Coupling Between Lysozyme and Glycerol Dynamics: Microscopic Insights from Molecular-Dynamics Simulations

We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics. (c) 2005 American Institute of Physics

Role of Hydrogen Bonds in the Fast Dynamics of Binary Glasses of Trehalose and Glycerol: a Molecular Dynamics Simulation Study

Trehalose-glycerol mixtures are known to be effective in the long time preservation of proteins. However, the microscopic mechanism of their effective preservation abilities remains unclear. In this article we present a molecular dynamics simulation study of the short time, less than 1 ns, dynamics of four trehalose-glycerol mixtures at temperatures below the glass transition temperature. We found that a mixture of 5% glycerol and 95% trehalose has the most suppressed short time dynamics (fast dynamics). This result agrees with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured via neutron scattering, and correlates with the experimentally observed enhancement of the stability of some enzymes at this particular concentration. Our microscopic analysis suggests. that the formation of a robust intermolecular hydrogen bonding network is most effective at this concentration and is the main mechanism for the suppression of the fast dynamics. (c) 2005 American Insititute of Physics

Coupling Between Lysozyme and Trehalose Dynamics: Microscopic Insights from Molecular-Dynamics Simulations

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems. (c) 2006 American Institute of Physics

How a Vicinal Layer of Solvent Modulates the Dynamics of Proteins

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk solvent at low temperatures, and communicates with it through a vicinal layer at physiological temperatures. A linear viscoelastic model elucidates the less-than-expected increase in the relaxation times observed in the backbone dynamics of the protein. The model further explains the increase in the flexibility of the protein once the transition takes place and the differences in the flexibility under the different solvent environments. Coupling between the vicinal layer and the protein fluctuations is necessary to interpret these observations. The vicinal layer is postulated to form once a threshold for the volumetric fluctuations in the protein to accommodate solvents of different sizes is reached. Compensation of entropic-energetic contributions from the protein-coupled vicinal layer quantifies the scaling of the dynamical transition temperatures in various solvents. The protein adapts different conformational routes for organizing the required coupling to a specific solvent, which is achieved by adjusting the amount of conformational jumps in the surface-group dihedrals

Evaluation of morphologi̇cal, yield and quality characters of bread wheat double haploid genotypes

Çalışmada farklı dönemlerde ıslah edilmiş ekmeklik buğday çeşitleri ve Namık Kemal Üniversitesi Ziraat Fakültesi Tarla Bitkileri Bölümü Tarafından kombinasyon ıslahı ile elde edilen F2 döllerinden anter kültürü ile geliştirilen double haploid hatlar ve bölgede yetiştirilen çeşitler materyal olarak kullanılmştır. Çalışmada fiziksel özellikler olarak; bitki boyu, başak uzunluğu, başaktaki dane sayısı, başak dane ağırlığı, başak ağırlığı, dane verimi ve başaklanma gün sayısı incelenmiş ve bunların hepsi de istatistiki olarak önemli bulunmuştur. Araştırılan özellikler bakımından kalite analizlerinde ise nem, süne zararı, embriyo kararması, protein oranı, gluten ve gluten indeks, sedimantasyon ve bekletilmiş sedimantasyon incelenmiş ve bu özelliklerin tamamı istatistiki olarak önemli bulunmuştur. Yapılan çalışmada gerek kalite gerekse fiziksel özellikler bakımından istenilen değerler veren double haploid melez Flamura85/Golia hattı tespit edilmiştir.In the study different periods have been breeding bread wheat varieties and Namık Kemal University established using the Faculty of Agronomy Department developed by anther culture of the resulting F2 progeny with a combination of breeding by double haploid as materials and their physical and quality characteristics of the double haploid lines derived from hybrids were examined. In the study the physical properties; plant height, spike length, grain piece in spike, spike grain weight, spike weight, grain yield and heading examined the number of days and all of them were statistically significant as well. In terms of quality of analysis investigated the characteristics of moisture, stink bug damage, embryo darkening, protein content, gluten and gluten index, sedimentation and suspended sedimentation was examined and found to be statistically significant all of these characters. In this study, desired values of the terms of quality and psysical properties that are resulted; hybrid double haploid line Flamura85/Golia was determined