Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-β-glucanase by molecular dynamics simulations

The dependence of some molecular motions in the enzyme 1,3-1,4-β-glucanase from Bacillus licheniformis on temperature changes and the role of the calcium ion in them were explored. For this purpose, two molecular dynamics simulated trajectories along 4 ns at low (300 K) and high (325 K) temperatures were generated by the GROMOS96 package. Several structural and thermodynamic parameters were calculated, including entropy values, solvation energies, and essential dynamics (ED). In addition, thermoinactivation experiments to study the influence of the calcium ion and some residues on the activity were conducted. The results showed the release of the calcium ion, which, in turn, significantly affected the movements of loops 1, 2, and 3, as shown by essential dynamics. These movements differ at low and high temperatures and affect dramatically the activity of the enzyme, as observed by thermoinactivation studies. The first two authors contributed equally to this work     

Is the impact of environmental noise visible in the dynamics of age-structured populations?

Climate change has ignited lively research into its impact on various population-level processes. The research agenda in ecology says that some of the fluctuations in population size are accountable for by the external noise (e.g. weather) modulating the dynamics of populations. We obeyed the agenda by assuming population growth after a resource-limited Leslie matrix model in an age-structured population. The renewal process was disturbed by superimposing noise on the development of numbers in one or several age groups. We constructed models for iteroparous and semelparous breeders so that, for both categories, the population growth rate was matching. We analysed how the modulated population dynamics correlates with the noise signal with different time-lags. No significant correlations were observed for semelparous breeders, whereas for iteroparous breeders high correlations were frequently observed with time-lags of 71 year or longer. However, the latter occurs under red-coloured noise and for low growth rates when the disturbance is on the youngest age group only. It is laborious to find any clear signs of the (red) noise- and age group-specific fluctuations if the disturbance influences older age groups only. These results cast doubts on the possibility of detecting the signature of external disturbance after it has modulated temporal fluctuations in age-structured populations.     

Influence of orthosteric ligand binding on the conformational dynamics of the β-2-adrenergic receptor via essential dynamics sampling simulation

The influence of the binding of orthosteric ligands on the conformational dynamics of the β-2-adrenoreceptor was identified using the molecular dynamics method. It was found that there was a small fraction of active states of the receptor in its apo (ligand free) ensemble. An analysis of the MD trajectories indicated that this spontaneous activation of the receptor was accompanied by the motion of its VI helix. Thus, the receptor’s constitutive activity is a direct result of its conformational dynamics. On the other hand, the binding of the full agonist resulted in a significant shift in the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized receptor in its inactive state. It is likely that the binding of the inverse agonists might be a universal method of the constitutive activity inhibition. Our results indicate that ligand binding redistributes preexisting conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux Model), rather than causes an induced fit. Therefore, the ensemble of the biologically relevant receptors conformations has been encoded in its spatial structure and individual conformations from that ensemble and might be used by the cell according to the physiological behavior.     

Solution dynamics of the 1,2,3,4,6-penta-O-acetyl-α-D-idopyranose ring

The anticoagulant properties of heparin are thought to derive from the inhibition of thrombin and other coagulation-related proteases by the binding of heparin to cofactors such as antithrombin III and heparin cofactor II. The apparent minimum native heparin sequence which can bind to antithrombin III is a highly sulfated pentasaccharide which contains a 2-O-sulfo-α-L-idopyranosyluronic acid residue. The idopyranosyl residue has the unusual property of existing in the solution state as a mixture of ring conformers. Whereas most hexopyranose sugars exist as a single chair conformer (eg D-glucose exists overwhelmingly as a 4C1 chair), the idopyranosyl ring is known to rapidly exchange between at least two and often more distinct conformations, depending on type and number of substituents (hydroxyl, carboxyl, sulfate, etc.) and solvent conditions (solvent pH, salt concentration, temperature). It is believed that this flexibility of the idopyranosyl residue in heparin is related to its binding specificity. In the past, coupling constants and molecular dynamics have been used to estimate the relative populations of conformers in iduronate and related compounds. Here we report extensive NMR measurements, including line shape analysis, T1ρ measurements, T1 and NOE measurements and spectral density mapping, which have been used to study the dynamics of conformer interconversion in model compounds related to idose and glucose. The findings presented here indicate that 1,2,3,4,6-peneta-O-acetyl-α-D-idopyranose can be reasonably well described as existing in a two-state equilibrium consisting of the 4C1 and 0S2 conformers. 13C NMR line shape analysis yields a ΔH+ of 40 kJ mol-1 and a ΔS‡ of 31 J mol-1 K-1 for the 4C1→0S2 interconversion and a ΔH‡ of 31 kJ mol-1 and a ΔS‡ of 13 J mol-1K-1 for the 0S2→4C1 interconversion. This corresponds to exchange rates of 22 and 128 MHz, respectively, at room temperature. This revised version was published online in November 2006 with corrections to the Cover Date.     

Sticking together? Falling apart? Exploring the dynamics of the interactome

Advances in techniques for the study of protein-protein interactions have dramatically improved our understanding of the interactome. However, we know little about the dynamics of this complex system. To better understand the dynamics of the interactome, it is important to consider what happens when single proteins are perturbed. Changes in protein abundance and post-translational modification can function as switches in the interactome, affecting protein-complex assembly and function. Changes in protein sequence or a dramatic increase in abundance might cause a promiscuous gain of interactions. These effects are not identical for all proteins and will differ depending on the number and type of interaction partners that a protein has.     

Characterization of the internal dynamics and conformational space of zinc-bound amyloid β peptides by replica-exchange molecular dynamics simulations

Amyloid β (Aβ) peptides and metal ions have been associated with the pathogenesis of Alzheimer’s disease. The conformational space of Aβ fragments of different length with and without binding of metal ions has been extensively investigated by replica-exchange molecular dynamics (REMD) simulation. However, only trajectories extracted at relatively low temperatures have been used for this analysis. The capability of REMD simulations to characterize the internal dynamics of such intrinsically disordered proteins (IDPs) as Aβ has been overlooked. In this work, we use an approach recently developed by Xue and Skrynnikov (J Am Chem Soc 133:14614–14628, 2011) to calculate NMR observables, including ¹⁵N relaxation rates and ¹⁵N–¹H nuclear Overhauser enhancement (NOE), from the high-temperature trajectory of REMD simulations for zinc-bound Aβ peptides. The time axis of the trajectory was rescaled to correct for the effect of the high temperature (408 K) compared with the experimental temperature (278 K). Near-quantitative agreement between simulated values and experimental results was obtained. When the structural properties and free-energy surfaces of zinc-bound Aβ_(1–40) and Aβ_(1–42) were compared at the physiological temperature 310 K it was found that zinc-bound Aβ_(1–42) was more rigid than Aβ_(1–40) at the C terminus, and its conformational transitions were also more preferred. The self-consistent results derived from trajectories at high and low temperatures demonstrate the capability of REMD simulations to capture the internal dynamics of IDPs.     

Computational analysis of the oscillatory dynamics in the processes of CO₂ assimilation and photorespiration

The computational analysis of the model system consisting of the processes of CO₂ assimilation and photorespiration shows the appearance of sustained oscillations in the system which might reflect their presence in photosynthesizing cells. Concentrations of CO₂ and O₂ oscillate in opposite phases causing Rubisco switching continuously between the carboxylase (CO₂ assimilation) and the oxygenase (photorespiration) reactions. The results of modeling are consistent with carbon isotopic and other observed data. They show that the oscillation period varies from about 1 s to 3 s depending on the values of parameters taken. Too high concentrations of O₂ suppress the oscillations.     

Structural dynamics of the amyloid β-protein monomer folding nucleus

Alzheimer's disease (AD) is linked to the aberrant assembly of the amyloid β-protein (Aβ). The (21)AEDVGSNKGA(30) segment, Aβ(21-30), forms a turn that acts as a monomer folding nucleus. Amino acid substitutions within this nucleus cause familial forms of AD. To determine the biophysical characteristics of the folding nucleus, we studied the biologically relevant acetyl-Aβ(21-30)-amide peptide using experimental techniques (limited proteolysis, thermal denaturation, urea denaturation followed by pulse proteolysis, and electron microscopy) and computational methods (molecular dynamics). Our results reveal a highly stable foldon and suggest new strategies for therapeutic drug development.     

Biomanipulation and food-web dynamics — the importance of seasonal stability

Responses of phytoplankton biomass were monitored in pelagic enclosures subjected to manipulations with nutrients (+N/P), planktivore roach (Rutilus rutilus) and large grazers (Daphnia) in 18 bags during spring, summer and autumn in mesotrophic Lake Gjersjøen. In general, the seasonal effects on phytoplankton biomass were more marked than the effects of biomanipulation. Primary top-down effects of fish on zooplankton were conspicuous in all bags, whereas control of phytoplankton growth by grazing was observed only in the nutrient-limited summer situation. The effect of nutrient additions was pronounced in summer, less in spring and autumn; additions of fish gave the most pronounced effect in spring. The phytoplankton/zooplankton biomass ratio remained high (10–100) in bags with fish, with the highest ratios in combination with fertilization. The ratio decreased in bags without fish to<2 in most bags, but a real grazing control was only observed in bags with addition ofDaphnia. No direct grazing effects could be observed on the absolute or relative biomass of cyanobacteria (mainlyOscillatoria agardhii). The share of cyanobacteria in total phytoplankton biomass was lowest in summer (7–26%), higher in spring (39–63%) and more than 90% in the autumn experiment. The development of the cyanobacterial biomass was rather synchronous in all bags in all the three experiments. A high biomass ofDaphnia gave no increase in the pool of dissolved nutrients in spring, a slight increase in summer and a pronounced increase in autumn. While a strong decrease in the P/C-cell quota of the phytoplankton was observed from spring to autumn, no effect of grazing or nutrient release could be related to this P/C-status. The experiments indicate that such systems, with high and stable densities of inedible cyanobacteria, are rather insensitive to short-term (3–4 weeks) biomanipulation efforts. This is supported by observations on the long-term development of the lake.

     

Pocket analysis of the full-length cholix toxin. An assessment of the structure–dynamics of the apo catalytic domain

Cholix toxin from Vibrio cholerae is the third member of the diphtheria toxin (DT) group of mono-ADP-ribosyltransferase (mART) bacterial toxins. It shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae DT. Cholix toxin is an important model for the development of antivirulence approaches and therapeutics against these toxins from pathogenic bacteria. Herein, we have used the high-resolution X-ray structure of full-length cholix complexed with NAD⁺ to describe the properties of the NAD⁺-binding pocket at the residue level, including the role of crystallographic water molecules in the NAD⁺ substrate interaction. The full-length apo cholix structure is used to describe the putative NAD⁺-binding site(s) and to correlate biochemical with crystallographic data to study the stoichiometry and orientation of bound NAD⁺ molecules. We quantitatively describe the NAD⁺ substrate interactions on a residue basis for the main 22 pocket residues in cholix_f, a glycerol and 5 contact water molecules as part of the recognition surface by the substrate according to the conditions of crystallization. In addition, the dynamic properties of an in silico version of the catalytic domain were investigated in order to understand the lack of electronic density for one of the main flexible loops (R-loop) in the pocket of X-ray complexes. Implications for a rational drug design approach for mART toxins are derived.     

“Neutral theory” and the dynamics of the evolution of “Modern” human morphology

There is a widespread assumption, even among those who reject the Synthetic Theory of Evolution, that the form of “modern”Homo sapiens is somehow superior to that of archaicHomo sapiens (Tattersall 2000). Those who accept the general outlook of evolutionary biology also tend to assume that “modern” form emerged because it was selected for, which also implies that it was better than that which preceded it. However, after years of using craniofacial measurements to compare human populations, I finally came to realize that, with only a few exceptions, the dimensions measured have no relation to differences in adaptation (Brace 1989, 1996, 2000; Brace et al., 1993). Elsewhere the conclusion has been supported that what is shown by craniometrics is selectively neutral on the average (Relethford 2002). With the documentation that approximately 95% of the genome is not functional, molecular genetics has proved to be useful in documenting the length of time of separation of related human populations by investigating the differences that have accumulated in the neutral parts of the genome. Not surprisingly, the picture revealed by the study of genetic differences is very similar to the one revealed by the study of craniometric differences (Brace et al., 2001). For this reason, the logic behind the “neutral theory” in molecular genetics is very similar to that applied to what happens to morphological characteristics when selection ceases (Brace 1963; Kimura 1968). The difference is that random changes in the neutral part of the genome have no other consequences. However, random changes in the genes that produce specific aspects of morphology will be visible even when selection is no longer controlling the particular trait in question. From an assessment of what random changes in genes controlling morphological traits are likely to do, it follows that the most likely change will probably be a reduction in the trait in question, i.e. the Probable Mutation Effect will produce structural reduction. When survival in the temperate zone during the last glaciation dependend on “obligatory cooking”, one of the unintended consequences was a reduction in the selective pressures maintaining a Middle Pleistocene-sized dentition. The result was a gradual reduction in tooth size and a conversion, of a Neanderthal-sized face into one of “modern” dimensions. The manufacture and use of string for snares and nets similarly reduced the selective pressures maintaining post-cranial levels of robustness and muscularity. The reduction in the latter resulted in the emergence of moderm post-cranial robustness out of what had been a Neanderthal level,in situ wherever the technology can be documented and without any need for invasions and replacements.     

Molecular dynamics simulations of the effect of the G-protein and diffusible ligands on the β2-adrenergic receptor

G-protein-coupled receptors have extraordinary therapeutic potential as targets for a broad spectrum of diseases. Understanding their function at the molecular level is therefore essential. A variety of crystal structures have made the investigation of the inactive receptor state possible. Recently released X-ray structures of opsin and the β₂-adrenergic receptor (β₂AR) have provided insight into the active receptor state. In addition, we have contributed to the crystal structure of an irreversible agonist-β₂ adrenoceptor complex. These extensive studies and biophysical investigations have revealed that agonist binding leads to a low-affinity conformation of the active state that is suggested to facilitate G-protein binding. The high-affinity receptor state, which promotes signal transduction, is only formed in the presence of both agonist and G-protein. Despite numerous crystal structures, it is not yet clear how ligands tune receptor dynamics and G-protein binding. We have now used molecular dynamics simulations to elucidate the distinct impact of agonist and inverse agonist on receptor conformation and G-protein binding by investigating the influence of the ligands on the structure and dynamics of a complex composed of β₂AR and the C-terminal end of the Gα_s subunit (GαCT). The simulations clearly showed that the agonist isoprenaline and the inverse agonist carazolol influence the ligand-binding site and the interaction between β₂AR and GαCT differently. Isoprenaline induced an inward motion of helix 5, whereas carazolol blocked the rearrangement of the extracellular part of the receptor. Moreover, in the presence of isoprenaline, β₂AR and GαCT form a stable interaction that is destabilized by carazolol.     

Going with the wind – Adaptive dynamics of plant secondary meristems

The developmental plasticity of organisms is a natural consequence of adaptation. Classical approaches targeting developmental processes usually focus on genetics as the essential factor underlying phenotypic differences. However, such differences are often based on the inherent plasticity of developmental programs. Due to their dependence on environmental stimuli, plants represent ideal experimental systems in which to dissect the contribution of genetic and environmental variation to phenotypic plasticity. An evident example is the vast repertoire of growth forms observed in plant shoot systems. A fundamental factor underlying the broadness of this repertoire is the activity of secondary meristems, namely the axillary meristems that give rise to side shoots, and the cambium essential for stem thickening. Differential activities of both meristem types are crucial to the tremendous variation seen in higher plant architecture. In this review, we discuss the role of secondary meristems in the adaptation of plant growth forms, and the ways in which they integrate environmental input. In particular, we explore potential approaches for dissecting the degree to which this flexibility and its consequences for plant architecture is genetically predetermined and how much it represents an adaptive value.     

A molecular dynamics simulation study of the effect of water–graphene interaction on the properties of confined water

The role of water in determining the structure and stability of biomacromolecules has been well studied. In this work, molecular dynamics simulations have been applied to investigate the effect of surface hydrophobicity on the structure and dynamics of water confined between graphene surfaces. In order to evaluate this effect, we apply various attractive/repulsive water–graphene interaction potentials (hydrophobicity). The properties of confined water are studied by applying a purely repulsive interaction potential between water–graphene (modelled as a repulsive r^?12 potential) and repulsive–attractive forces (modelled as an LJ(12-6) potential). Compared to the case of a purely repulsive graphene–water potential, the inclusion of repulsive–attractive forces leads to formation of sharp peaks for density and the number of hydrogen bonds. Also, it was found that repulsive–attractive graphene–water potential caused slower hydrogen bonds dynamics and restricted the diffusion coefficient of water. Consequently, it was found that hydrogen bond breakage and formation rate with the repulsive r^?12 potential model, will increase compared to the corresponding water confined with the LJ(12-6) potential.     

Molecular dynamics investigation of the ω-current in the Kv1.2 voltage sensor domains

Voltage sensor domains (VSD) are transmembrane proteins that respond to changes in membrane voltage and modulate the activity of ion channels, enzymes, or in the case of proton channels allow permeation of protons across the cell membrane. VSDs consist of four transmembrane segments, S1-S4, forming an antiparallel helical bundle. The S4 segment contains several positively charged residues, mainly arginines, located at every third position along the helix. In the voltage-gated Shaker K(+) channel, the mutation of the first arginine of S4 to a smaller uncharged amino acid allows permeation of cations through the VSD. These currents, known as ω-currents, pass through the VSD and are distinct from K(+) currents passing through the main ion conduction pore. Here we report molecular dynamics simulations of the ω-current in the resting-state conformation for Kv1.2 and for four of its mutants. The four tested mutants exhibit various degrees of conductivity for K(+) and Cl(-) ions, with a slight selectivity for K(+) over Cl(-). Analysis of the ion permeation pathway, in the case of a highly conductive mutant, reveals a negatively charged constriction region near the center of the membrane that might act as a selectivity filter to prevent permeation of anions through the pore. The residues R1 in S4 and E1 in S2 are located at the narrowest region of the ω-pore for the resting state conformation of the VSD, in agreement with experiments showing that the largest increase in current is produced by the double mutation E1D and R1S.