The calculation of partial specific volumes of proteins in 8 M urea solution

The native GCN4 leucine-zipper domain does not uniquely specify a dimeric oligomerization state

The dimerization domain of the yeast transcription factor GCN4, one of the first coiled-coil proteins to be structurally characterized at high resolution, has served as the basis for numerous fundamental studies on α-helical folding. Mutations in the GCN4 leucine zipper are known to change its preferred oligomerization state from dimeric to trimeric or tetrameric; however, the wild-type sequence has been assumed to encode a two-chain assembly exclusively. Here we demonstrate that the GCN4 coiled-coil domain can populate either a dimer or trimer fold, depending on environment. We report high-resolution crystal structures of the wild-type sequence in dimeric and trimeric assemblies. Biophysical measurements suggest populations of both oligomerization states under certain experimental conditions in solution. We use parallel tempering molecular dynamics simulations on the microsecond time scale to compare the stability of the dimer and trimer folded states in isolation. In total, our results suggest that the folding behavior of the well-studied GCN4 leucine-zipper domain is more complex than was previously appreciated. Our results have implications in ongoing efforts to establish predictive algorithms for coiled-coil folds and the selection of coiled-coil model systems for design and mutational studies where oligomerization state specificity is an important consideration.

Serge Timasheff: the man with a genius for solutions in biology

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Stabilizing effect of sucrose against irreversible denaturation of rabbit muscle lactate dehydrogenase

Measurements of the kinetics of activity loss by rabbit muscle lactate dehydrogenase in acetate-chloride buffer, pH 5.0, I 0.20, have shown that the enzyme exhibits greater stability against irreversible inactivation when the buffer is supplemented with sucrose (0.1 M-0.5 M). On the basis of sedimentation equilibrium distributions obtained for enzyme in the absence and presence of sucrose (0.5 M), the lactate dehydrogenase is essentially dimeric in both environments. The observed stabilization of enzyme activity has therefore been considered in terms of the space-filling effects of sucrose on an isomerization equilibrium between native and unfolded forms of dimeric lactate dehydrogenase, which precedes irreversible inactivation of the unfolded isomer. Interpretation of the kinetic results on that basis has led to the conclusion that the initial stage of enzyme unfolding entails a minor change in volume and/or asymmetry of the lactate dehydrogenase that gives rise to a 4% increase in the second virial coefficient describing excluded volume interactions between dimeric enzyme and sucrose.

Tumour necrosis factor is a compact trimer

Recombinant produced human tumour necrosis factor (TNF) has been studied to characterise the subunit structure of the protein. TNF is shown to be a trimer Mr 52000 in which the subunits are associated in a compact, triangular form. In secondary structure it belongs to the all-beta class of proteins. It has high thermodynamic stability and the unfolded subunits can fold and associate spontaneously to form native, biologically active TNF.

Physicochemical properties of oilseed proteins

This review attempts to consolidate the information on the physicochemical properties of proteins from groundnut, soybean, sesame seed, mustard seed, rapeseed, sunflower seed, cottonseed, and other oilseeds. It deals with the extraction and characterization of the oilseed proteins and describes the methods for isolation of the various protein fractions and determination of their physicochemical characteristics. Also discussed are the subunit composition of the oligomeric proteins, their hydrodynamic properties, and the effect of denaturants on these proteins. The similarity in the properties of the proteins from various oilseed materials is discussed. The review article aims to indicate the gaps in our knowledge about the physicochemical properties of oilseed proteins and suggests areas for future investigation.

The Hofmeister effect and the behaviour of water at interfaces

Starting from known properties of non-specific salt effects on the surface tension at an air-water interface, we propose the first general, detailed qualitative molecular mechanism for the origins of ion-specific (Hofmeister) effects on the surface potential difference at an air-water interface; this mechanism suggests a simple model for the behaviour of water at all interfaces (including water-solute interfaces), regardless of whether the non-aqueous component is neutral or charged, polar or non-polar. Specifically, water near an isolated interface is conceptually divided into three layers, each layer being I water-molecule thick. We propose that the solute determines the behaviour of the adjacent first interfacial water layer (I1); that the bulk solution determines the behaviour of the third interfacial water layer (I3), and that both I1 and I3 compete for hydrogen-bonding interactions with the intervening water layer (I2), which can be thought of as a transition layer. The model requires that a polar kosmotrope (polar water-structure maker) interact with I1 more strongly than would bulk water in its place; that a chaotrope (water-structure breaker) interact with I1 somewhat less strongly than would bulk water in its place; and that a non-polar kosmotrope (non-polar water-structure maker) interact with I1 much less strongly than would bulk water in its place. We introduce two simple new postulates to describe the behaviour of I1 water molecules in aqueous solution. The first, the 'relative competition' postulate, states that an I1 water molecule, in maximizing its free energy (--delta G), will favour those of its highly directional polar (hydrogen-bonding) interactions with its immediate neighbours for which the maximum pairwise enthalpy of interaction (--delta H) is greatest; that is, it will favour the strongest interactions. We describe such behaviour as 'compliant', since an I1 water molecule will continually adjust its position to maximize these strong interactions. Its behaviour towards its remaining immediate neighbours, with whom it interacts relatively weakly (but still favourably), we describe as 'recalcitrant', since it will be unable to adjust its position to maximize simultaneously these interactions.(ABSTRACT TRUNCATED AT 400 WORDS)