Cu(II)-binding properties of a cytochrome c with a synthetic metal-binding site: His-X3-His in an alpha-helix

A metal-binding site consisting of two histidines positioned His-X3-His in an alpha-helix has been engineered into the surface of Saccharomyces cerevisiae iso-1-cytochrome c. The synthetic metal-binding cytochrome c retains its biological activity in vivo. Its ability to bind chelated Cu(II) has been characterized by partitioning in aqueous two-phase polymer systems containing a polymer-metal complex, Cu(II)IDA-PEG, and by metal-affinity chromatography. The stability constant for the complex formed between Cu(II)IDA-PEG and the cytochrome c His-X3-His site is 5.3 x 10(4) M-1, which corresponds to a chelate effect that contributes 1.5 kcal mol-1 to the binding energy. Incorporation of the His-X3-His site yields a synthetic metal-binding protein whose metal affinity is sensitive to environmental conditions that alter helix structure or flexibility.

Characterization of His-X3-His sites in alpha-helices of synthetic metal-binding bovine somatotropin

Variants of bovine somatotropin have been engineered to contain synthetic metal-binding sites consisting of two solvent-exposed histidines separated by a single turn of an alpha-helix (His-X3-His variants). The affinities of these proteins for Cu(II) were characterized by measuring their partition coefficients in an aqueous two-phase polymer system. The partition coefficients were used to generate binding constants for formation of a complex between the engineered metal-binding site and Cu(II) chelated to an iminodiacetic acid derivative of polyethylene glycol. For three His-X3-His variants described here, these constants range from 2 x 10(4) to 1.6 x 10(6) M-1. The metal affinity of a His-X3-His site depends on the rigidity of the helix into which the site is engineered. The affinities of the His-X3-His sites for Cu(II) are large enough to dramatically increase not only the partitioning of these proteins in aqueous two-phase systems, but also their retention times on a metal-affinity chromatography column. Both these features can greatly facilitate the purification of engineered proteins. Criteria for choosing positions for incorporating metal-binding sites are discussed.

Engineering enzymes for non-aqueous solvents

Enzymes may be redesigned to permit catalysis in non-aqueous solvents by engineering their amino acid sequences, thereby altering their physical and chemical properties to suit the new solvent environment. The interactions that contribute to protein stability in non-aqueous solvents are discussed in the context of attempting to identify possible approaches to constructing enzymes which exhibit enhanced stability in non-aqueous media. These approaches are illustrated by several examples where protein engineering has resulted in enzymes that are better suited for catalysis in organic solvents.

Metal affinity precipitation of proteins

Proteins containing multiple surface-accessible histidine residues can be precipitated using small quantities of bis-copper chelates. The chelates serve to crosslink the proteins, presumably via the accessible histidines, leading to the formation of large, insoluble complexes. When excess copper chelate is used to carry out the precipitation, the resulting precipitate has a stoichiometry of 1:1 copper:accessible histidine. The precipitation is analogous to antibody-antigen precipitin reactions and can be described qualitatively using simple equilibrium theory developed for those systems. Human hemoglobin contains a large number of surface histidines and is efficiently precipitated by the copper salt CuSO4 as well as by bis-copper chelates. Sperm whale myoglobin contains many fewer surface histidines and is precipitated only by the bis-chelates. The effects of the number of accessible histidines on the protein, the chain length separating the two chelates, and the pH on the precipitation reaction have been investigated.

Protein design for non-aqueous solvents

Improving protein stability in unnatural and suboptimal environments is a promising application of protein engineering technology. Carefully designed amino acid alterations may lead to dramatic positive effects on the stability of proteins under highly perturbing conditions, such as in non-aqueous solvents. Applications of biocatalysts and proteins with specific binding capabilities in the chemical industry have been severely limited by constraints placed on the solvent environment. With the advent of convenient methods for altering the amino acid composition and even synthesizing entirely new protein molecules, it is worthwhile to consider engineering proteins for stability in non-aqueous solvents. In order to identify the features that a protein would need for stability in organic media, we have been studying the structure and properties of the hydrophobic protein crambin. Crambin is unique in that it is soluble and stable in very high concentrations of polar organic solvents. Crambin and its water-soluble homologs offer a powerful demonstration of protein engineering for non-aqueous solvents. This paper describes the structural features that contribute to crambin's special properties. Based on these observations and consideration of how non-aqueous solvents affect the interactions important in protein folding, a set of rules for designing non-aqueous solvent-stable proteins is proposed.

Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2

The structures and hydrogen exchange properties of the mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2 have been studied by high-resolution nuclear magnetic resonance. Both the adenine-adenine and thymine-thymine mismatches are intercalated in the duplexes. The structures of these self-complementary duplexes are symmetric, with the two strands in equivalent positions. The evidence indicates that these mismatches are not stably hydrogen bonded. The mismatched bases in both duplexes are in the anti conformation. The mismatched thymine nucleotide in d(CCCTGGG)2 is intercalated in the duplex with very little distortion of the bases or sugar-phosphate backbone. In contrast, the bases of the adenine-adenine mismatch in d(CCCAGGG)2 must tilt and push apart to reduce the overlap of the amino groups. The thermodynamic data show that the T-T mismatch is less destabilizing than the A-A mismatch when flanked by C-G base pairs in this sequence, in contrast to their approximately equal stabilities when flanked by A-T base pairs in the sequence d(CAAAXAAAG.CTTTYTTTG) where X and Y = A, C, G, and T [Aboul-ela, F., Koh, D., & Tinoco, I., Jr. (1985) Nucleic Acids Res. 13, 4811]. Although the mechanism cannot be determined conclusively from the limited data obtained, exchange of the imino protons with solvent in these destabilized heteroduplexes appears to occur by a cooperative mechanism in which half the helix dissociates.

Analytical affinity chromatography. II. Rate theory and the measurement of biological binding kinetics

Affinity chromatography can be used to measure equilibrium constants and kinetics of biological interactions. The local-equilibrium theory presented in the preceding paper is extended to include mass transfer and kinetic effects. Solutions for both zonal and frontal elution are presented. For highly nonlinear isotherms, the frontal elution method is preferred. Experiments with bovine serum albumin binding to immobilized Reactive Blue show that the binding kinetics inside the porous gel are several orders of magnitude slower than typical biological binding reactions in solution. The temperature dependence of the kinetic constants indicate that the binding may still be diffusion-controlled.