PDBsum entry 2q1e

Protein fibril

PDB id: 2q1e

Contents

Protein chains

109 a.a.

Ligands

SO4

Waters ×443

PDB id:

2q1e

Name:

Protein fibril

Title:

Altered dimer interface decreases stability in an amyloidogenic kappa1 bence jones protein.

Structure:

Amyloidogenic immunoglobulin light chain protein al-09. Chain: a, b, c, d. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mutant of vk1 o18/o8 germline. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.55Å R-factor: 0.166 R-free: 0.206

Authors:

J.R.Thompson,M.Ramirez-Alvarado,E.M.Baden

Key ref:

E.M.Baden et al. (2008). Altered dimer interface decreases stability in an amyloidogenic protein. J Biol Chem, 283, 15853-15860. PubMed id: 18400753 DOI: 10.1074/jbc.M705347200

Date:

24-May-07 Release date: 08-Apr-08

Protein chains

A2NI60  (A2NI60_HUMAN) -  BRE (Fragment) from Homo sapiens

Seq: 108 a.a.

Struc: 109 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

DOI no: 10.1074/jbc.M705347200

J Biol Chem 283:15853-15860 (2008)

PubMed id: 18400753

Altered dimer interface decreases stability in an amyloidogenic protein.

E.M.Baden, B.A.Owen, F.C.Peterson, B.F.Volkman, M.Ramirez-Alvarado, J.R.Thompson.

ABSTRACT

Amyloidoses are devastating and currently incurable diseases in which the process of amyloid formation causes fatal cellular and organ damage. The molecular mechanisms underlying amyloidoses are not well known. In this study, we address the structural basis of immunoglobulin light chain amyloidosis, which results from deposition of light chains produced by clonal plasma cells. We compare light chain amyloidosis protein AL-09 to its wild-type counterpart, the kappaI O18/O8 light chain germline. Crystallographic studies indicate that both proteins form dimers. However, AL-09 has an altered dimer interface that is rotated 90 degrees from the kappaI O18/O8 dimer interface. The three non-conservative mutations in AL-09 are located within the dimer interface, consistent with their role in the decreased stability of this amyloidogenic protein. Moreover, AL-09 forms amyloid fibrils more quickly than kappaI O18/O8 in vitro. These results support the notion that the increased stability of the monomer and delayed fibril formation, together with a properly formed dimer, may be protective against amyloidogenesis. This could open a new direction into rational drug design for amyloidogenic proteins.

Selected figure(s)

Figure 2.
FIGURE 2. In vitro fibril formation indicated shorter lag time for AL-09. a, ThT fluorescence measured at 1, 24, and 120 h indicated that AL-09 ( ) formed fibrils within 24 h, whereas I O18/O8 ( ) did not (error bars were ± S.D. for n = 5; ^*, p value 0.05). Even after 120 h, I O18/O8 had not formed fibrils (^**, p value 0.0079). Complete amyloid formation kinetics followed by ThT fluorescence is included in supplemental Fig. S2 online. b, electron micrograph of AL-09 at 24 h (scale bar, 500 nm), confirming fibril formation. c, I O18/O8 fibril formation at 215 h (scale bar 100 nm) confirms the earliest time point at which ThT fluorescence enhancement occurred (supplemental Fig. S2 online).

Figure 3.
FIGURE 3. Crystal structures revealed different dimer interfaces for I O18/O8 (a) and AL-09 (b). c, superposition of I O18/O8 (blue and cyan) and AL-09 (brown and salmon) dimers illustrated that AL-09 had a 90° rotation from the canonical (germline-like) interface. d, arrangement of key interface residues was significantly disrupted upon superposition of I O18/O8 (blue) and AL-09 (brown) monomers. The presence of the second monomers for I O18/O8 (cyan) and AL-09 (salmon) showed that a canonical dimer interface in AL-09 was sterically impossible, given the conformation of F98 (yellow highlight). e, stereo images of I O18/O8 2F[o]-F[c] electron density (at 1 contouring). The images show the electron density around Trp-35.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 15853-15860) copyright 2008.

Figures were selected by an automated process.