Modification of the substrate specificity of an acyl-acyl carrier protein thioesterase by protein engineering.

The plant acyl-acyl carrier protein (ACP) thioesterases (TEs) are of biochemical interest because of their roles in fatty acid synthesis and their utilities in the bioengineering of plant seed oils. When the FatB1 cDNA encoding a 12:0-ACP TE (Uc FatB1) from California bay, Umbellularia californica (Uc) was expressed in Escherichia coli and in developing oilseeds of the plants Arabidopsis thaliana and Brassica napus, large amounts of laurate (12:0) and small amounts of myristate (14:0) were accumulated. We have isolated a TE cDNA from camphor (Cinnamomum camphorum) (Cc) seeds that shares 92% amino acid identity with Uc FatB1. This TE, Cc FatB1, mainly hydrolyzes 14:0-ACP as shown by E. coli expression. We have investigated the roles of the N- and C-terminal regions in determining substrate specificity by constructing two chimeric enzymes, in which the N-terminal portion of one protein is fused to the C-terminal portion of the other. Our results show that the C-terminal two-thirds of the protein is critical for the specificity. By site-directed mutagenesis, we have replaced several amino acids in Uc FatB1 by using the Cc FatB1 sequence as a guide. A double mutant, which changes Met-197 to an Arg and Arg-199 to a His (M197R/R199H), turns Uc FatB1 into a 12:0/14:0 TE with equal preference for both substrates. Another mutation, T231K, by itself does not effect the specificity. However, when it is combined with the double mutant to generate a triple mutant (M197R/R199H/T231K), Uc FatB1 is converted to a 14:0-ACP TE. Expression of the double-mutant cDNA in E. coli K27, a strain deficient in fatty acid degradation, results in accumulation of similar amounts of 12:0 and 14:0. Meanwhile the E. coli expressing the triple-mutant cDNA produces predominantly 14:0 with very small amounts of 12:0. Kinetic studies indicate that both wild-type Uc FatB1 and the triple mutant have similar values of Km,app with respect to 14:0-ACP. Inhibitory studies also show that 12:0-ACP is a good competitive inhibitor with respect to 14:0-ACP in both the wild type and the triple mutant. These results imply that both 12:0- and 14:0-ACP can bind to the two proteins equally well, but in the case of the triple mutant, the hydrolysis of 12:0-ACP is severely impaired. The ability to modify TE specificity should allow the production of additional "designer oils" in genetically engineered plants.     

Structural and functional basis of protein phosphatase 5 substrate specificity

The serine/threonine phosphatase protein phosphatase 5 (PP5) regulates hormone- and stress-induced cellular signaling by association with the molecular chaperone heat shock protein 90 (Hsp90). PP5-mediated dephosphorylation of the cochaperone Cdc37 is essential for activation of Hsp90-dependent kinases. However, the details of this mechanism remain unknown. We determined the crystal structure of a Cdc37 phosphomimetic peptide bound to the catalytic domain of PP5. The structure reveals PP5 utilization of conserved elements of phosphoprotein phosphatase (PPP) structure to bind substrate and provides a template for many PPP–substrate interactions. Our data show that, despite a highly conserved structure, elements of substrate specificity are determined within the phosphatase catalytic domain itself. Structure-based mutations in vivo reveal that PP5-mediated dephosphorylation is required for kinase and steroid hormone receptor release from the chaperone complex. Finally, our data show that hyper- or hypoactivity of PP5 mutants increases Hsp90 binding to its inhibitor, suggesting a mechanism to enhance the efficacy of Hsp90 inhibitors by regulation of PP5 activity in tumors.Protein phosphatase 5 (PP5) has pleiotropic roles in cellular signaling, including DNA damage repair, proliferation of breast cancer cells, circadian cycling, response to cytotoxic stresses, Rac-dependent potassium ion channel activity, and activation of steroid hormone receptors [e.g., glucocorticoid receptor (GR) and estrogen receptor] (1, 2). It is a member of the phosphoprotein phosphatase (PPP) family of serine/threonine phosphatases, which has members that share a highly conserved catalytic core and catalytic mechanism dependent on two metal ions, commonly Mn²⁺. Most PPP family members exhibit high, nonspecific phosphatase activity. Specificity is provided by a large cohort of regulatory and other interacting proteins that function to inhibit basal activity and recruit substrates, thereby finely tuning the enzymes (3). This combinatorial approach enables a small number of catalytic subunits to have the breadth of specificity equivalent to that seen in kinases, which are greater in number by an order of magnitude. Structures of complexes between regulatory and catalytic domains have illuminated the importance of regulatory subunits in facilitating substrate recruitment (3). However, to date, there is no structural information describing how a substrate binds at the active site of a PPP; therefore, a central question remains of how local interactions between the substrate and the catalytic domain contribute to the molecular basis of dephosphorylation.PP5 is unique among the PPP family because it has a low basal activity caused by an autoinhibitory N-terminal tetratricopeptide (TPR) domain (4). Its activity is promoted by a number of cellular factors, including fatty acids and the molecular chaperone heat shock protein 90 (Hsp90) (5), both of which release autoinhibition by interacting with the TPR domain (6, 7). Many established PP5 substrates are dependent on Hsp90 for their activation (known as Hsp90 clients). In addition to a requirement for Hsp90’s chaperone activity, it is likely that these PP5 substrates require Hsp90 to act as a molecular bridge to bring the catalytic domain of PP5 in close proximity to enable dephosphorylation, which has been shown for the Hsp90 cochaperone Cdc37 (8). In such cases, Hsp90 performs a role similar to that observed by the regulatory subunits of the PP1 and PP2A family (3).The cochaperone Cdc37 regulates the activation of Hsp90 client kinases by distinguishing between client and nonclient kinases (9) and recruiting the former to Hsp90 (10). Many of these kinases are oncogenes; therefore, the molecular details of their activation are of considerable interest in cancer therapy. Activation is dependent on a cycle of Cdc37-Ser13 phosphorylation by the constitutively active kinase CK2 (11, 12) and dephosphorylation by PP5 (8). The mechanisms by which Cdc37 phosphorylation and dephosphorylation regulate kinase activation are not understood.To understand the molecular determinants of the phospho-Ser13 Cdc37-PP5 interaction, we determined the 2.3-Å crystal structure of a Cdc37 phosphomimetic peptide bound to the catalytic domain of PP5. The structure reveals how PP5 uses conserved elements of PPP structure to bind substrate, whereas in vitro and in vivo analyses indicate that, despite being highly conserved, elements of substrate specificity are determined within the phosphatase catalytic domain itself.     

Prediction and experimental validation of enzyme substrate specificity in protein structures

Structural Genomics aims to elucidate protein structures to identify their functions. Unfortunately, the variation of just a few residues can be enough to alter activity or binding specificity and limit the functional resolution of annotations based on sequence and structure; in enzymes, substrates are especially difficult to predict. Here, large-scale controls and direct experiments show that the local similarity of five or six residues selected because they are evolutionarily important and on the protein surface can suffice to identify an enzyme activity and substrate. A motif of five residues predicted that a previously uncharacterized Silicibacter sp. protein was a carboxylesterase for short fatty acyl chains, similar to hormone-sensitive-lipase–like proteins that share less than 20% sequence identity. Assays and directed mutations confirmed this activity and showed that the motif was essential for catalysis and substrate specificity. We conclude that evolutionary and structural information may be combined on a Structural Genomics scale to create motifs of mixed catalytic and noncatalytic residues that identify enzyme activity and substrate specificity.As the list of known genes grows exponentially, the elucidation of their function remains a major bottleneck and lags far behind the production of sequences (1–5). The best approach remains to search computationally for functionally characterized sequence homologs, ideally with greater than 50% sequence identity (6). Binding specificity, however, is sensitive to subtle amino acid differences, and the transfer of substrate between related enzymes is prone to errors when sequence identity is below 65–80% (7–9). These thresholds vary from case to case: Some orthologs will maintain identical functions down to 25% sequence identify (9), whereas paralogs can take on highly diverse activities (10). Other difficulties that plague annotation transfer between homologs are that individual small molecules may each bind to multiple and distinct molecular pockets (11), that different residues can support similar chemistries (12), and that activity can vary even when catalytic residues are conserved (13–18). To raise annotation accuracy, Structural Genomics (19) made structural information widely available and spurred the development of annotation methods dependent on local chemical and physical environments (20), sequence and structural comparisons (21), or 3D templates (22). In the case of the latter, these methods search between proteins for local structural similarities over a few signature residues that represent the telltale parts of a functional site, so-called “3D templates” (3, 14, 18, 22–24). The residue composition of 3D templates is critical, however, and derived from experiments (25) or from analyses of functional sites and determinants (14, 15, 26). The sensitivity and specificity of template-based annotations still needs to be established experimentally (27, 28), but retrospective controls suggest they often predict enzyme catalytic activity (14, 16, 17, 29, 30).Here, to extend the functional resolution of 3D template annotations to substrates, we exploit Evolutionary Tracing (ET) (31, 32). ET ranks sequence positions by the tendency of their evolutionary variations to correlate with major or with minor divergences. Top-ranked ET sequence positions are the most evolutionarily and, presumably, functionally important, and indeed they map out functional sites and specificity determinants (33) accurately enough to efficiently design mutations that block or swap functions among homologs in vitro (34–36) or in vivo (37, 38).Accordingly, given a query protein of unknown function, the ET Annotation pipeline (ETA) builds a 3D template from five or six top-ranked ET residues that also cluster together on surface regions of protein structures (31, 32). ETA then searches already annotated protein structures, the targets, for those that match the query 3D template (Fig. 1 and Movie S1). False positive matches are common but can be recognized because they typically (i) involve unimportant residues in the target (39), (ii) are not reciprocated back to the query (40), and (iii) point to multiple proteins that each bear unrelated functions. With appropriate specificity filters to eliminate these false positives, ETA identified enzyme activity down to the first three Enzyme Commission (EC) levels with 92% accuracy (40), as well as in nonenzymes (41) in large-scale Structural Genomics retrospective controls. The prediction of substrate specificity remains an open question and further requires accurate identification of the fourth and last EC level (42) presumably by adding a more discriminating use of 3D template residues than is sufficient to specify a general chemical process (43). Some sequence methods (29, 30) and other structure methods (14, 44) have aimed to predict all four EC levels, but to our knowledge they have not been directly tested on de novo predictions of substrate specificity.Open in a separate windowFig. 1.ETA accurately determines substrate specificity. (A) The ET algorithm is applied to a protein from Sulfolobus tokadaii strain 7 (green, PDB ID code 2eer, chain A) to identify evolutionarily important residues. A cluster of 10 or more important residues is identified and a Template Picker algorithm further selects five or six residues to act as a template that is used to probe a target library of proteins with known functions. Paired-distance matching algorithm identifies regions in protein structures in the target library that are similar to the template. Found matches are next passed to the SVM, which identifies significant matches based on geometric and evolutionary similarities. ETA repeats all these steps reciprocally, generating templates from target structures and searching for matches in the query protein. Following this protocol, ETA suggests four matches: alcohol dehydrogenase from Saccharomyces cerevisae (blue left, PDB ID code 2hcy), alcohol dehydrogenase from S. solfataricus (blue middle, PDB ID code 1r37), human class II alcohol dehydrogenase (blue right, PDB ID code 3cos), and NADP(H)-dependent cinnamyl alcohol dehydrogenase from S. cerevisae (red, PDB ID code 1piw) to the query protein. (B) The most seen function among matches, alcohol dehydrogenase activity (EC 1.1.1.1), is identified with high confidence with a confidence value of 1.125 as calculated in the box. (C) Comparison of PPV versus confidence score binned at <1, =1, and >1 for both six-residue templates (Left) and five-residue templates (Right) when considering only matches of <30% sequence identity. For more detail, see Fig. S1. (D) Comparison of PPV when predictions are made using ETA or the closest structural match (TM-align). Horizontal axis shows the maximum sequence identity of matches for proteins depicted in corresponding bars; the vertical axis is the PPV for each bin range.In this study, we improve the functional resolution of the ETA pipeline to identify relevant functional homology down to very low sequence identity and add substrate specificity to its large-scale predictions. We then experimentally validate the predictions and show that both catalytic and noncatalytic residues are essential for 3D templates to pinpoint activity and substrate specificity.     

On the specificity of DNA-protein interactions.

In this paper we summarize the various factors that must be considered in establishing the operational specificity of the binding of a protein regulator of gene expression to a DNA target site. We consider informational (combinatorial) aspects of binding-site specification, actual recognition mechanisms, and the thermodynamics of target-site selection against a background of competing pseudospecific and non-(sequence)-specific DNA binding sites. The results provide insight into the design, specification, and possibly the evolution of regulatory proteins and their chromosomal binding targets, as well as into practical aspects of the design of regulatory-protein isolation schemes and physicochemical regulatory considerations in vivo.     

Aromatic substrate specificity of browning by cultures of the Legionnaires' disease bacterium.

When the Legionnaires' disease (LD) bacterium is grown on supplemented Mueller-Hinton agar, brown pigmentation of the medium occurs. Since this browning may result from tyrosinase-mediated formation of melanin, we supplemented yeast-extract agar with various aromatic precursors of melanin and inoculated it with eight strains of the LD bacterium. Browning occurred with growth of each LD strain of the bacterium on yeast-extract agar enriched with 2.5 mmol/L of L-phenylalanine or L-tyrosine but not without such enrichment. Equimolar D-phenylalanine or D-tryosine in yeast-extract agar did not enhance browning. The LD bacterium may possess L-phenylalanine hydroxylase activity, but it does not use D-aromatic amino acids effectively in pigment production.     

Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serinethreonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.     

Control of oligomeric enzyme thermostability by protein engineering.

The ability to control the resistance of an enzyme to inactivation due to exposure to elevated temperatures is essential for the understanding of thermophilic behavior and for developing rational approaches to enzyme stabilization. By means of site-directed mutagenesis, point mutations have been engineered in the dimeric enzyme yeast triosephosphate isomerase that improve its thermostability. Cumulative replacement of asparagine residues at the subunit interface by residues resistant to heat-induced deterioration and approximating the geometry of asparagine (Asn-14----Thr-14 and Asn-78----Ile-78) nearly doubled the half-life of the enzyme at 100 degrees C, pH 6. Moreover, in an attempt to model the deleterious effects of deamidation, we show that replacement of interfacial Asn-78 by an aspartic acid residue increases the rate constant of irreversible thermal inactivation, drastically decreases the reversible transition temperature, and reduces the stability against dilution-induced dissociation.     

Alteration of substrate specificity for the endoribonucleolytic cleavage of RNA by the Tetrahymena ribozyme.

A shortened form of the intervening sequence of the self-splicing RNA from Tetrahymena thermophila catalyzes sequence-specific cleavage of RNA. Cleavage site selection involves a base-pairing interaction between the substrate RNA and a binding site within the intervening sequence. Single-base changes in this binding site were previously shown to alter substrate specificity in a predictable manner. To examine the generality with which substrate specificity can be altered, six variant catalytic RNAs (ribozymes) have been produced with two- or three-base changes in the active site. Each ribozyme cleaves its predicted substrate. The conditions required for good reactivity and for discrimination against cleavage at mismatched sites vary and were independently determined for each ribozyme.     

Protein interactions and ligand binding: From protein subfamilies to functional specificity

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as “specificity determining positions” (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.     

An electrostatic mechanism for substrate guidance down the aromatic gorge of acetylcholinesterase.

Electrostatic calculations based on the recently solved crystal structure of acetylcholinesterase (acetylcholine acetylhydrolase, EC 3.1.1.7) indicate that this enzyme has a strong electrostatic dipole. The dipole is aligned with the gorge leading to its active site, so that a positively charged substrate will be drawn to the active site by its electrostatic field. Within the gorge, aromatic side chains appear to shield the substrate from direct interaction with most of the negatively charged residues that give rise to the dipole. The affinity of quaternary ammonium compounds for aromatic rings, coupled with this electrostatic force, may work in concert to create a selective and efficient substrate-binding site in acetylcholinesterase and explain why the active site is situated at the bottom of a deep gorge lined with aromatic residues.     

Effect of side chain-backbone electrostatic interactions on the stability of alpha-helices.

An apparent discrepancy between the observed stability of the C-peptide alpha-helix of ribonuclease A and that computed from the Zimm-Bragg parameters sigma and s (obtained by the host-guest technique) is resolved. Side chain-backbone ion-dipole interactions play a role in both systems. However, they are averaged out in the random copolymers used to determine sigma and s for charged residues such as glutamic acid but not in the specific-sequence copolymer, namely, the C-peptide, where they contribute significantly to the helix stability. In considering a specific-sequence alpha-helix, its intrinsic stabilizing free energy (expressed in terms of sigma and s) must be augmented by position-dependent stabilizing long-range electrostatic interactions.     

Sequence specificity in aflatoxin B1--DNA interactions.

The activated form of aflatoxin B1 (AFB1) causes covalent modification primarily of guanine residues, leading to alkali-labile sites in DNA. A simple extension of the Maxam-Gilbert procedure for sequence analysis permits the identification of alkali-labile sites induced by AFB1 and determination of the frequency of alkali-labile AFB1 modifications at particular sites on a DNA fragment of known sequence. Using this strategy, we have investigated the influence of flanking nucleotide sequences on AFB1 modification in a number of DNA fragments of known sequence. Our results show that certain guanine residues in double-stranded DNA are preferentially attacked by AFB1 over others in a manner predictable from a knowledge of vicinal nucleotide sequences. The observed in vitro sequence specificity is independent of a number of tested parameters and is likely to occur in vivo.     

Effects of hydrodynamics and leukocyte-endothelium specificity on leukocyte-endothelium interactions.

In vivo microscopy was used to assess the relative contribution of hydrodynamic forces (network topography and shear rate) and the specificity for leukocytes to interact with venular endothelium as determinants of leukocyte-endothelium interactions. To ascertain this, microvascular networks in the rat and rabbit mesentery were examined under normograde and mechanically induced retrograde flows to determine the effect of reversed flow on leukocyte-endothelium interactions in arterioles and venules. The data indicate that retrograde perfusion under hemodynamic (red blood cell velocity and shear rate) states equivalent to normograde flow significantly increased leukocyte marginating flux in arterioles (from 0 to 0.5 cells/5 sec) and decreased flux significantly in venules (from 1.0 to 0.2 cells/5 sec). The increased flux in arterioles under retrograde conditions, however, was significantly lower than the flux in venules under normograde conditions and the decreased flux in venules during retrograde flow was significantly greater than the flux in arterioles during normograde flow. This apparent discrepancy appears to be the result of a heterogeneous distribution of adhesive receptors on vascular endothelium. Furthermore, marginating leukocytes in arterioles made only brief contact with the endothelium before being swept away while marginating leukocytes in venules during normal and retrograde perfusion rolled along the vascular wall, with similar velocities in both directions. In conclusion, although hydrodynamic forces are important in facilitating leukocyte margination through mechanisms of radial migration, it is leukocyte-endothelium specificity in venules that ultimately determines leukocyte-endothelium interactions.     

Phosphorylation of a UDP-glucuronosyltransferase regulates substrate specificity

UDP-glucuronosyltransferase (UGT) isozymes catalyze detoxification of numerous chemical toxins present in our daily diet and environment by conjugation to glucuronic acid. The special properties and enzymatic mechanism(s) that enable endoplasmic reticulum-bound UGT isozymes to convert innumerable structurally diverse lipophiles to excretable glucuronides are unknown. Inhibition of cellular UGT1A7 and UGT1A10 activities and of [33P]orthophosphate incorporation into immunoprecipitable proteins after exposure to curcumin or calphostin-C indicated that the isozymes are phosphorylated. Furthermore, inhibition of UGT phosphorylation and activity by treatment with PKCepsilon-specific inhibitor peptide supported PKC involvement. Co-immunoprecipitation, colocalization by means of immunofluorescence, and cross-linking studies of PKCepsilon and UGT1A7His revealed that the proteins reside within 11.4 angstroms of each other. Moreover, mutation of three PKC sites in each UGT isozyme demonstrated that T73A/G and T202A/G caused null activity, whereas S432G-UGT1A7 caused a major shift of its pH-8.5 optimum to 6.4 with new substrate selections, including 17beta-estradiol. S432G-UGT1A10 exhibited a minor pH shift without substrate alterations. PKCepsilon involvement was confirmed by the demonstration that PKCepsilon overexpression enhanced activity of UGT1A7 but not of its S432 mutant and the conversion of 17beta-[14C]estradiol by S432G-UGT1A7 but not by UGT1A7. Consistent with these observations, treatment of UGT1A7-transfected cells with PKCepsilon-specific inhibitor peptide or general PKC inhibitors increased 17beta-estradiol catalysis between 5- and 11-fold, with parallel decreases in phosphoserine-432. Here, we report a mechanism involving PKC-mediated phosphorylation of UGT such that phosphoserine/threonine regulates substrate specificity in response to chemical exposures, which possibly confers survival benefit.     

Conversion of human choriogonadotropin into a follitropin by protein engineering.

Human reproduction is dependent upon the actions of follicle-stimulating hormone (hFSH), luteinizing hormone (hLH), and chorionic gonadotropin (hCG). While the alpha subunits of these heterodimeric proteins can be interchanged without effect on receptor-binding specificity, their beta subunits differ and direct hormone binding to either LH/CG or FSH receptors. Previous studies employing chemical modifications of the hormones, monoclonal antibodies, or synthetic peptides have implicated hCG beta-subunit residues between Cys-38 and Cys-57 and corresponding regions of hLH beta and hFSH beta in receptor recognition and activation. Since the beta subunits of hCG or hLH and hFSH exhibit very little sequence similarity in this region, we postulated that these residues might contribute to hormone specificity. To test this hypothesis we constructed chimeric hCG/hFSH beta subunits, coexpressed them with the human alpha subunit, and examined their ability to interact with LH and FSH receptors and hormone-specific monoclonal antibodies. Surprisingly, substitution of hFSH beta residues 33-52 for hCG beta residues 39-58 had no effect on receptor binding or stimulation. However, substitution of hFSH beta residues 88-108 in place of the carboxyl terminus of hCG beta (residues 94-145) resulted in a hormone analog identical to hFSH in its ability to bind and stimulate FSH receptors. The altered binding specificity displayed by this analog is not attributable solely to the replacement of hCG beta residues 108-145 or substitution of residues in the "determinant loop" located between hCG beta residues 93 and 100.     

Substrate specificity of the protein tyrosine phosphatases.

The substrate specificity of a recombinant protein tyrosine phosphatase (PTPase) was probed using synthetic phosphotyrosine-containing peptides corresponding to several of the autophosphorylation sites in epidermal growth factor receptor (EGFR). The peptide corresponding to the autophosphorylation site, EGFR988-998, was chosen for further study due to its favorable kinetic constants. The contribution of individual amino acid side chains to the binding and catalysis was ascertained utilizing a strategy in which each amino acid within the undecapeptide EGFR988-998 (DADEpYLIPQQG) was sequentially substituted by an Ala residue (Ala-scan). The resulting effects due to singular Ala substitution were assessed by kinetic analysis with two widely divergent homogeneous PTPases. A "consensus sequence" for PTPase recognition may be suggested from the Ala-scan data as DADEpYAAPA, and the presence of acidic residues proximate to the NH2-terminal side of phosphorylation is critical for high-affinity binding and catalysis. The Km value for EGFR988-998 decreased as the pH increased, suggesting that phosphate dianion is favored for substrate binding. The results demonstrate that chemical features in the primary structure surrounding the dephosphorylation site contribute to PTPase substrate specificity.     

Combinatorial protein engineering by incremental truncation

We have developed a combinatorial approach, using incremental truncation libraries of overlapping N- and C-terminal gene fragments, that examines all possible bisection points within a given region of an enzyme that will allow the conversion of a monomeric enzyme into its functional heterodimer. This general method for enzyme bisection will have broad applications in the engineering of new catalytic functions through domain swapping and chemical synthesis of modified peptide fragments and in the study of enzyme evolution and protein folding. We have tested this methodology on Escherichia coli glycinamide ribonucleotide formyltransferase (PurN) and, by genetic selection, identified PurN heterodimers capable of glycinamide ribonucleotide transformylation. Two were chosen for physical characterization and were found to be comparable to the wild-type PurN monomer in terms of stability to denaturation, activity, and binding of substrate and cofactor. Sequence analysis of 18 randomly chosen, active PurN heterodimers revealed that the breakpoints primarily clustered in loops near the surface of the enzyme, that the breaks could result in the deletion of highly conserved residues and, most surprisingly, that the active site could be bisected.