PDBsum entry 2cw1

De novo protein

PDB id: 2cw1

Contents

Protein chain

65 a.a.

PDB id:

2cw1

Name:

De novo protein

Title:

Solution structure of the de novo-designed lambda cro fold protein

Structure:

Sn4m. Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: chemically synthesized

NMR struc:

10 models

Authors:

Y.Isogai,Y.Ito,T.Ikeya,Y.Shiro,M.Ota

Key ref:

Y.Isogai et al. (2005). Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein. J Mol Biol, 354, 801-814. PubMed id: 16289118 DOI: 10.1016/j.jmb.2005.10.005

Date:

15-Jun-05 Release date: 13-Dec-05

Protein chain

No UniProt id for this chain

Struc: 65 a.a.

DOI no: 10.1016/j.jmb.2005.10.005

J Mol Biol 354:801-814 (2005)

PubMed id: 16289118

Design of lambda Cro fold: solution structure of a monomeric variant of the de novo protein.

Y.Isogai, Y.Ito, T.Ikeya, Y.Shiro, M.Ota.

ABSTRACT

One of the classical DNA-binding proteins, bacteriophage lambda Cro, forms a homodimer with a unique fold of alpha-helices and beta-sheets. We have computationally designed an artificial sequence of 60 amino acid residues to stabilize the backbone tertiary structure of the lambda Cro dimer by simulated annealing using knowledge-based structure-sequence compatibility functions. The designed amino acid sequence has 25% identity with that of natural lambda Cro and preserves Phe58, which is important for formation of the stably folded structure of lambda Cro. The designed dimer protein and its monomeric variant, which was redesigned by the insertion of a beta-hairpin sequence at the C-terminal region to prevent dimerization, were synthesized and biochemically characterized to be well folded. The designed protein was monomeric under a wide range of protein concentrations and its solution structure was determined by NMR spectroscopy. The solved structure is similar to that of a monomeric variant of natural lambda Cro with a root-mean-square deviation of the polypeptide backbones at 2.1A and has a well-packed protein core. Thus, our knowledge-based functions provide approximate but essential relationships between amino acid sequences and protein structures, and are useful for finding novel sequences that are foldable into a given target structure.

Selected figure(s)

Figure 4.
Figure 4. NMR analyses of solution structure of designed Cro monomer. (a) 1H-15N HSQC spectrum of SN4m. (b) Short-range NOE connectivity. The left notations of aH, NN and ab indicate Ha-HN, HN-HN and Hb-HN, respectively. (c) b-Structural topology. Only the unambiguous NOE connectivity between the backbone CaH and NH protons on separate b-strands are indicated by arrows. Hydrogen bonds included in the structure calculations are indicated by broken lines.

Figure 6.
Figure 6. Solution structures of designed Cro monomer. (a) Stereo representation of the ten energy-minimized NMR structures of SN4m. Each of the ten backbone traces is superimposed on the average structure to minimize the RMSD of the backbone atoms (0.63 Å) and displayed with the hydrophobic residue side-chains (Leu5, Leu7, Phe10, Val11, Leu23, Leu25, Leu29, Ile30, Val33, Leu34, Leu38, Val40, Val42, Ile50, Val52, Ile54, Ile59, and Phe63) in pink bars. (b) Comparison between the average solution structure of SN4m and the X-ray crystallographic structure of the natural l Cro monomer (1orc) in stereo representation. The average NMR structure (red) is superimposed on the natural Cro monomer structure (white) with the minimal backbone RMSD of 2.1 Å.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 801-814) copyright 2005.

Figures were selected by an automated process.