title: Local and long-range structural effects caused by the removal of the N-terminal polypeptide fragment from immunoglobulin L chain lambda.
abstract: The 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.
authors.affiliation: Department of Biostatistics and Medical Informatics, Collegium Medicum, Jagiellonian University, 17 Kopernika St, Kraków, 31-501 Poland.
authors.forename: Marcin
authors.initials: M
authors.lastname: Król
authors.forename: Irena
authors.initials: I
authors.lastname: Roterman
authors.forename: Barbara
authors.initials: B
authors.lastname: Piekarska
authors.forename: Leszek
authors.initials: L
authors.lastname: Konieczny
authors.forename: Janina
authors.initials: J
authors.lastname: Rybarska
authors.forename: Barbara
authors.initials: B
authors.lastname: Stopa
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D004396:Coloring Agents / Q000737:chemistry; D003198:Computer Simulation; D003224:Congo Red / Q000737:chemistry; D004220:Disulfides / Q000737:chemistry; D010450:Endopeptidases / Q000494:pharmacology; D006358:Hot Temperature; D006801:Humans; D007128:Immunoglobulin Fragments / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification; D007135:Immunoglobulin Variable Region / Q000737:chemistry / Q000235:genetics; D007146:Immunoglobulin lambda-Chains / Q000737:chemistry* / Q000235:genetics; D008024:Ligands; D008958:Models, Molecular; D009194:Myeloma Proteins / Q000652:urine; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012697:Serine Endopeptidases; D013329:Structure-Activity Relationship; D014357:Trypsin / Q000494:pharmacology
chemical_list: D004396:Coloring Agents; D004220:Disulfides; D007128:Immunoglobulin Fragments; D007135:Immunoglobulin Variable Region; D007146:Immunoglobulin lambda-Chains; D008024:Ligands; D009194:Myeloma Proteins; D003224:Congo Red; D010450:Endopeptidases; D012697:Serine Endopeptidases; D014357:Trypsin