the determination of gyration radius is a strong research for configuration of a macromolecule. italso reflects molecular compactness shape. in this work, to characterize the behavior of theprotein, we observe quantities such as the radius of gyration and the average energy. we studiedthe changes of these factors as a function of temperature for acetylcholine receptor protein in gasphase with n...

In recent work, a new method for using the outputs of molecular dynamics simulations to generate enhanced inputs for EXAFS analysis of nanoparticles was reported. Although currently limited to the first coordination shell, the method was demonstrated to improve both the quality of the fit, and the cross-correlation of the EXAFS data with that from TEM and XRD. Here we discuss further the justif...

disposition and transportation of anticancer drugs by human serum albumin (hsa) affects their bioavailability, distribution and elimination. in this study, the interaction of a set of anticancer drugs with hsa was investigated by molecular dynamics and molecular docking simulations. the drugs' activities were analyzed according to their docking scores, binding sites and structural descriptors. ...

The complete 3D nonlinear dynamic problem of extensible, flexible risers conveying fluid is considered. For describing the dynamics of the system, the Newtonian derivation procedure is followed. The velocity field inside the pipe formulated using hydrostatic and Bernoulli equations. The hydrodynamic effects of external fluids are taken into consideration through the nonlinear drag forces in var...

Human immunodeficiency virus type 1 (HIV-1) protease inhibitors comprise an important class of drugs used in HIV treatments. However, mutations of protease genes accelerated by low fidelity of reverse transcriptase yield drug resistant mutants of reduced affinities for the inhibitors. This problem is considered to be a serious barrier against HIV treatment for the foreseeable future. In this st...

body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (i). 348 mhz 1h nmr spectra of (i) have been investigated over the temperature range of 25° to -160°c. two conformation processes affect the 1h nmr spectrum of (i). iterative force-field calculations on the conformations and conformational interconversion paths of (i) give results consisten...

potassium channels allow potassium flux and are essential for the generation of electric current acrossexcitable membranes. potassium channels are also the targets of various intracellular controlmechanisms; such that the suboptimal regulation of channel function might be related to pathologicalconditions. realistic studies of ion current in biologic channels present a major challenge for compu...

In translation, elongation factor Tu (EF-Tu) molecules deliver aminoacyl-tRNAs to the mRNA-programmed ribosome. The GTPase activity of EF-Tu is triggered by ribosome-induced conformational changes of the factor that play a pivotal role in the selection of the cognate aminoacyl-tRNAs. We present a 6.7-A cryo-electron microscopy map of the aminoacyl-tRNA x EF-Tu x GDP x kirromycin-bound Escherich...

The light-harvesting apparatus of the purple bacterial photosynthetic unit consists of a pool of peripheral light-harvesting complexes that transfer excitation energy to a reaction center (RC) via the surrounding pigment-protein complex LH1. Recent electron microscopy and atomic force microscopy studies have revealed that RC-LH1 units of Rhodobacter sphaeroides form membrane-bending dimeric com...