To Probe the Conformational Adaptability of Conserved G-P-G-R Segment in the V3 Loop of HIV-1

Abstract

To design an effective HIV vaccine it is important to study the relationship between sequence diversity and conformations of principal neutralizing determinant (PND) peptides, the hypervariable region of gp120. Two fragments 318-327 and 315-329 of gp120 are mapped as PND and can induce HIV-1 specific cytotoxic lymphocyte activity that could kill virus infected cells. Consequently, the design of more ordered and biologically relevant conformation of immunogenic region from gp120-V3 loop may aid in the design of more effective immunogens for HIV-1 vaccine development. In order to enlighten optimal structural preferences we have explored the conformational adaptability of two fragments from V3 loop of gp120 that contains G-P-G-R sequence encompassing mainly the crown region. Nuclear Magnetic Resonance (NMR) spectroscopy and molecular dynamics (MD) simulations have been used to map out the conformation in diverse solvent systems such as water and hexafluroacetone (HFA). In HFA, the larger fragment, 315-329 shows some degree of inclination towards the formation of secondary structure. This indicates that length of the fragment is crucial in attaining secondary structure, which may be responsible for V3 loop’s hypervariable status. However, in water, both the fragments do not show any specific conformational preferences.