Defining the HIV Capsid Binding Site of Nucleoporin 153

Abstract

The interaction between the HIV-1 capsid (CA) and human nucleoporin 153 (NUP153) is vital for delivering the HIV-1 preintegration complex into the nucleus via the nuclear pore complex. The interaction with CA requires a phenylalanine/glycine-containing motif in the C-terminus of NUP153. This study used molecular modeling and biochemical assays to determine the amino acids of NUP153 that are essential for its interactions with CA. Molecular dynamics, FoldX, and PyRosetta simulations delineated the minimal CA binding motif of NUP153 based on the known structure of NUP153 bound to the HIV-1 CA hexamer. Computational predictions were experimentally validated by testing the interaction of NUP153 with CA using an in vitro binding assay and a cell-based TRIM-NUP153C restriction assay. This multidisciplinary approach identified eight amino acids from P1411 to G1418 that stably engage with CA, with significant correlations between molecular models and empirical experiments. Specifically, P1411, V1414, F1415, T1416, F1417, and G1418 were confirmed as critical amino acids required to interact NUP153 with CA. IMPORTANCEHuman immunodeficiency virus (HIV) can infect non-dividing cells by interacting with host nuclear pores. The host nuclear pore protein NUP153 directly interacts with the HIV capsid to promote viral nuclear entry. This study used a multidisciplinary approach combining computational and experimental techniques to map the essential amino acids of NUP153 required for HIV capsid interaction. This approach revealed that the HIV capsid interacts specifically with only six amino acids of NUP153, suggesting other FG-containing motifs could also interact with the capsid. Based on molecular modeling, naturally occurring polymorphisms in human and non-human primates would be predicted to prevent NUP153 interaction with capsid, potentially protecting from HIV infection.