A Prediction of the Structure of Tobacco-Mosaic-Virus Protein

Abstract

The location of amino acid residues within the tobacco mosaic virus protein subunit is discussed. Sequence data, X-ray crystallographic measurements, and the availability of specific residues for enzymic, immunological or chemical reaction are amongst the information used to trace roughly how the tobacco mosaic virus polypeptide chain winds in and out from the virus axis. Published rules for predicting secondary structure are then applied to obtain a diagram of the course of the polypeptide chain. This map should be useful for the interpretation of X-ray diffraction data and already permits an outline of the main features of the inner third of subunit to be suggested.Tobacco mosaic virus (TMV) protein presents a difficult problem for X-ray crystallographic structure determination. It can be crystallised as disks [1,2] but the asymmetric unit is very large (about 600000 daltons) and oriented gels of the virus itself are not sufficiently ordered to yield information to atomic resolution. Therefore, as an aid to the interpretation of current X-ray results, we attempt here to make deductions about the structure of the protein subunit from other available evidence. Such deductions impose limitations on the range of interactions between amino acid residues that may be proposed to explain other experimental data and, of course, the work also represents an exploration of the current state of the art of protein structure prediction.TMV protein is an unusually favourable subject for structure prediction because so much is already known about it. The information summarised here was obtained by many methods, the most important of which is X-ray crystallography, but also including electron microscopy, amino acid sequencing, titration studies and studies of the chemical, enzymic and immunological reactivity of various amino acid residues. The secondary structure of the polypeptide chain is then predicted, using the rules of Chou and Fasman [3,4]. Together these results enable us to propose a diagram of the approximate path of the polypeptide chain. Earlier attempts at partial TMV protein structure prediction have been made by Schiffer and Edmundson [5], and Leberman [7]. We gladly acknowledge that our thinking is based upon the labours of many people, not always explicitly mentioned here. In particular we acknowledge our debt to the crystallographic studies of Dr K. C. Holmes and his colleagues, started in Cambridge and continued, more recently, in Heidelberg. Low-Resolution Structural InformationThe TMV protein subunit contains 158 amino acid residues and has a molecular weight of 17493 [8,9]. Electron microscope and X-ray studies upon the virus (reviewed by Klug and Caspar [lo] and more recently by Barrett et al. [ll]) show that each subunit can be contained within a sector-shaped domain, like a slice of cake, within an angle of about 22". It extends radially from about 20 8, to about 90 8, from the virus helix axis, and is about 25 8, high. The RNA fits between the protein subunits in a groove at a radius of about 40 A,...

Circular‐Dichroism and Absorption Spectroscopic Studies on Specific Aromatic Residues Involved in the Different Modes of Aggregation of Tobacco‐Mosaic‐Virus Protein

“…Earlier observations soggested Tyr-139 to be involved in the transformation of A-protein to double discs [21]. This finding has been confirmed by preliminary determinations of the threedimensional structure of TMV-protein vulgare which prove the C-terminal sequence to be exposed in the surface of the molecule [19,20]. A clear-cut relation of the observed structural effects to certain amino acid residues interacting in the different modes of aggregation is expected from mutant studies.…”

“…Considering the tentative three-dimensional folding of the protein the contributions of Tyr-2, Phe-35, Phe-87, and Trp-152 to the rotatory strength cannot be important due to their distance from other chromophores [19,20]. The clustering of the aromatic residues may explain the observation that dichroic absorption of phenylalanine chromophores seems to be influenced by all structural changes under consideration ( Fig.…”

“…This interpretation is confirmed by model studies with diketopiperazines [40] which have shown that high-intensity negative bands at 1 > 290 nm are generated by strong interactions of one tryptophan residue with another aromatic sidechain. From the tentative structure of the protein [19,20] both chromophores are expected to be sufficiently close to show strong interaction. This interaction is gradually diminished in the processes of aggregation and vanishes upon transforming the double disc to the helix (Fig.…”

“…Recent low-resolution electron density studies [ 191 and predictions of the three-dimensional structure on the basis of all presently available structural data [20] are not sufficient to definitely determine the regions of the TMV-protein molecule involved in the transconformation process which precedes or accompanies aggregation. The observed differences in the nearultraviolet CD spectra for the different states of aggregation strongly indicate aromatic residues to be involved in the aggregation processes.…”

Hormone-receptor interactions: a study of the binding of hormone-substituted tobacco mosaic virus to membrane vesicles by dynamic light scattering and by transient electric bi-refringence

“…68 of each capsomer are the only amino groups available for substitution in the intact virus (for a recent review of TMV structure and chemistry, see Ref. 1). …”