The small heat shock protein (sHSP) from Methanococcus jannaschii (Mj Hsp16.5) forms a monodisperse 24mer and each of its monomer contains two flexible N- and C-terminals and a rigid α-crystallin domain with an extruding β-strand exchange loop. The minimal α-crystallin domain with a β-sandwich fold is conserved in sHSP family, while the presence of the β-strand exchange loop is divergent. The function of the β-strand exchange loop and the minimal α-crystallin domain of Mj Hsp16.5 need further study. In the present study, we constructed two fragment-deletion mutants of Mj Hsp16.5, one with both the N- and C-terminals deleted (ΔNΔC) and the other with a further deletion of the β-strand exchange loop (ΔNΔLΔC). ΔNΔC existed as a dimer in solution. In contrast, the minimal α-crystallin domain ΔNΔLΔC became polydisperse in solution and exhibited more efficient chaperone-like activities to prevent amorphous aggregation of insulin B chain and fibril formation of the amyloidogenic peptide dansyl-SSTSAA-W than the mutant ΔNΔC and the wild type did. The hydrophobic probe binding experiments indicated that ΔNΔLΔC exposed much more hydrophobic surface than ΔNΔC. Our study also demonstrated that Mj Hsp16.5 used different mechanisms for protecting different substrates. Though Mj Hsp16.5 formed stable complexes with substrates when preventing thermal aggregation, no complexes were detected when preventing aggregation under non-heat-shock conditions. Proteins 2014; 82:1156–1167. © 2013 Wiley Periodicals, Inc.