AbstractThe role of the N‐terminal polypeptide fragment of the immunoglobulin l‐chain in V domain packing stability, and the flexibility of the whole chain was approached by molecular dynamics simulation. The observations were supported by experimental analysis. The N‐terminal polypeptide fragment appeared to be the low‐stability packing element in the V domain. At moderately elevated temperature it may be replaced at its packing locus by Congo red and then removed by proteolysis. After removal of Congo red by adsorption to (diethylamino)ethyl (DEAE) cellulose, the stability of complete L chain and of L chain devoid of the N‐terminal polypeptide fragment were compared. The results indicated that the N‐terminal polypeptide fragment plays an essential role in the stability of the V domain. Its removal makes the domain accessible for ANS and Congo red dye binding without heating. The decreased domain stability was registered in particular as increased root mean square (RMS) fluctuation and higher susceptibility to proteolytic attack. The long‐range effect was most clearly manifested at 340 K as independent V and C domain fluctuation in the l‐chain devoid of the N‐terminal polypeptide fragment. This is likely due to the lack of direct connections between the N‐ and C‐termini of the V domain polypeptide. In a complete V domain the connection involves residues 8–12 and 106–110 in particular. Partial or complete disruption of this connection increases the freedom of V domain rotation, while its increased cohesion strengthens the coupling of the V and C domains, making the whole L chain less flexible. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 189–200, 2003