Protein Engineering Design and Selection - current issue

Mutation analysis in UGT1A9 suggests a relationship between substrate and catalytic residues in UDP-glucuronosyltransferases

Patana, A.-S., Kurkela, M., Finel, M., Goldman, A. — 2008-08-15

UDP-glucuronosyltransferases (UGTs) catalyze the transfer of glucuronic acid from UDP-glucuronic acid to endo- and xenobiotics in our body. UGTs belong to the GT1 family of glycosyltransferases and many GT1s use a serine protease-like catalytic mechanism in which an Asp-His pair deprotonates a hydroxyl on the aglycone for nucleophilic attack on the sugar donor. The pair in human UGTs could be H37 and either D143 or D148 (UGT1A9 numbering). However, H37 is not totally conserved, being replaced by either Pro or Leu in UGT1A4 and UGT2B10. We therefore investigated the role of H37, D143 and D148 in UGT1A9 by site-directed mutagenesis, activity and kinetic measurements with several substrates. The results suggest that H37 is not critical in N-glucuronidation, but is so in O-glucuronidation. The V_max of the H37A mutant was much less affected in N- than O-glucuronidation, while the reverse was true for the Asp mutations, particularly D143A. We suggest that this is due to the opposing properties of O- and N- nucleophiles. O-nucleophiles require the histidine to deprotonate them so that they become effective nucleophiles, while N-nucleophiles develop a formal positive charge during the reaction (RNH₂⁺–GlcA), and thus require a negatively charged residue to stabilize the transition state.

Structural principles of the broad substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T--role of amino acid residues at positions 260 and 262

Grishin, A.M., Akparov, V.K., Chestukhina, G.G. — 2008-08-15

An influence of residues at positions 260 and 262 on a broad substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T (CPT) has been studied by means of site-directed mutagenesis. The structure of the S1'-site of CPT is similar to those of pancreatic carboxypeptidases A (CPA) and B (CPB); however, the enzyme is capable of cleaving off C-terminal hydrophobic (like CPA), C-terminal positively charged (like CPB), and negatively charged residues. The spatial alteration of the S1' site hydrophobic area in CPT by an insertion of one residue in the active site loop with Tyr255 by analogy with CPA and CPB did not change the enzyme specificity. The introduction of Ile262 (CPT D260G/T262I) led to a statistically significant reduction in activity towards charged substrates. The removal of a negative (CPT D260G) and placement of a positive charge (CPT D260G/T262K and CPT D260G/T262R) in the S1' site shifted the specificity of the variants towards substrates with C-terminal Glu. The selectivity profile was 64:1.7:1 for wild-type CPT, 815:115:1 for CPT D260G, 3270:1060:1 for CPT D260G/T262K and 1:2.4:0 for CPT D260G/T262R for substrates with C-terminal Leu, Glu and Arg, respectively. The obtained results confirm the important role of the amino acid residues at positions 260 and 262 in determination of the CPT substrate specificity.

Self-assembling multimeric integrin {alpha}5{beta}1 ligands for cell attachment and spreading

Kreiner, M., Li, Z., Beattie, J., Kelly, S.M., Mardon, H.J., van der Walle, C.F. — 2008-08-15

Substrates utilising clustered arginine–glycine–aspartic acid (RGD) ligand displays support greater cell adhesion over random displays. However, cell adhesion to integrin 5β1 requires the synergy site on the 9th type III fibronectin domain (FIII) in addition to RGD on the 10th FIII domain. Here, we have designed and expressed soluble protein chimeras consisting of an N-terminal 9th–10th FIII domain pair, IgG-derived hinge and leucine zipper-derived helix; the latter mutated to yield di-, tri- and tetrameric coiled coils and thus self-assembling, multimeric integrin 5β1 ligands. A unique C-terminal cysteine was appended to the helix to facilitate ‘anchoring’ of the chimeras with a defined orientation on a surface. Size-exclusion chromatography and circular dichroism demonstrated that the chimeras self-assembled as multimers in solution with defined secondary structures predicted from theoretical calculations. Biotinylation via a thioether bond was used to selectively bind the chimeras to streptavidin-coated surfaces, each of which was then shown to bind integrin 5β1 by surface plasmon resonance. Spreading of fibroblasts to surfaces derivatised with the chimeras was found to proceed in the order: tetramer > trimer > dimer > monomer. Thus, we describe novel polyvalent integrin 5β1 ligands for facile derivatisation of substrates to improve cell adhesion in vitro.

Structural simulation and protein engineering to convert an endo-chitosanase to an exo-chitosanase

2008-08-15

To obtain an enzyme for the production of chito-disaccharides (GlcN₂) by converting endo-chitosanase to exo-chitosanase, we chose an endo-chitosanase from Bacillus circulans MH-K1 (Csn) as the candidate for protein engineering. Using molecular modeling, two peptides with five amino acids (PCLGG) and six amino acids (SRTCKP) were designed and inserted after the positions of D¹¹⁵ and T²²² of Csn, respectively. The inserted fragments are expected to form loops that might protrude from opposite walls of the substrate-binding cleft, thus forming a ‘roof’ over the catalytic site that might alter the product specificity. The chimeric chitosanase (Chim-Csn) and wild-type chitosanase (WT-Csn) were both over-expressed in Escherichia coli and purified nearly to homogeneity. The products formed from chitosan were analyzed by ESI-MS (electrospray ionization-mass spectrometry). A mixture of GlcN₂, GlcN₃ and GlcN₄ was obtained with WT-Csn, whereas Chim-Csn formed, with a smaller catalytic rate (3% of WT-Csn activity), GlcN₂ as the dominant product. Measurements of viscosity showed that, with similar amounts of enzyme activity, Chim-Csn catalyzed the hydrolysis of chitosan with a smaller rate of viscosity decrease than WT-Csn. The results indicate that, on inserting two surface loops, the endo-type chitosanase was converted into an exo-type chitosanase, which to our knowledge is the first chitosanase that releases GlcN₂ from chitosan as the dominant product.

A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution

Hidalgo, A., Schliessmann, A., Molina, R., Hermoso, J., Bornscheuer, U. T. — 2008-08-15

Protein engineering is currently performed either by rational design, focusing in most cases on only a few positions modified by site-directed mutagenesis, or by directed molecular evolution, in which the entire protein-encoding gene is subjected to random mutagenesis followed by screening or selection of desired phenotypes. A novel alternative is focused directed evolution, in which only fragments of a protein are randomised while the overall scaffold of a protein remains unchanged. For this purpose, we developed a PCR technique using long, spiked oligonucleotides, which allow randomising of one or several cassettes in any given position of a gene. This method allows over 95% incorporation of mutations independently of their position within the gene, yielding sufficient product to generate large libraries, and the possibility of simultaneously randomising more than one locus at a time, thus originating recombination. The high efficiency of this method was verified by creating focused mutant libraries of Pseudomonas fluorescens esterase I (PFEI), screening for altered substrate selectivity and validating against libraries created by error-prone PCR. This led to the identification of two mutants within the OSCARR library with a 10-fold higher catalytic efficiency towards p-nitrophenyl dodecanoate. These PFEI variants were also modelled in order to explain the observed effects.

NMR-detected conformational exchange observed in a computationally designed variant of protein G{beta}1

Crowhurst, K. A., Mayo, S. L. — 2008-08-15

Detailed biophysical characterization of computationally designed proteins has become increasingly important in order to thoroughly understand the properties of these variants compared with wild-type and to apply this knowledge to future designs. The protein dynamics and structural properties of a computationally designed variant (1.5) of the β1 domain of streptococcal protein G (Gβ1) were measured using multinuclear NMR methods. Results from relaxation, diffusion and hydrogen exchange experiments indicate that the variant weakly self-associates at NMR concentrations, with evidence for multiple binding sites. Although comparison of fast (ps–ns) timescale motions shows only small differences in dynamics between 1.5 and wild-type, results from the measurement of intermediate (µs–ms) timescale motions are very different. Significant backbone conformational exchange has been observed in the variant at positions all along the sequence, whereas the wild-type Gβ1 shows little evidence for this type of motion. This increased conformational exchange in 1.5 has been attributed to core overpacking resulting from the incorporation of two large hydrophobic side chains and the loss of an aromatic T-stacking interaction. These data highlight, in detail, the potential consequences of incorporating major perturbations in the core of a protein and the need to carry out more detailed analyses of the biophysical properties of designed proteins in order to better understand and predict the effects of mutations.