Depth dependent dynamics in the hydration shell of a protein

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition that corresponds to the onset of amplified atomic fluctuations in proteins. The number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling inversely with depth index at physiological temperatures while the diffusive escape is highly reduced below the transition. A depth independent orientational memory loss is obtained for the average dipole vector of the water molecules within the sphere when the protein is functional. While below the transition temperature, the solvent is in a glassy state, acting as a solid crust around the protein, inhibiting any large scale conformational fluctuations. At the transition, most of the hydration shell unfreezes and water molecules collectively make the protein more flexible.Comment: Journal of Chemical Physics in pres

The limits of filopodium stability

Filopodia are long, finger-like membrane tubes supported by cytoskeletal filaments. Their shape is determined by the stiffness of the actin filament bundles found inside them and by the interplay between the surface tension and bending rigidity of the membrane. Although one might expect the Euler buckling instability to limit the length of filopodia, we show through simple energetic considerations that this is in general not the case. By further analyzing the statics of filaments inside membrane tubes, and through computer simulations that capture membrane and filament fluctuations, we show under which conditions filopodia of arbitrary lengths are stable. We discuss several in vitro experiments where this kind of stability has already been observed. Furthermore, we predict that the filaments in long, stable filopodia adopt a helical shape

Some observations on the behavior of the Langley model rotor blade

The design of the model rotor and the comparative study of coupled beam theory and the finite element analysis performed earlier at the Aerostructures Directorate by Robert Hodges and Mark Nixon is examined. Attention is focused upon two matters: (1) an examination of the small discrepancies between twist angle predictions under pure torque and radial loading, and (2) an assessment of nonclassical effects in bending behavior. The primary objective is understanding, particularly with regard to cause and effect relationships. Understanding, together with the simple, affordable nature of the coupled beam analysis, provides a sound basis for design

The efficiency of fan-pad cooling system in greenhouse and building up of internal greenhouse temperature map

During summer periods, high temperature values that are being formed in greenhouses can greatly influence the efficiency of production workers and also decrease the productivity of plants grown there. A greenhouse production without the cooling systems can be sustained at the desirable level by imposing summer restrictions in the areas with warm climate, and by starting cooling in the areas with cold climate. A statement can be made regarding both utility and efficiency of fan-pad cooling systems that they tend to go up in the areas with low relative air humidity. The present study has been carried out in order to either prove or disprove this statement. We have attempted to create a map of internal greenhouse temperature distribution via determining the system’s efficiency. As a result of this study, it was determined that since air temperature and relative humidity in the air tend to decrease during summer months by using fan-pad cooling system, temperatures in the greenhouse can be consequently lowered down to 10-12°C. Statistical analysis revealed remarkable differences (

Driving calmodulin protein towards conformational shift by changing ionization states of select residues

Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes

The effects of different irrigation methods on root distribution, intensity and effective root depth of young dwarf apple trees

The aim of this study is to determine the effects of different irrigation methods (drip, subsurface drip, surface and under-tree micro sprinkler) on the root distribution, intensity and effective root depth of “Williams Pride” and “Jersey Mac” apple cultivars budded on M9, rapidly grown in Isparta Region. The rootstocks were shallow root system and their root distribution was placed near trunk center and accumulated in diameter of 0.5 m and depth of 0.4 m of soil volume as bowl shape. The root intensity was reduced gradually away from surface and trunk; the root distribution was uniform in all irrigation methods used in the study. In other words, the effect of irrigation methods on root distribution was similar. Generally, the amount of “Williams Pride” root was higher than that of “Jersey Mac” variety. Therefore, these varieties have partial effect on root of the rootstock. Also, effective root depth was increased during the experimental years. Over the years, effective root depths obtained were 28.4 - 36.6 cm in 2006; 32.3 - 42.5 cm in 2007 and 37.1 - 45.2 cm in 2008, respectively. As a result, effective root depths for irrigation of the varieties can be taken as 40 - 45 cm until 3 years old

Anharmonicity and self-similarity of the free energy landscape of protein G

The near-native free energy landscape of protein G is investigated through 0.4 microseconds-long atomistic molecular dynamics simulations in explicit solvent. A theoretical and computational framework is used to assess the time-dependence of salient thermodynamical features. While the quasi-harmonic character of the free energy is found to degrade in a few ns, the slow modes display a very mild dependence on the trajectory duration. This property originates from a striking self-similarity of the free energy landscape embodied by the consistency of the principal directions of the local minima, where the system dwells for several ns, and of the virtual jumps connecting them.Comment: revtex, 6 pages, 5 figure

Effects of different irrigation programs on yield and quality parameters of eggplant (Solanum melongena L.) under greenhouse conditions

This study was carried out to determine the effects of different irrigation programs on yield and quality parameters of eggplant under greenhouse conditions, using Class A pan evaporation calculations and different plant-pan coefficients. Irrigation water was applied through drip irrigation method twice a week during the growing period. Irrigation treatments consisted of five plant-pan coefficients (S1: kcp = nonirrigation, S2: kcp = 0.50, S3: kcp = 0.75, S4: kcp = 1.00 and S5: kcp = 1.25). The amount of irrigation water ranged between 95.2 and 238.7 mm among the treatments. Evapotranspiration (ET) values varied from 93.1 to 466.3 mm for the treatments. The highest yield was obtained from the S3 and S4 treatments. A significant polynomial correlation was obtained between the yield and irrigation water, and between the yield and ET (P < 0.01). This indicated that when irrigation water and ET increased, yield also increased to a certain point. However, when the amount of irrigation water exceeded the plant water requirement, eggplant yield decreased. Yield response factor (Ky) was determined as 0.81. Since Ky < 1, eggplants were not sensitive to water deficiency. In addition, the highest water use efficiency (WUE) and irrigation water use efficiency (IWUE) values were calculated in the S3 (12.9 kgm-3) and S2 (44.2 kgm-3) treatments, while the lowest WUE and IWUE values were calculated in the S5 (7.9 and 15.5 kgm-3) treatment to which the highest irrigation water was applied. This finding indicated that WUE and IWUE values decreased with the increasing irrigation water and ET. These results suggested that S3 (kcp = 0.75) treatment can be the most appropriate irrigation program for eggplant with higher yield and WUE under greenhouse conditions.Key words: Eggplant, yield response factor, water use efficiency, Class A pan, evapotranspiration

Functional modes of proteins are among the most robust ones

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. Moreover, it may also pave the way for the development of methods allowing to predict such motions accurately.Comment: 4 pages, 5 figure

Classical, semiclassical, and quantum investigations of the 4-sphere scattering system

A genuinely three-dimensional system, viz. the hyperbolic 4-sphere scattering system, is investigated with classical, semiclassical, and quantum mechanical methods at various center-to-center separations of the spheres. The efficiency and scaling properties of the computations are discussed by comparisons to the two-dimensional 3-disk system. While in systems with few degrees of freedom modern quantum calculations are, in general, numerically more efficient than semiclassical methods, this situation can be reversed with increasing dimension of the problem. For the 4-sphere system with large separations between the spheres, we demonstrate the superiority of semiclassical versus quantum calculations, i.e., semiclassical resonances can easily be obtained even in energy regions which are unattainable with the currently available quantum techniques. The 4-sphere system with touching spheres is a challenging problem for both quantum and semiclassical techniques. Here, semiclassical resonances are obtained via harmonic inversion of a cross-correlated periodic orbit signal.Comment: 12 pages, 5 figures, submitted to Phys. Rev.