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K M Shokat

Publications and source records attributed to K M Shokat.

30 records · Page 2Linked to original sources
PubMed1998

A molecular gate which controls unnatural ATP analogue recognition by the tyrosine kinase v-Src.

Engineered proteins with specificity for unnatural substrates or ligands are useful tools for studying or manipulating complex biological systems. We have engineered the prototypical tyrosine kinase v-Src to accept an unnatural ATP analogue N6-(benzyl) ATP in order to identify v-Src's direct cellular substrates. Here we have used molecular modeling to analyze the binding mode of N6-(benzyl) ATP. Based on this modeling we proposed that a new ATP analogue (N6-(2-phenethyl) ATP might be a better substrate than N6-(benzyl) ATP for the I338G mutant of v-Src. In fact the newly proposed analogue (N6-(2-phenethyl) ATP is a somewhat improved substrate for the engineered kinase (kcat = 0.6 min-1, KM = 8 microM). We also synthesized and screened three analogues of N6-(benzyl) ATP: N6-(2-methylbenzyl), ATP N6-(3-methylbenzyl), and ATP N6-(4-methylbenzyl) ATP to further probe the dimensions and shape of the introduced pocket. Results from screening newly synthesized ATP analogues agreed well with our modeling predictions. We conclude that rather than engineering a 'new' pocket by mutation of Ile 338 in v-Src to the smaller Ala or Gly residues, the I338G and I338A mutants possess a 'path' for the N6 substituent on ATP to gain access to an existing pocket in the ATP binding site. We expect to be able to extend the engineering of v-Src's ATP specificity to other kinase families based on our understanding of the binding modes of ATP analogues to engineered kinases.

Adenosine Triphosphate↗
PubMed1998

Engineering Src family protein kinases with unnatural nucleotide specificity.

BACKGROUND: Protein kinases play a central role in controlling diverse signal transduction pathways in all cells. The identification of the direct cellular substrates of individual protein kinases remains the key challenge in the field. RESULTS: We describe the protein engineering of v-Src to produce a kinase which preferentially uses an ATP analog, N6-(benzyl) ATP, as a substrate, rather than the natural v-Src substrate, ATP. The sidechain of a single residue (Ile338) controls specificity for N6-substituted ATP analogs in the binding pocket of v-Src. Elimination of this sidechain by mutation to glycine produces a v-Src kinase which preferentially utilizes N6-(benzyl) ATP as a phosphodonor substrate. Our engineering strategy is generally applicable to the Src family kinases: mutation of the corresponding residue (Thr339 to glycine) in the Fyn kinase confers specificity for N6-(benzyl) ATP on Fyn. CONCLUSIONS: The v-Src tyrosine kinase has been engineered to exhibit specificity for an unnatural ATP analog, N6-(benzyl) ATP, even in a cellular context where high concentrations of natural ATP are present (1-5 mM), where preferential use of the ATP analog by the mutant kinase is essential. The mutant v-Src transfers phosphate more efficiently with the designed unnatural analog than with ATP. As the identical mutation in the Src-family kinase Fyn confers on Fyn the ability to recognize the same unnatural ATP analog, our strategy is likely to be generally applicable to other protein kinases and may help to identify the direct targets of specific kinases.

Adenosine Triphosphate↗
PubMed1997

Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates.

Protein phosphorylation plays a central role in controlling many diverse signal transduction pathways in all cells. Novel protein kinases are identified at a rapid rate using homology cloning methods and genetic screens or selections; however identification of the direct substrates of kinases has proven elusive to genetic methods because of the tremendous redundancy and overlapping of substrate specificities among protein kinases. We describe the development of a protein engineering-based method to identify the direct substrates of the prototypical protein tyrosine kinase v-Src, which controls fibroblast transformation by the Rous sarcoma virus. To differentiate the substrates of v-Src from all other kinase substrates, we mutated the ATP binding site of v-Src such that the engineered v-Src uniquely accepted an ATP analog. We show that the engineered v-Src kinase displayed catalytic efficiency with the ATP analog, N(6)-(cyclopentyl) ATP, which is similar to the wild-type kinase catalytic efficiency with ATP itself. However, the N(6)-(cyclopentyl) ATP analog was not accepted by the wild-type kinase. Furthermore, the engineered v-Src exhibited the same protein target specificity as wild-type v-Src despite the proximity of the reengineered nucleotide binding site to the phosphoacceptor binding site. The successful engineering of v-Src's active site to accept a unique nucleotide analog provides a unique handle by which the direct substrates of one kinase (v-Src) can be traced in the presence of any number of cellular kinases.

Amino Acid Sequence↗
PubMed1995

Antigen-induced B-cell death and elimination during germinal-centre immune responses.

During an immune response, hypermutation of immunoglobulin genes in B cells proliferating within germinal centres (GCs) generates variant antibodies that react with higher affinity against either foreign or self antigens. Several experiments suggest that self-reactive B cells may be censored at this stage of the immune response, but the rarity of these cells and the dynamic nature of GC reactions have prevented direct analysis. We have developed a new approach to visualize the fate of antigen-specific B cells during GC reactions by seeding an ongoing immune response with lysozyme-specific B cells from immunoglobulin-gene transgenic animals. Administration of soluble antigen at the peak of the GC response rapidly eliminates lysozyme-specific GC B cells in two waves of apoptosis, one within the GC and a second in cells that have redistributed to lymphoid zones that are rich in T cells. Elimination of these cells is inhibited by constitutive expression of the follicular lymphoma proto-oncogene bcl-2. These findings reveal censoring steps that may normally prevent affinity maturation of autoantibodies to systemic autoantigens, and might be used by pathogenic microorganisms or in clinical strategies to interfere with antibody responses.

Amino Acid Sequence↗
PubMed1995

Tyrosine kinases: modular signaling enzymes with tunable specificities.

Cytoplasmic tyrosine kinases are composed of modular domains; one (SH1) has catalytic activity, the other two (SH2 and SH3) do not. Kinase specificity is largely determined by the binding preferences of the SH2 domain. Attaching the SH1 domain to a new SH2 domain, via protein-protein association or mutation, can thus dramatically change kinase function.

Protein-Tyrosine Kinases↗
PubMed1994

Immunoglobulin signal transduction guides the specificity of B cell-T cell interactions and is blocked in tolerant self-reactive B cells.

The specificity of antibody (Ab) responses depends on focusing helper T (Th) lymphocyte signals to suitable B lymphocytes capable of binding foreign antigens (Ags), and away from nonspecific or self-reactive B cells. To investigate the molecular mechanisms that prevent the activation of self-reactive B lymphocytes, the activation requirements of B cells specific for the Ag hen egg lysozyme (HEL) obtained from immunoglobulin (Ig)-transgenic mice were compared with those of functionally tolerant B cells isolated from Ig-transgenic mice which also express soluble HEL. To eliminate the need for surface (s)Ig-mediated Ag uptake and presentation and allow the effects of sIg signaling to be studied in isolation, we assessed the ability of allogeneic T cells from bm12 strain mice to provide in vivo help to C57BL/6 strain-transgenic B cells. Interestingly, non-tolerant Ig-transgenic B cells required both allogeneic Th cells and binding of soluble HEL for efficient activation and Ab production. By contrast, tolerant self-reactive B cells from Ig/HEL double transgenic mice responded poorly to the same combination of allogeneic T cells and soluble HEL. The tolerant B cells were nevertheless normally responsive to stimulation with interleukin 4 and anti-CD40 Abs in vitro, suggesting that they retained the capacity to respond to mediators of T cell help. However, the tolerant B cells exhibited a proximal block in the sIg signaling pathway which prevented activation of receptor-associated tyrosine kinases in response to the binding of soluble HEL. The functional significance of this sIg signaling defect was confirmed by using a more potent membrane-bound form of HEL capable of triggering sIg signaling in tolerant B cells, which markedly restored their ability to collaborate with allogeneic Th cells and produce Ab. These findings indicate that Ag-specific B cells require two signals for mounting a T cell-dependent Ab response and identify regulation of sIg signaling as a mechanism for controlling self-reactive B cells.

Animals↗
PubMed1991

The generation of antibody combining sites containing catalytic residues.

To expand the scope of antibody-catalysed reactions to those involving rate-limiting proton abstraction, such as elimination, isomerization and condensation reactions, we developed a new strategy--hapten charge complementarity. A hapten containing a benzyl ammonium group was used to elicit a specific base, a carboxylate, in the combining site of an antibody that catalysed a beta-elimination reaction. This was the first example of the use of a hapten to elicit a specific catalytic residue in an antibody combining site. A variety of kinetic and chemical modification experiments strongly suggest that a specific Asp or Glu residue in the combining site is responsible for catalysis. Preliminary results indicate that in addition to charge-charge complementarity, the nucleophilic reactivity of amino acid residues (Ser, Thr, Lys, Asp, Glu, Cys) in antibodies can be used as a selection tool. Antibodies were raised against a reactive epoxide group to elicit an antibody containing a uniquely reactive carboxylate or thiol group. Antibodies which bind the epoxide do catalyse a beta-elimination reaction, indicating the presence of a specific base in the combining site. Antibodies elicited to two closely related haptens do not catalyse the beta-elimination reaction.

Antibodies↗
PubMed1989

A new strategy for the generation of catalytic antibodies.

The high binding affinity and specificity of antibodies for a wide range of ligands has recently been exploited in the generation of catalysts for acyl-transfer reactions, carbon-carbon bond forming and carbon-carbon bond cleaving reactions. In addition, a number of strategies are emerging for the generation of catalytic antibodies including transition state stabilization, catalysis by approximation, and the introduction of catalytic groups or cofactors into antibody combining sites. An important goal in the design of catalytic antibodies is the development of general rules relating hapten structure to the corresponding catalytic groups in the antibody combining site. We report here that electrostatic interactions between a hapten and the complementary antibody can be exploited to generate catalytic amino-acid side chains in an antibody-combining site. The antibody-catalysed reaction, a beta-elimination reaction, exhibits saturation kinetics, substrate specificity, competitive inhibition by hapten, and specific inactivation by a reagent that modifies carboxylate residues.

Antibodies↗
PubMed1987

Does the bifunctional uridylate synthase channel orotidine 5'-phosphate? Kinetics of orotate phosphoribosyltransferase and orotidylate decarboxylase activities fit a noninteracting sites model.

Uridylate synthase is a bifunctional protein that first forms orotidine 5'-phosphate (OMP) from orotate via its orotate phosphoribosyltransferase activity (EC 2.4.2.10) and then converts OMP to uridine 5'-phosphate (UMP) via the OMP decarboxylase activity (EC 4.1.1.23). A computer modeling analysis of the experiments that led to the proposal [Traut, T.W., & Jones, M.E. (1977) J. Biol. Chem. 252, 8374-8381] that uridylate synthase channels intermediate OMP suggests that the experimental results do not demonstrate preferential use of OMP generated in the bifunctional complex as against exogenous OMP. This analysis shows that the experimentally observed amounts of [6-14C]UMP from [6-14C]orotate in the presence of various amounts of exogenous [7-14C]OMP agree well with the amounts predicted by the computer simulations. Thus we conclude that uridylate synthase does not channel OMP. Additionally, the subsequent suggestion that channeling of OMP occurs to protect the intermediate from degradation by a nucleotidase [Traut, T.W. (1980) Arch. Biochem. Biophys. 200, 590-594] seems unlikely. The appropriate computer simulation demonstrates that low transient levels of OMP and protection of the intermediate are provided for strictly by the kinetic parameters of orotate phosphoribosyltransferase, OMP decarboxylase, and the nucleotidase. Additionally, calculations show that, in both sets of published experiments, the concentration of transient OMP greatly exceeded the concentration of OMP decarboxylase active sites. Thus, channeling of OMP by the bifunctional complex cannot be invoked to explain the evolution of uridylate synthase, and that event must be the result of some other selective pressure.

Carboxy-Lyases↗
PubMedDate not supplied

Acquisition of inhibitor-sensitive protein kinases through protein design.

Protein phosphorylation is the major post-translational modification used by eukaryotic cells to control cellular signaling. Protein kinases have emerged as attractive drug targets because heightened protein kinase activity has been associated with several proliferative diseases, most notably cancer and restenosis. Until now, it has been very difficult to confirm the utility of protein kinases as inhibitor targets because very few small molecules that selectively inhibit one particular kinase are known. Discovery of highly specific kinase inhibitors has been slow because the protein family contains approximately 2000 members, all of which share a conserved active site fold. Recent work in several laboratories has sought to circumvent the problem of kinase structural degeneracy by engineering drug sensitivity into Src family tyrosine kinases and mitogen-activated protein kinases through site-directed mutagenesis. By introducing a unique non-naturally occurring amino acid into a conserved region of the enzyme's binding site, a target protein kinase can be rapidly sensitized to a small molecule. Introduction of the engineered kinase into a cell line or animal model should greatly expedite the investigation of protein kinase inhibition as a viable drug treatment. The purpose of this review is to summarize these recent advances in protein kinase drug sensitization.

Animals↗