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81.
Apoflavodoxin from the sulfate reducing bacteria Desulfovibrio desulfuricans is a small, acidic protein with a net charge of -19 at neutral pH. Here, we show that monovalent cations in biologically relevant amounts have dramatic effects on apoflavodoxin stability. The effect is largest for Gdm(+) and decreases as a function of increased cation charge density (Gdm(+)>NH(4)(+)K(+) approximately Cs(+) approximately Na(+)>Li(+)). A linear correlation of stabilizing effects with cation hydration properties suggests an important role of dehydration in efficient cation interaction with the protein. The effects on stability are due to preferential binding of one cation to native apoflavodoxin and results in an increase in thermal midpoint of 20 degrees C and the free energy of unfolding (at 20 degrees C) increases fivefold. Tuning of biophysical properties (such as folding and ligand/cofactor binding) of acidic proteins by cation binding may be important in vivo. 相似文献
82.
应用小波熵分析大鼠脑电信号的动态变化特性 总被引:19,自引:0,他引:19
应用小波熵(一种新的信号复杂度测量方法)分析大鼠在不同生理状态下脑电复杂度的动态时变特性。采用慢性埋植电极记录自由活动大鼠的皮层EEG,使用多分辨率小波变换将EEG信号分解为δ、θ、α和β四个分量,求得随时间变化的小波熵。结果表明:在清醒、慢波睡眠和快动眼睡眠三种生理状态下,EEG的小波熵之间存在显著差别,并且在不同时期其值与各个分解分量之间具有不同的关系,其中,慢波睡眠期小波熵还具有较明显的变化节律,反映了EEG微状态中慢波和纺锤波的互补性。由此可见,小波熵既能区别长时间段EEG复杂度之间的差别,又能反映EEG微状态的快速变化特性。 相似文献
83.
Fei Li Milind Gangal Celina Juliano Elliot Gorfain Susan S Taylor David A Johnson 《Journal of molecular biology》2002,315(3):459-469
While there is no question that ligands can induce large-scale domain movements that narrow (close) the active-site cleft of the catalytic (C) subunit of cAMP-dependent protein kinase (cAPK), the results from small-angle X-ray scattering, protein footprinting, and thermostability studies are inconsistent with regard to which ligands induce these movements. This inconsistency suggests a greater complexity of cAPK conformational dynamics than is generally recognized. As an initial step to study this issue in relation to the catalysis, a new method to measure cAPK domain closure was developed, and the state of domain closure and the local segmental flexibility at major steps of the cAPK catalytic cycle were examined with site-directed labeling and fluorescence spectroscopy. To achieve this, a C subunit mutant (F239C/C199A) was engineered that allowed for fluorescein 5-maleimide (donor) conjugation of F239C in the large lobe and tetramethylrhodamine (acceptor) conjugation of C343 in the small lobe. Domain closure was assessed as an increase in the efficiency of energy transfer between donor and acceptor. The anisotropy decay of fluoroscein 5-maleimide, conjugated to a site of cysteine substitution (K81C) in the small lobe of the C subunit was used to assess the local backbone flexibility around the B helix. The effects of substrate/pseudosubstrate (ATP and PKI(5-24)), a fragment of protein kinase inhibitor) and products (ADP and phosphorylated PKS) on domain closure and B helix flexibility were measured. The results show that domain closure is not tightly coupled to the flexibility around K81C. Moreover, although substrates/pseudosubstrate and products independently close the active-site cleft, only the substrates substantially decreased the backbone flexibility around the B helix. Because this order-to-disorder transition coincides with the phosphoryl transfer transition, the results suggest the existence of an internal entropy contribution to catalysis. 相似文献
84.
Aim Species distribution models are invaluable tools in biogeographical, ecological and applied biological research, but specific concerns have been raised in relation to different modelling techniques in terms of their validity. Here we compare two fundamentally different approaches to species distribution modelling, one based on simple occurrence data where the lack of an ecological framework has been criticized, and the other firmly based in socio‐ecological theory but requiring highly detailed behavioural information that is often limited in availability. Location (Sub‐Saharan) Africa. Methods We used two distinct techniques to predict the realized distribution of a model species, the vervet monkey (Cercopithecus aethiops Linnaeus, 1758). A maximum entropy model was produced taking 13 environmental variables and presence‐only data from 174 sites throughout Africa as input, with an additional 58 sites retained to test the model. A time‐budget model considering the same environmental variables was constructed from detailed behavioural data on 20 groups representing 14 populations, with presence‐only data from the remaining 218 sites reserved to test model predictions on vervet monkey occurrence. Both models were further validated against a reference species distribution map as drawn up by the African Mammals Databank. Results Both models performed well, with the time budget and maximum entropy algorithms correctly predicting vervet monkey presence at 78.4% and 91.4% of their respective test sites. Similarly, the time‐budget model correctly predicted presence and absence at 87.4% of map pixels against the reference distribution map, and the maximum entropy model achieved a success rate of 81.8%. Finally, there was a high level of agreement (81.6%) between the presence–absence maps produced by the two models, and the environmental variables identified as most strongly driving vervet monkey distribution were the same in both models. Main conclusions The time‐budget and maximum entropy models produced accurate and remarkably similar species distribution maps, despite fundamental differences in their conceptual and methodological approaches. Such strong convergence not only provides support for the credibility of current results, but also relieves concerns about the validity of the two modelling approaches. 相似文献
85.
Mutual information and entropy transfer analysis employed on two inactive states of human beta-2 adrenergic receptor (β2-AR) unraveled distinct communication pathways. Previously, a so-called “highly” inactive state of the receptor was observed during 1.5 microsecond long molecular dynamics simulation where the largest intracellular loop (ICL3) was swiftly packed onto the G-protein binding cavity, becoming entirely inaccessible. Mutual information quantifying the degree of correspondence between backbone-Cα fluctuations was mostly shared between intra- and extra-cellular loop regions in the original inactive state, but shifted to entirely different regions in this latest inactive state. Interestingly, the largest amount of mutual information was always shared among the mobile regions. Irrespective of the conformational state, polar residues always contributed more to mutual information than hydrophobic residues, and also the number of polar-polar residue pairs shared the highest degree of mutual information compared to those incorporating hydrophobic residues. Entropy transfer, quantifying the correspondence between backbone-Cα fluctuations at different timesteps, revealed a distinctive pathway directed from the extracellular site toward intracellular portions in this recently exposed inactive state for which the direction of information flow was the reverse of that observed in the original inactive state where the mobile ICL3 and its intracellular surroundings drove the future fluctuations of extracellular regions. 相似文献
86.
A simple method of making a type of orthogonal contrasts among treatments for unbalanced two-way classification data has been described. The method begins with the direct use of absorbing equations, derived from normal equations. Then it is shown that the single components of the treatment sum of squares, adjusted for blocks, are independently distributed. 相似文献
87.
88.
C. D. Mathers 《Biometrical journal. Biometrische Zeitschrift》1984,26(1):33-38
The heterogeneous Poisson process with discretized exponential quadratic rate function is considered. Maximum likelihood estimates of the parameters of the rate function are derived for the case when the data consists of numbers of occurrences in consecutive equal time periods. A likelihood ratio test of the null hypothesis of exponential quadratic rate is presented. Its power against exponential linear rate functions is estimated using Monte Carlo simulation. The maximum likelihood method is compared with a log-linear least squares techniques. An application of the technique to the analysis of mortality rates due to congenital malformations is presented. 相似文献
89.
S. A. FRANK 《Journal of evolutionary biology》2009,22(8):1563-1585
We typically observe large‐scale outcomes that arise from the interactions of many hidden, small‐scale processes. Examples include age of disease onset, rates of amino acid substitutions and composition of ecological communities. The macroscopic patterns in each problem often vary around a characteristic shape that can be generated by neutral processes. A neutral generative model assumes that each microscopic process follows unbiased or random stochastic fluctuations: random connections of network nodes; amino acid substitutions with no effect on fitness; species that arise or disappear from communities randomly. These neutral generative models often match common patterns of nature. In this paper, I present the theoretical background by which we can understand why these neutral generative models are so successful. I show where the classic patterns come from, such as the Poisson pattern, the normal or Gaussian pattern and many others. Each classic pattern was often discovered by a simple neutral generative model. The neutral patterns share a special characteristic: they describe the patterns of nature that follow from simple constraints on information. For example, any aggregation of processes that preserves information only about the mean and variance attracts to the Gaussian pattern; any aggregation that preserves information only about the mean attracts to the exponential pattern; any aggregation that preserves information only about the geometric mean attracts to the power law pattern. I present a simple and consistent informational framework of the common patterns of nature based on the method of maximum entropy. This framework shows that each neutral generative model is a special case that helps to discover a particular set of informational constraints; those informational constraints define a much wider domain of non‐neutral generative processes that attract to the same neutral pattern. 相似文献
90.
Marko Popovic 《Journal of biological education》2018,52(3):294-300
All living structures, from archaea to human, are open thermodynamic systems analysed through nonequilibrium thermodynamics. Nonequilibrium thermodynamics is a field with important applications to life sciences, which is very often left out of life science courses. A three-step method is suggested to make an easy introduction of nonequilibrium thermodynamics to life science students. The first step is to introduce the Prigogine equation dS = deS + diS, and explain the meaning of the entropy exchange with the surroundings deS and internal entropy generation in the system diS. The second step is to show that the Prigogine equation is connected to the equilibrium thermodynamics already known to students. This can be done by deriving the Clausius inequality dS ≥ dq/T, from the Prigogine equation applied to reversible and irreversible processes in closed systems. Reversible and irreversible processes are discussed separately and the results are then combined into the Clausius inequality. The third step is to introduce the fact that the Prigogine equation has a variety of applications in life sciences. This would give the students an opportunity to understand the entropy balance of physiological processes in cells and organisms. The import and accumulation of entropy, entropy generation, and entropy export could be made easier for students to adopt. 相似文献