The zinc finger motifs in retroviral nucleocapsid (NC) proteins are essential for viral replication. Disruption of these Cys-X 2 -Cys-X 4 -His-X 4 -Cys zinc-binding structures eliminates infectivity. To determine if N-ethylmaleimide (NEM) can inactivate human immunodeficiency virus type 1 (HIV-1) or simian immunodeficiency virus (SIV) preparations by alkylating cysteines of NC zinc fingers, we treated infectious virus with NEM and evaluated inactivation of infectivity in cell-based assays. Inactivation was rapid and proportional to the NEM concentration. NEM treatment of HIV-1 or SIV resulted in extensive covalent modification of NC and other internal virion proteins. In contrast, viral envelope glycoproteins, in which the cysteines are disulfide bonded, remained intact and functional, as assayed by high-performance liquid chromatography, fusion-from-without analyses, and dendritic cell capture. Quantitative PCR assays for reverse transcription intermediates showed that NEM and 2,2-dipyridyl disulfide (aldrithiol-2), a reagent which inactivates retroviruses through oxidation of cysteines in internal virion proteins such as NC, blocked HIV-1 reverse transcription prior to the formation of minusstrand strong-stop products. However, the reverse transcriptase from NEM-treated virions remained active in exogenous template assays, consistent with a role for NC in reverse transcription. Since disruption of NC zinc finger structures by NEM blocks early postentry steps in the retroviral infection cycle, virus preparations with modified NC proteins may be useful as vaccine immunogens and probes of the role of NC in viral replication.Retroviral nucleocapsid (NC) proteins are critically involved in multiple steps of the retroviral replication cycle, both as a domain within the Gag polyprotein and in the mature protein form (reviewed in reference 19). As part of the Gag precursor, NC functions include recognition and packaging of the viral genome (50, 64) and possibly the placement of the tRNA on the primer-binding site (22). Once it is liberated from the Gag polyprotein by the viral protease, the small and highly basic NC protein functions as a chaperone during reverse transcription and integration and also protects newly synthesized viral DNA (vDNA) (10,13,14,26,49,50,64).In all orthoretroviruses, the NC protein contains one or two zinc finger domains with the common sequence motif Cys-X 2 -Cys-X 4 -His-X 4 -Cys, which binds a zinc ion in a tetrahedral coordination complex (6,7,16,58). Genetic or chemical disruption of the zinc finger domain emphasizes its critical role in virus replication. Site-directed mutagenesis studies indicate that these zinc finger structures within NC are required for essential functions in the viral replication cycle (29,32,33). Additionally, reagents with sufficient oxidative potential have been shown to disrupt the zinc finger structure in vitro (51,60) and are also capable of inactivating human immunodeficiency virus type 1 (HIV-1) (52). These observations suggested that selective covalent mod...