Viral incorporation of cyclophilin A (CS PA) during the assembly of human immunodeficiency virus type-1 (HIV-1) is crucial for efficient viral replication, CyPA binds to the previously identified Gly-Pro(90) site of the capsid protein p24, but its role remained unclear. Here we report two new interaction sites between cyclophilins and p24, Both are located in the C-terminal domain of p24 around Gly-Pro(157) and Gly-Pro(224). Peptides corresponding to these regions showed higher affinities (K-d similar to 0.3 mu M) for both CyPA and cyclophilin B than the best peptide derived from the Gly-Pro(90) site (similar to 8 mu M) and thus revealed new sequence motifs flanking Gly-Pro that are important for tight interaction of peptide ligands with cyclophilins. Between CS PA and an immature (unprocessed) form of p24, a K-d of similar to 8 mu M was measured, which corresponded with the K-d of the best of the Gly-Pro(90) peptides, indicating an association via this site, Processing of immature p24 by the viral protease, yielding mature p24, elicited a conformational change in its C-terminal domain that was signaled by the covalently attached fluorescence label acrylodan. Consequently, CyPA and cyclophilin B bound with much higher affinities (similar to 0.6 and 0.25 mu M) to the new, i.e. maturation-generated sites. Since this domain is essential for p24 oligomerization and capsid cone formation, CyPA bound to the new sites might impair the regularity of the capsid cone and thus facilitate in vivo core disassembly after host infection.