Experimental and theoretical studies of the three‐dimensional structure of human interleukin‐4

Abstract

The structure of human interleukin 4 (IL-4) was predicted utilizing a series of experimental and theoretical techniques. Circular Dichroism (CD) spectroscopy indicated that IL-4 belonged to the all alpha-helix class of protein structures. Secondary structure prediction, site-directed mutagenesis, and CD spectroscopy suggested a predominantly alpha-helical structure, consistent with a four-helix bundle structural motif. A human/mouse IL-4 chimera was constructed to qualitatively evaluate alternative secondary structure predictions. The four predicted helices were assembled into tertiary structures using established algorithms. The mapping of three disulfide bridges in IL-4 provided additional constraints on possible tertiary structures. Using accessible surface contact area as a criterion, the most suitable structures were right handed all antiparallel four-helix bundles with two overhand loop connections. Successful loop closure and incorporation of the three disulfide constraints were possible while maintaining the expected shape, solvent accessibility, and steric interactions between loops and helices. Lastly, energy minimization was used to regularize the chain.

Origins of structural diversity within sequentially identical hexapeptides

“…This has begun to change-algorithms directed at predicting the secondary structure locations in a/a proteins are more accurate than their unbiased counterparts (Kneller et al, 1990;Presnell et al, 1992). In a prediction of the structure of IL-4 (Curtis et al, 1991) in advance of the NMR structure determination (Smith et al, 1992), the helical regions of this a / a protein were predicted with 90% fidelity. Second, peptide fragment databases of the types constructed by Unger et al (1989) or Rooman et al (1992) could be improved.…”

Proposed three-dimensional structure for the cellular prion protein.

“…Tertiary structures were generated by investigating the plausible arrangements of the a-helices via a combinatorial packing approach (20,34). This approach was developed based on the original concept of the packing of a-helices proposed by Crick (35).…”

“…Although the problem ofpredicting protein structure from the amino acid sequence information alone remains unsolved, recent advances in secondary and tertiary structure prediction of proteins have shown that reasonable structures can often be proposed by using a heuristic approach in conjunction with experimental data (18). For all-a-helical proteins, this approach has been applied to generate low-resolution structural models for a number of proteins (19)(20)(21). Some of the structural features proposed by these methods have been verified by subsequent x-ray or NMR experiments (22).…”

The high-resolution, three-dimensional solution structure of human interleukin-4 determined by multidimensional heteronuclear magnetic resonance spectroscopy

“…In the present article, residues are numbered from the N-terminal Glu as residue 1, so that the natural IL-4 sequence starts at residue 5 . In addition, the two potential N-linked glycosylation sites at Asn 42 and Asn 109 in the natural sequence were changed to Asp by site-directed mutagenesis to prevent hyperglycosylation in the yeast host (Curtis et al, 1991). Samples for NMR contained 2 mM 15N-or l3C/I5N-labeled IL-4, pH 5.7, dissolved in either 90% Hz0/10% D2O or 99.996% D2O.…”