An analytical approach based on Gaussian network model (GNM) is proposed for predicting the rotational dynamics of proteins. The method, previously shown to successfully reproduce X-ray crystallographic temperature factors for a series of proteins is extended here to predict bond torsional mobilities and reorientation of main chain amide groups probed by 15N-H nuclear magnetic resonance (NMR) r...

Çîroka bi navê Leyla û Mecnûn, ya ku di eslê xwe de çîrokeke gelêrî ye, ji aliyê gelek helbestkarên Rojhilata Naverast ve wek menzûm qalibê mesnewiyê hatiye vehonandin. Herçend beriya wî jî ev çîrok farisî hatibe hûnandîn Nîzamiyê Gencewî mesnewîya Mecnûnê li dinyayê navdar berbelav kiriye. Ev çîroka hesbestkaran tirkî kurdî mesnewî honandin. Heman Fuzûlî “Leyla wû Mecnûn” tirkî, Sewadî Di vê x...

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolv...

Amyloid fibril formation by proteins leads to variety of degenerative disorders called amyloidosis. While these disorders are topic of extensive research, effective treatments are still unavailable. Thus in present study, two anti-tuberculosis drugs, i.e., pyrazinamide (PYZ) and D-cycloserine (DCS), also known for treatment for Alzheimer's dementia, were checked for the anti-aggregation and ant...

A protein, designated as Sgl, showing a muramidase lytic activity to the cell wall of the Gram-positive bacterium Micrococcus lysodeikticus was isolated for the first time from plasma of Escherichia coli-immunized fifth instar Schistocerca gregaria. The isolated Sgl was detected as a single protein band, on both native- and SDS-PAGE, has a molecular weight of ∼15.7 kDa and an isoelectric point ...

We have investigated effects of excluded volume interactions on the translational diffusion of hydrodynamically anisotropic molecules. For that, we have performed rigid-body Brownian dynamics simulations of aqueous solutions of hen egg-white lysozyme (HEWL), at concentrations ranging from 1.25 mg/mL to 250 mg/mL and evaluated the lysozyme's self-diffusion. In the long time limit (above 1 μs), t...

In this study, we developed a simple and efficient Bacillus subtilis genome editing method in which targeted gene(s) could be inactivated by single-stranded PCR product(s) flanked by short homology regions and in-frame deletion could be achieved by incubating the transformants at 42°C. In this process, homologous recombination (HR) was promoted by the lambda beta protein synthesized under the c...

We examine temperature dependent picosecond dynamics as a function of structure and function for lysozyme and cytochrome c using temperature dependent terahertz permittivity measurements. A double Arrhenius temperature dependence with activation energies E1 ~ 0.1 kJ/mol and E2 ~10 kJ/mol fits the native state response. The higher activation energy is consistent with the so-called protein dynami...