTI) as measured by the Novel Pliance System, which consists of a flexible 32 x 32 capacitive sensor mat (each sensor 1.5 cm2) interfaced with a PC, was sampled at 10Hz. The participants were measured in their own wheelchair with a new Jay Active seat cushion. RESULTS: The repeated measures MANOVA showed a difference in the PP and PTI between the static and dynamic measurements (Wilk's = .00, p < .05). Follow-up dependent t tests yielded a difference in PP (t = 5.40, p < 0.025) and no difference in the PTI between static and dynamic conditions (t = 1.45, p > 0.025). The PP during static seating (mean = 16.2 +/- 5.0 kPa [121 +/- 37.5 mmHg]) was less than during dynamic seat interface pressures during wheelchair locomotion (20.03 +/- 6.6 kPa [152.3 +/- 49.5 mmHg]). PP varied by up to 42% during the wheelchair locomotion cycle. The PTI was similar between static (30.1 +/- 9.3 kPa [225.75 +/- 69 mmHg]) and dynamic conditions (36.2 +/- 18.1 kPa [271 +/- 135.7 mmHg]). CONCLUSIONS: The results from this study are consistent with some of the previous work on the nondisabled and a single case study, but with greater external validity because of the nature of the sample chosen and the methodology employed. PPs were greater during dynamic wheelchair locomotion compared with static seating interface pressures, with the peak varying up to 42% during the wheelchair locomotion cycle. The PTI indicates that the cumulative effect of the loading was comparable between conditions. The question that remains is whether this dynamic loading, resulting in a change in PP throughout the cycle, has a significant effect on tissue health.

Adult↗
PubMed1996

A comparison of structural and dynamic properties of different simulation methods applied to SH3.

The dynamic and static properties of molecular dynamics simulations using various methods for treating solvent were compared. The SH3 protein domain was chosen as a test case because of its small size and high surface-to-volume ratio. The simulations were analyzed in structural terms by examining crystal packing, distribution of polar residues, and conservation of secondary structure. In addition, the "essential dynamics" method was applied to compare each of the molecular dynamics trajectories with a full solvent simulation. This method proved to be a powerful tool for the comparison of large concerted atomic motions in SH3. It identified methods of simulation that yielded significantly different dynamic properties compared to the full solvent simulation. Simulating SH3 using the stochastic dynamics algorithm with a vacuum (reduced charge) force field produced properties close to those of the full solvent simulation. The application of a recently described solvation term did not improve the dynamic properties. The large concerted atomic motions in the full solvent simulation as revealed by the essential dynamics method were analyzed for possible biological implications. Two loops, which have been shown to be involved in ligand binding, were seen to move in concert to open and close the ligand-binding site.

Algorithms↗
PubMed1998

Fast dynamic contrast enhanced MR imaging of cervical carcinoma.

The first pass phase of contrast material is most important to study vascularization and perfusion of tissue and can be studied using dynamic magnetic resonance (MR) imaging. The purpose of this prospective study was to evaluate the usefulness of pre-contrast vs. post-contrast and fast dynamic MR imaging in the pre-operative staging of cervical carcinomas. To assess the normal onset of enhancement of the uterus and cervix 15 volunteers underwent dynamic MR imaging. Forty-two consecutive patients with invasive cervical cancer underwent pre-operative evaluation using MR imaging. The results of the MR examinations were correlated with clinical (FIGO) staging under anaesthesia (n = 42) and with histopathological findings after operation (n = 26). The staging results of pre-contrast T1-weighted and T2-weighted turbo spin-echo (TSE) MR images, pre-contrast MR images plus post-contrast enhanced (two dimensional fast low angle shot (FLASH 2-D) post contrast), pre-contrast MR images plus post-contrast enhanced plus fast dynamic enhanced (single slice turbo fast low angle shot (turbo FLASH)) MR images compared to histopathology (n = 26) were 77%, 81% and 85% respectively. The improvement was statistically not significant. The result of MR staging compared to clinical staging (n = 42) with pre-contrast MR images was correct in 79% of the cases. Pre-contrast MR images combined with post-contrast MR images did not significantly improve staging accuracy (83%). Pre-contrast plus post-contrast plus fast dynamic MR imaging improved staging to 91%. However, the improvement was only statistically significant for one reader (P = 0.01), whereas the improvement of the second reader was not significant (P = 0.07). The single slice turbo FLASH images showed enhancement of all squamous cell carcinomas (n = 32) with an average onset of 5s (range 4-8s) during the first 45s of bolus injection of gadolinium. The normal cervix showed enhancement with an average of 10s (range 6-14 s). FLASH 2-D post-contrast images showed less intense enhancement of the cervical tumours with respect to the parametria and other surrounding structures. Fast dynamic MR imaging and to a lesser degree post-contrast MR imaging showed a higher level of confidence than pre-contrast MR. Fast dynamic MRI compared with clinical staging (n = 42) was correct in 91% (38/42) and to histopathology in 85% (22/26). Comparison of clinical staging with histopathology was 85% (22/26). In conclusion, fast dynamic MR imaging is superior to post-contrast and pre-contrast MR imaging and is at least as good as clinical staging in the evaluation of cervical carcinoma.

Adult↗
PubMed2002

Infant perceptual and conceptual categorization: the roles of static and dynamic stimulus attributes.

Infants' categorization of animals and vehicles based on static vs. dynamic attributes of stimuli was investigated in five experiments (N=158) using a categorization habituation-of-looking paradigm. In Experiment 1, 6-month-olds categorized static color images of animals and vehicles, and in Experiment 2, 6-month-olds categorized dynamic point-light displays showing only motions of the same animals and vehicles. In Experiments 3, 4, and 5, 6- and 9-month-olds were tested in an habituation-transfer paradigm: half of the infants at each age were habituated to static images and tested with dynamic point-light displays, and the other half were habituated to dynamic point-light displays and tested with static images. Six-month-olds did not transfer. Only 9-month-olds who were habituated to dynamic displays showed evidence of category transfer to static images. Together the findings show that 6-month-olds categorize animals and vehicles based on static and dynamic information, and 9-month-olds can transfer dynamic category information to static images. Transfer, static vs. dynamic information, and age effects in infant categorization are discussed.

Age Factors↗
PubMed1997

Auditory dynamic range derived from the mean rate-intensity function in the cat.

Loudness change is perceived over a far greater range than the discrimination range of single afferents-the "dynamic range problem" [1]. However, earlier neural count models have not fully considered how variability in the dynamic ranges, thresholds, spontaneous rates, and saturation rates of these afferents may affect overall dynamic range. In the present model, all four of these characteristics appear in a logistic rate-intensity function that fits well with sigmoidally firing cat neurons (a double logistic fits well with sloping-saturating units). These equations were averaged statistically over parameter distributions for each of three spontaneous rate groups. An average over these groups (weighted by relative group size) was used to compute discriminability for a patch of basilar membrane. The upper limit on dynamic range for a patch one critical band wide at 8 kHz was 89 dB SPL, less than implied by psychophysics [2]. A two-channel model extended the upper limit by only 3 dB, and splitting the population into four channels did not improve this limit. Seven channels, optimally combined, provided a dynamic range nearly equal to that of an ideal observer that treats each fiber as a separate channel. Moreover, the contribution of sloping-saturating units to discriminability was not as great as popularly expected. Changing the variances of fiber dynamic ranges did not strongly affect overall dynamic range in any of these computations. In sum, when the distributions of neural parameters are taken into account, local pooling can greatly mitigate the "dynamic range problem."

Animals↗
PubMedDate not supplied

Effect of dynamic glutaraldehyde fixation on the viscoelastic properties of bovine pericardial tissue.

We have previously proposed dynamic fixation as an alternative method to fix a porcine aortic heart valve xenograft with better tissue fixation and better preservation of its natural biomechanical properties. Bovine pericardium was fixed under dynamic conditions, low pressures (< 4 mmHg) and low vibration rate (1.2 Hz) in a 0.5% glutaraldehyde phosphate buffer (pH 7.4, 0.2 M). After fixation, tensile testing (i.e. relaxation and stress-strain curves) was performed at low and high extension rates (3 and 30 mm s(-1)) and tissue denaturation temperatures were determined by the hydrothermal isometric tension method. Conventional fresh and statically fixed pericardium were used as controls. In this instance, we found no significant biomechanical differences between the dynamically and statically fixed pericardial tissue (e.g. moduli and stress relaxation). However, differences in tissue extensibility were delineated, since the extensibility of the dynamically fixed tissue was closer to that of the fresh tissue compared to that of the statically fixed tissue. The final relaxation rate of the dynamically fixed tissue (-3.5 +/- 1.0% of stress remaining per log(second)) was similar to that of the statically fixed tissue (-3.2 +/- 0.60% log(s(-1))) and significantly lower than the fresh tissue(-9.5 +/- 1.2% log(s(-1))). The denaturation temperatures of the dynamically fixed pericardial tissue (mean +/- SD) (86.0 +/- 1.2 degrees C) and the statically fixed (85.2 +/- 1.6 degrees C) were similar but significantly higher than that of the untreated (fresh) valves (69.3 +/- 0.4 degrees C). The results suggest a similar degree of internal cross-linking for both statically and dynamically fixed pericardium. Although fundamental structural differences exist between both porcine and bovine xenograft tissue, how these differences contribute to biomechanical differences in the effects of dynamic versus static fixation remain to be explained.

Animals↗
PubMed2002

Estimating auditory neuronal dynamic range using a fitted function.

To obtain the dynamic range of an auditory afferent, the neuron's firing rate is plotted versus stimulus level, and the dynamic range is taken as the difference between the threshold for evoked firing, and the level at which firing rate saturates. Those dynamic range endpoints are typically defined in terms of the neuron's spontaneous firing rate and its maximum firing rate, according to a plurality of schemes, each of which depends on user-chosen sets of numerical criteria. The dynamic ranges predicted by some of these schemes are compared for the first time, and the resulting estimates can differ by a factor of 2. A step can be taken towards standardizing the measurement of neuronal dynamic range, if dynamic range is incorporated into a rate-level function as a parameter. To build this function, it is first assumed that the neuron's rate-level response reaches half its maximum at a level half-way between the threshold and the level at saturation, i.e. at threshold plus half the dynamic range. Then the firing rates at threshold and at threshold plus dynamic range are defined according to the most popular of the endpoint schemes. The resulting equation produces credible estimates of neuronal properties when fitted, and correctly predicts the behavior of the slope of the empirical rate-level plot [McGee, 1983. M.S. thesis, Creighton University; Ohlemiller et al., 1991. J. Acoust. Soc. Am. 90, 274-287]. Thus, despite not being deterministic, the new equation has remarkable predictive power. When two of the rate-level functions are added and weighted, the resulting equation fits sloping-saturating data better than any functions presently employed.

Animals↗
PubMed1998

Quantification of synovistis by MRI: correlation between dynamic and static gadolinium-enhanced magnetic resonance imaging and microscopic and macroscopic signs of synovial inflammation.

Dynamic and static gadolinium-diethylenetriaminepentaacetic acid(Gd-DTPA)-enhanced magnetic resonance imaging (MRI) were evaluated as measures of joint inflammation in arthritis, by a comparison with macroscopic and microscopic signs of synovitis. Furthermore, the importance of the size of the evaluated synovial areas was investigated, as was the optimal time for enhancement measurements. Seventeen rheumatoid arthritis knees and 25 osteoarthritis knees, scheduled for arthroscopy or arthrotomy, were included. Macroscopic and microscopic synovial inflammation as well as nine histologic tissue characteristics were graded at four preselected biopsy sites. Preoperative T1-weighted dynamic fast low angle shot and static spin-echo Gd-enhanced MRI were performed. The dynamic enhancement rate and the static enhancement were measured in the entire synovial membrane of a preselected slice as well as at the four biopsy sites, and compared to synovial pathology. The rate of early enhancement of the total synovial membrane of the preselected slice, determined by dynamic MRI, was highly correlated with microscopic evidence of active inflammation (Spearman p = 0.73; p < 10(-7). Dynamic MRI could distinguish knees with and without synovial inflammation with a high predictive value (0.81-0.90). Moderate and severe inflammation could not be differentiated. The early enhancement rate was correlated with histologic features of active inflammation, particularly vessel proliferation and mononuclear leucocyte infiltration. Dynamic evaluation of small synovial sections at the biopsy sites and static spin-echo MRI resulted in considerably weaker correlations to histologic inflammation than dynamic evaluation of the total synovium. The optimal time for enhancement measurements was one-half to one minute after Gd injection, as the highest correlation coefficients to histologic inflammation were observed in this interval. Dynamic MRI can be used to determine synovial inflammation. Evaluation of large synovial areas one-half to one minute after Gd injection best reflects joint inflammation.

Adult↗
PubMed1998

Self-organization and dynamics reduction in recurrent networks: stimulus presentation and learning.

Freeman's investigations on the olfactory bulb of the rabbit showed that its signal dynamics was chaotic, and that recognition of a learned stimulus is linked to a dimension reduction of the dynamics attractor. In this paper we address the question whether this behavior is specific of this particular architecture, or if it is a general property. We study the dynamics of a non-convergent recurrent model-the random recurrent neural networks. In that model a mean-field theory can be used to analyze the autonomous dynamics. We extend this approach with various observations on significant changes in the dynamical regime when sending static random stimuli. Then we propose a Hebb-like learning rule, viewed as a self-organization dynamical process inducing specific reactivity to one random stimulus. We numerically show the dynamics reduction during learning and recognition processes and analyze it in terms of dynamical repartition of local neural activity.

Journal Article↗
PubMed1995

Regulation of microtubule dynamic instability by tubulin-GDP.

The regulation of the spontaneous transitions between growth and shortening of microtubules is central to the biological function of dynamic instability. Here we examine the effects of controlled amounts of tubulin-GDP (Tu-GDP) on the dynamic properties of microtubules in vitro. The transphosphorylation equilibrium between GTP, GDP, UTP, and UDP in the presence of nucleoside-5'-diphosphate kinase (NDPK) was used to fix the ratio chi D = [Tu-GDP]/([Tu-GTP]) + [Tu-GDP]) in solution. Lower levels of Tu-GDP (chi D < 0.6) produce only a small increase in the apparent critical concentration, Cc'. However, at chi D > 0.6 a dramatic increase in Cc is observed. At steady state of assembly, low levels of Tu-GDP (chi D < 0.5) cause a significant reduction of the dynamic length redistribution of the microtubule population. The principal observable effect of Tu-GDP on the empirical parameters of microtubule dynamic instability is to decrease the duration of individual phases of microtubule growth and shortening, with relatively little effect on the intrinsic rates of growth and shortening. Observations in dark-field video microscopy reveal that the irregularities in the rates of growth (and shortening) are increased in the presence of Tu-GDP. At elevated levels of Tu-GDP, pauses occur frequently during the growth phase, microtubule dynamics cease to conform to a clear two-phase process, and the extents of growth and shortening excursions are strongly attenuated. The experimental results are well reproduced by computer simulation, using mechanisms defined in the lateral cap model for dynamic instability [Martin, S. R., Schilstra, M. J., & Bayley, P. M. (1993) Biophys. J. 65, 578-596], which includes the binding of Tu-GDP to the microtubule end in competition with Tu-GTP. In the presence of Tu-GDP, the growing-state lifetime is significantly attenuated, and the microtubule length versus time excursions simulated by the model show irregularities and complex multistate behavior, including pauses, as observed experimentally. These results suggest that Tu-GDP can modulate microtubule dynamics significantly under conditions where little bulk microtubule disassembly is induced. Tu-GDP therefore appears to exemplify the action of a relatively simple factor with the potential capability for regulation of microtubule dynamics in a cellular environment.

Computer Simulation↗
PubMed2000

Active site dynamics in the lead-dependent ribozyme.

Conformational dynamics are an important property of ribozymes and other RNA molecules but there is currently only limited information on the relationship between dynamics and RNA function. A recent structural study of the lead-dependent ribozyme, known as the leadzyme, showed significant dynamics at the active site and indicated that a structural rearrangement is required for the reaction to proceed from the ground to the transition state. In this work, microsecond-to-millisecond dynamics of the leadzyme are probed by analysis of the power dependence of (13)C NMR relaxation times in the rotating frame (T(1)(rho)). These results revealed a wide range of conformational dynamics for various residues in the leadzyme. For residue A25 in the active site, the power dependence of T(1)(rho) yielded an exchange lifetime similar to that previously measured by line-shape analysis, and provides an important calibration of this T(1)(rho) methodology for probing the dynamics of macromolecules. Strong evidence was also found for a previously suggested dynamic network of hydrogen bonds stabilizing the GAAA tetraloop motif. Within the active site of the leadzyme, internal motions are observed on a wide variety of time scales, suggesting a complex landscape of accessible states, and potential correlations between observed motions and catalytic function are discussed. These results demonstrate that the power dependence of (13)C T(1)(rho) relaxation times provides a valuable method for probing dynamics in nucleic acids.

Adenine Nucleotides↗
PubMed2004

SERCA structural dynamics induced by ATP and calcium.

We have used time-resolved phosphorescence anisotropy (TPA) to probe rotational dynamics of the rabbit skeletal sarcoplasmic reticulum Ca-ATPase (SERCA), to test the hypothesis, generated from X-ray crystallography, that large-scale structural changes are induced by Ca in this system. Previous TPA studies on SERCA used primarily erythrosin 5'-isothiocyanate (ErITC), which binds to the nucleotide-binding domain and inactivates the enzyme. To investigate rotational dynamics of the active enzyme, we labeled SERCA with erythrosin 5'-iodoacetamide, which binds to the phosphorylation domain and has a minimal effect on the calcium-dependent ATPase activity. In the absence of nucleotide and the presence of calcium, TPA results were similar to those observed previously with ErITC, consistent with the global uniaxial rotation of SERCA monomers and oligomers and small amplitude internal protein dynamics. The removal of Ca had only a slight effect, while the addition of adenosine 5'-triphosphate (ATP) increased the amplitude of internal dynamics and changed the probe's orientation, corresponding to tilting of the phosphorylation domain by at least 20 degrees . Ca partially reversed the ATP effects. A nonhydrolyzable ATP analogue had the same effects as ATP, showing that the observed changes were not dependent on active ion transport. Computational analysis indicates that these ligands affect primarily the internal dynamics of the enzyme, with negligible effects on global dynamics and enzyme association. Melittin, which has been shown to aggregate and inhibit SERCA, eliminated the nucleotide-induced internal dynamics and increased the final anisotropy. We propose that (i) the large Ca-dependent structural changes suggested by SERCA crystallography are more dependent on ATP than on Ca and (ii) aggregation-induced inhibition of SERCA is due to the functional coupling between global and internal protein dynamics.

Adenosine Triphosphate↗
PubMed2005

Protein dynamics in living cells.

A protein's structure is most often used to explain its function, but function also depends on dynamics. To date, protein dynamics have been studied only in vitro under dilute solution conditions where solute concentrations are typically less than 10 g/L, yet proteins function in a crowded environment where the solute concentration can exceed 400 g/L. Does the intracellular environment affect protein dynamics? The answer will help in assessing the biological significance of the NMR-derived dynamics data collected to date. We investigated fast protein dynamics inside living Escherichia coli by using in-cell NMR. The backbone dynamics of apocytochrome b5 were quantified using {1H}-15N nuclear Overhauser effect (nOe) measurements, which characterize motions on the pico- to nanosecond time scale. The overall trend of backbone dynamics remains the same in cells. Some of the nOe values differ, but most of the differences track the increased intracellular viscosity rather than a change in dynamics. Therefore, it appears that dilute solution steady-state {1H}-15N nOe measurements provide biologically relevant information about pico- to nanosecond backbone motion in proteins.

Escherichia coli↗
PubMed2005

Backbone and side chain dynamics of mutant calmodulin-peptide complexes.

The mechanism of long-range coupling of allosteric sites in calcium-saturated calmodulin (CaM) has been explored by characterizing structural and dynamics effects of mutants of calmodulin in complex with a peptide corresponding to the smooth muscle myosin light chain kinase calmodulin-binding domain (smMLCKp). Four CaM mutants were examined: D95N and D58N, located in Ca2+-binding loops; and M124L and E84K, located in the target domain-binding site of CaM. Three of these mutants have altered allosteric coupling either between Ca2+-binding sites (D58N and D95N) or between the target- and Ca2+-binding sites (E84K). The structure and dynamics of the mutant calmodulins in complex with smMLCKp were characterized using solution NMR. Analysis of chemical shift perturbations was employed to detect largely structural perturbations. 15N and 2H relaxation was employed to detect perturbations of the dynamics of the backbone and methyl-bearing side chains of calmodulin. The least median squares method was found to be robust in the detection of perturbed sites. The main chain dynamics of calmodulin are found to be largely unresponsive to the mutations. Three mutants show significantly perturbed dynamics of methyl-bearing side chains. Despite the pseudosymmetric location of Ca2+-binding loop mutations D58N and D95N, the dynamic response of CaM is asymmetric, producing long-range perturbation in D58N and almost none in D95N. The mutations located at the target domain-binding site have quite different effects. For M124L, a local perturbation of the methyl dynamics is observed, while the E84K mutation produces a long-range propagation of dynamic perturbations along the target domain-binding site.

Allosteric Site↗
PubMed2006

Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy.

Calmodulin is a central mediator of calcium-dependent signal transduction pathways and regulates the activity of a large number of diverse targets. Calcium-dependent interactions of calmodulin with regulated proteins are of generally high affinity but of quite variable thermodynamic origins. Here we investigate the influence of the binding of the calmodulin-binding domain of calmodulin kinase I on the fast internal dynamics of calcium-saturated calmodulin. NMR relaxation was used to probe motion on the backbone (viewed through the backbone amide NH group) and the side chains (viewed through methyl groups). The distribution of the amplitudes of side chain dynamics is trimodal. The microscopic details of side chain motion are compared with those of a thermodynamically and structurally similar complex of calmodulin with the calmodulin-binding domain of the smooth muscle myosin light chain kinase. While there are no significant differences in backbone dynamics and no net change in methyl-bearing side chain dynamics, a large redistribution of the amplitude of methyl dynamics is observed between the two complexes. The variation in dynamics was largely localized to the heterogeneously dynamic target-binding interface, suggesting that differential dynamics of the binding surface plays a functional role in the high-affinity binding interactions of calmodulin. These results begin to reveal a fundamental role for residual protein entropy in molecular recognition by calmodulin.

Amino Acid Sequence↗
PubMed1998

Backbone and side chain dynamics of uncomplexed human adipocyte and muscle fatty acid-binding proteins.

Adipocyte lipid-binding protein (A-LBP) and muscle fatty acid-binding protein (M-FABP) are members of a family of small ( approximately 15 kDa) cytosolic proteins that are involved in the metabolism of fatty acids and other lipid-soluble molecules. Although highly homologous (65%) and structurally very similar, A-LBP and M-FABP display distinct ligand binding characteristics. Since ligand binding may be influenced by intrinsic protein dynamical properties, we have characterized the backbone and side chain dynamics of uncomplexed (apo) human A-LBP and M-FABP. Backbone dynamics were characterized by measurements of 15N T1 and T2 values and ¿1H¿-15N NOEs. These data were analyzed using model-free spectral density functions and reduced spectral density mapping. The dynamics of methyl-containing side chains were charaterized by measurements of 2H T1 and T1rho relaxation times of 13C1H22H groups. The 2H relaxation data were analyzed using the model-free approach. For A-LBP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 42 methyl groups. For M-FABP, 15N relaxation data were obtained for 111 residues and 2H relaxation data were obtained for 53 methyl groups. The intrinsic flexibilities of these two proteins are compared, with particular emphasis placed on binding pocket residues. There are a number of distinct dynamical differences among corresponding residues between the two proteins. In particular, many residues display greater backbone picosecond to nanosecond and/or microsecond to millisecond time scale mobility in A-LBP relative to M-FABP, including F57, K58, and most residues in alpha-helix 2 (residues 28-35). Variations in the dynamics of this region may play a role in ligand selectivity. The side chains lining the fatty acid binding pocket display a wide range of motional restriction in both proteins. Side chains showing distinct dynamical differences between the two proteins include those of residues 20, 29, and 51. This information provides a necessary benchmark for determining dynamical changes induced by ligand binding and may ultimately lead to an enhanced understanding of ligand affinity and selectivity among fatty acid-binding proteins.

Adipocytes↗