Drug–protein interaction with Vpu from HIV-1: proposing binding sites for amiloride and one of its derivatives

Vpu is an 81-amino-acid auxiliary protein of the genome of HIV-1. It is proposed that one of its roles is to enhance particle release by self-assembling to form water-filled channels enabling the flux of ions at the site of the plasma membrane of the infected cell. Hexamethylene amiloride has been shown to block Vpu channel activity when the protein is reconstituted into lipid bilayers. In a docking approach with monomeric, pentameric and hexameric bundle models of Vpu corresponding to the transmembrane part of the protein, a putative binding site of hexamethylene amiloride is proposed and is compared with the site for the nonpotent amiloride. The binding mode for both ligands is achieved by optimizing hydrogen bond interactions with serines. Binding energies and binding constants are the lowest for protonated hexamethylene amiloride in the pentameric bundle. Figure The proposed binding site of the Vpu channel blocker hexamethylene amiloride within the lumen of the Vpu bundle. The bundle is a homo-pentamer with each monomer consisting of the first 32 amino acids of Vpu including the transmembrane part of the protein which is encoded by HIV-1. The bundle atoms are shown in their van der Waals representation and the helix backbone in a ribbon representation. Residues Trp-23 and Ser-24 are highlighted as sticks. Hexamethylene amiloride is shown in yellow (C atoms) and blue (N atoms)     

Polar Mixing Optical Phonon Spectra in Wurtzite GaN Cylindrical Quantum Dots： Quantum Size and Dielectric Effects

The interface-optical-propagating （IO-PR） mixing phonon modes of a quasi-zero-dimensional （QOD） wurtzite cylindrical quantum dot （QD） structure are derived and studied by employing the macroscopic dielectric continuum model. The analytical phonon states of IO-PR mixing modes are given. It is found that there are two types of IO-PR mixing phonon modes, i.e. p-IO//z-PR mixing modes and the z-IO//p-PR mixing modes existing in QOD wurtzite QDs. And each IO-PR mixing modes also have symmetrical and antisymmetrieal forms. Via a standard procedure of field quantization, the Frohlich Hamiltonians of electron-（IO-PR） mixing phonons interaction are obtained. Numerical calculations on a wurtzite GaN cylindrical QD are performed. The results reveal that both the radial-direction size and the axial-direction size as well as the dielectric matrix have great influence on the dispersive frequencies of the IO-PR mixing phonon modes. The limiting features of dispersive curves of these phonon modes are discussed in depth. The phonon modes ＂reducing＂ behavior of wurtzite quantum confined systems has been observed obviously in the structures. Moreover, the degenerating behaviors of the IO-PR mixing phonon modes in wurtzite QOD QDs to the IO modes and PR modes in wurtzite Q2D QW and QID QWR systems are analyzed deeply from both of the viewpoints of physics and mathematics.