Comparison of two crystal structures of TGF-β2: the accuracy of refined protein structures

Abstract

Transforming growth factor-fl is a multifunctional cell-growth regulator and is a member of the TGF-fl superfamily of cytokines. Each monomer is 112 amino acids long and the mature active form is a 25 kDa homodimer. Recently, the crystal structure of TGF-fl2 has been determined independently in two laboratories [Daopin, Piez, Ogawa & Davies (1992). Science, 257, 369-373; Schlunegger & Grfitter (1992). Nature (London), 358,[430][431][432][433][434] and subsequently refined to higher resolutions [Daopin, Li & Davies (1993). Proteins Struct. Funct. Genet. In the press; Schlunegger & Griitter (1993). J. Mol. Biol. In the press]. A detailed structural comparison shows that the two structures are nearly identical with the differences mostly located on the mobile regions of the molecule. The r.m.s, differences between the two structures are 0.10 A for 104 pairs of C a atoms, 0.15 A for 434 pairs of main-chain atoms, 0.33 A for 860 out of 890 pairs of protein atoms and a correlation of 90% between the temperature B factors of all protein atoms. Based on a comparison of the water molecules, a B value of 60.0 A 2 is recommended as the cut off for modeling new waters. The structural identity is striking because in one case the material was expressed in vivo in CHO cells whereas in the other case it was expressed in E. coli and had to be refolded in vitro. The overall coordinate errors are estimated to be 0.21/~ from the Luzzati plot, 0.18 A from the O' A plot, 0.24 A with Cruickshank's equations and 0.25 A using the empirical method of Perry & Stroud. These estimates are comparable to the r.m.s, structure superposition. The r.m.s. differences correlate very well with the crystallographic B values and the relation is best described with the Cruickshank formula. In addition to the estimation of an overall error, a new application of the Cruickshank formula is presented here to estimate the local errors.

How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding

“…It is believed that in general 0.5 Å reflects the amount of positional uncertainty expected from crystal structures determined at around 2.0 Å resolution. 38 Motions where only side-chain rotation is involved are ignored and treated as no conformational change case (class I). If the maximum C α displacement falls between 0.5 Å and 2.0 Å that pair is classified as class II (moderate conformational change).…”

The crystal structure of TGF‐β3 and comparison to TGF‐β2: Implications for receptor binding

“…(1992) and Schlunegger and Griitter (1992). Because both structures are more or less identical (Daopin et al, 1994), even though the proteins were folded by different routes, we focus on the comparison with the structure of human TGF-02 purified from Escherichia coli and folded in vitro (Brookhaven Protein Data Bank accession code 1TFG). Human TGF-fi2 and TGF-03 share 79% sequence identity.…”

Alteration of citrine structure by hydrostatic pressure explains the accompanying spectral shift

“…Because protein molecules have dimensions of tens to hundreds of angstroms, subangstrom positional perturbations may naïvely appear insignificant (2). However, if one considers two objects interacting through a Lennard-Jones potential that are separated by 3.5 Å and moves them together by just 0.1 Å, the potential energy between these objects will change by (1/3.4 6 )/ (1/3.5 6 ) ϭ 1.…”