Protein glycosylation.

Glycan structures can modulate the biological properties and functions of glycoproteins. This has been shown by investigation of the biological activities and glycan structures of several recombinant glycoproteins. Glycan structures of glycoproteins differ according to the species and tissue producing them, and selection of an appropriate host-cell type can generate recombinant glycoproteins with new characteristics.     

Protein densities.

The calculation of protein densities from atomic coordinates is not straight-forward and requires very careful attention to the determination of the protein-solvent boundary. Interior densities are more readily obtained and are in reasonable agreement with those estimated from solvent accessibility studies. The interior of globular proteins has very significant density inhomogenities on a scale of 100--1000 A3. The interior densities range from less than 0.5 g/cm3 to over 3 g/cm3. The low local densities are primarily associated with clusters of nonpolar sidechains while the high local density regions arise from the protein backbone secondary structures: helices and beta sheets. We show a rough correlation between local density and local polarity.     

Protein design.

Several noteworthy papers have been published in the past year in which the creation of interesting novel proteins, either by de novo design or the redesign of existing proteins, has been reported. Highlights include the successful design of proteins for binding specific ligands.     

Protein redesign.

It has been demonstrated that, for a number of proteins, it is possible to dramatically alter the connectivities between elements of secondary structure. Remarkably large loop insertions are tolerated and many redesigns have generated proteins that successfully fold to stable, active structures. Some redesigns have been entirely the choice of the investigators, whereas others have incorporated a randomization and selection step to identify optimal sequences. These studies have provided basic guidelines for the rational manipulation of protein structure and stability, they have allowed the dissection of folding pathways and they have generated proteins with the potential for practical therapeutic applications.     

Protein metal-binding sites.

Metal ions have a role in a variety of important functions in proteins including protein folding, assembly, stability, conformational change, and catalysis. The presence or absence of a given metal ion is crucial to the conformation or activity of over one third of all proteins. Recent developments have been made in the understanding and design of metal-binding sites in proteins, an important and rapidly advancing area of protein engineering.     

Protein synthesis rhythm.

The three-dimensional structure of a protein molecule appears to depend on the amino acid sequence of the protein in an as yet incompletely described manner. If the amino acid sequence is replaced by a numerical sequence of values representing a physical or chemical property of amino acids, the resulting numerical sequence is amenable to autocorrelation analysis. Further, if certain geometrical parameters are calculated from the three-dimensional structure of a protein to form a configurational series, pairs of property series and configurational series can be analyzed by cross-correlation techniques. The data base for the analysis was the three-dimensional structures of ten proteins as determined by X-ray crystallography. Such analysis yields the result that the hydrophobicity of an amino acid residue in a protein influences the orientation angle of the amino acid side chain. This result is consistent with the widely current “oil-drop” model of protein structure. Hydrophobicity also appears to influence the backbone dihedral angle φ, but not ψ Such a directional effect cannot be explained by a current model of information transfer in protein helices. The magnitude of the cross correlations does not appear to be satisfactory for construction of a transfer function model for the prediction of general features of protein structure from amino acid sequences.     

Protein solubility modeling.

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process.     

Protein structure similarities.

Comparison of protein structures can reveal distant evolutionary relationships that would not be detected by sequence information alone. This helps to infer functional properties. In recent years, many methods for pairwise protein structure alignment have been proposed and are now available on the World Wide Web. Although these methods have made it possible to compare all available protein structures, they also highlight the remaining difficulties in defining a reliable score for protein structure similarities.     

Protein engineering for thermostability.

Studies with small, monomeric proteins indicate that, to some extent, the effects of amino acid substitutions can be predicted. However, conformational and other changes may complicate the prediction. Site-directed mutagenesis is leading both to a better understanding of protein stability and to the production of more stable proteins.     

Protein folding in vitro.

It is becoming increasingly evident that intermediates observed in protein folding in vitro may be closely related to conformational states that are important in various intracellular processes. This review focuses on recent advances in in vitro protein-folding studies with particular reference to the molten globule state, which is purported to be a common and distinct intermediate of protein folding.     

Protein interaction with ice.

Many organisms have evolved novel mechanisms to minimize freezing injury due to extracellular ice formation. This article reviews our present knowledge on the structure and mode of action of two types of proteins capable of ice interaction. The antifreeze proteins inhibit ice crystal formation and alter ice growth habits. The ice nucleation proteins, on the other hand, provide a proper template to stimulate ice growth. The potential applications of these proteins in different industries are discussed.