PDBsum entry 1kd9

De novo protein

PDB id: 1kd9

Contents

Protein chains

36 a.a.

35 a.a.

35 a.a.

Waters ×174

PDB id:

1kd9

Name:

De novo protein

Title:

X-ray structure of the coiled coil gcn4 acid base heterodimer acid- d12la16l base-d12la16l

Structure:

Gcn4 acid base heterodimer acid-d12la16l. Chain: a, c, f. Synonym: gabh all. Engineered: yes. Other_details: coiled coil acid strand. Gcn4 acid base heterodimer base-d12la16l. Chain: b, d, e. Synonym: gabh bll. Engineered: yes.

Source:

Synthetic: yes. Other_details: the peptide was chemically synthesized.. Other_details: the peptide was chemically synthesized.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.10Å R-factor: 0.242 R-free: 0.296

Authors:

A.E.Keating,V.N.Malashkevich,B.Tidor,P.S.Kim

Key ref:

A.E.Keating et al. (2001). Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils. Proc Natl Acad Sci U S A, 98, 14825-14830. PubMed id: 11752430 DOI: 10.1073/pnas.261563398

Date:

12-Nov-01 Release date: 28-Nov-01

Protein chains

No UniProt id for this chain

Struc: 35 a.a.

Protein chain

No UniProt id for this chain

Struc: 35 a.a.

Protein chains

No UniProt id for this chain

Struc: 34 a.a.

DOI no: 10.1073/pnas.261563398

Proc Natl Acad Sci U S A 98:14825-14830 (2001)

PubMed id: 11752430

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils.

A.E.Keating, V.N.Malashkevich, B.Tidor, P.S.Kim.

ABSTRACT

An important goal in biology is to predict from sequence data the high-resolution structures of proteins and the interactions that occur between them. In this paper, we describe a computational approach that can make these types of predictions for a series of coiled-coil dimers. Our method comprises a dual strategy that augments extensive conformational sampling with molecular mechanics minimization. To test the performance of the method, we designed six heterodimeric coiled coils with a range of stabilities and solved x-ray crystal structures for three of them. The stabilities and structures predicted by the calculations agree very well with experimental data: the average error in unfolding free energies is <1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations <0.7 A. We have also tested the method on a series of homodimers derived from vitellogenin-binding protein. The predicted relative stabilities of the homodimers show excellent agreement with previously published experimental measurements. A critical step in our procedure is to use energy minimization to relax side-chain geometries initially selected from a rotamer library. Our results show that computational methods can predict interaction specificities that are in good agreement with experimental data.

Selected figure(s)

Figure 1.
Fig. 1. Helical wheel diagram of the heterodimeric coiled coil GABH. Substitutions of Val, Ile, and Leu were made at positions d12 and a16 (yellow boxes) to give six peptides: A[LI]B[LL], A[LL]B[LL], A[IV]B[LL], A[LL]B[IV], A[LI]B[IV], and A[IV]B[IV] (notation: Acid[d12a16]Base[d12a16]). The linear sequence is: Ac-(E/K)VKQL(E/K)A(E/K)VEEd12(E/K)S(E/K)a16WHL(E/K)N(E/K)VARL(E/K)K(E/K)NAEC(E/K)A-NH[2]; the ACID peptide has E and the BASE peptide has K at positions in parentheses.

Figure 6.
Fig. 6. Superposition of the x-ray and MIN-FULL-calculated structures. The structures shown correspond to the first entries in Table 3 for each peptide. The view is from the C terminus of the peptide and includes positions a16 and d12.

Figures were selected by the author.