Insights from the interfaces of HIV-1 envelope (ENV) trimer viral protein GP160 (GP120-GP41)
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HIV-1, Envelope, Trimer, Glycoprotein, GP160, GP120, GP41, Protein Interface, Van Der Waals
Abstract
The Human Immunodeficiency Virus (HIV-1) type 1 viral protein is a life threatening virus causing HIV/AIDS in infected humans. The HIV-1 envelope (ENV) trimer glycoprotein GP160 (GP120-GP41) is gaining attention in recent years as a potential vaccine candidate for HIV-1/AIDS. However, the sequence variation and charge polarity at the interacting sites across clades is a short coming faced in the development of an effective HIV-1 vaccine. We analyzed the interfaces in terms of its interface area, interface size, and interface energies (van der Waals, hydrogen bonds, and electrostatics). The interfaces were divided as dominant (>60%) and subdominant (<60%) based on van der Waals contribution to total energies. 88% of GP120 and 74% of GP41 interfaces are highly pronounced with van der Waals energy having large interfaces with interface size (98 ± 65 (GP120) and 73 ± 65 (GP41)) and interface area (882 ± 1166Å2 (GP120) and 921 ± 1288Å2 (GP41)). Nevertheless, 12% of GP120 and 26% of GP41 interfaces have subdominant van der Waals energies having small interfaces with interface size (58 ± 20 (GP120) and 27 ± 9 (GP41)) and interface area (581 ± 1605Å2 (GP120) and 483 ± 896Å2 (GP41)). It was interesting to observe GP41 small interfaces with subdominant van der Waals are stabilized by electrostatics (r2=0.63) without hydrogen bonds (r2=0). However, GP120 small interfaces were found to have two fold more hydrogen bonds (r2=0.59) than electrostatics (r2=0.20). Therefore, our previous finding stating that small protein-protein interfaces rich in electrostatics holds true in case of GP41 whereas not with GP120 protein interfaces.
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