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Slama JT, Radziejewski C, Oruganti S, Kaiser ET. Semisynthetic enzymes: characterization of isomeric flavopapains with widely different catalytic efficiencies. J Am Chem Soc. 106:1984;6778-6785.
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Radziejewski C, Ballou DP, Kaiser ET. Catalysis of N-alkyl-1,4-dihydronicotinamide oxidation by a flavopapain: rapid reaction in all catalytic steps. J Am Chem Soc. 107:1985;3352-3354.
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Hilvert D, Hatanaka Y, Kaiser ET. A highly active thermophilic semisynthetic flavoenzyme. J Am Chem Soc. 100:1988;682-689.
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Chen CB, Sigman DS. Chemical conversion of a DNA-binding protein into a site-specific nuclease. Science. 237:1987;1197-1201.
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Sluka JP, Horvath SJ, Bruist MF, Simon MI, Dervan PB. Synthesis of a sequence specific DNA-cleaving peptide. Science. 238:1987;1129-1132.
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Sluka, J.P.1
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0028846429
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Drosophila engrailed-1,10-phenanthroline chimeras as probes of homeodomain-DNA complexes
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Pan CQ, Landgraf R, Sigman DS. Drosophila engrailed-1,10-phenanthroline chimeras as probes of homeodomain-DNA complexes. Protein Sci. 4:1995;2279-2288.
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Pan, C.Q.1
Landgraf, R.2
Sigman, D.S.3
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27
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Structure of the E, coli Fis-DNA complex probed by protein conjugated with 1,10-phenanthroline Cu(I) complex
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Pan CQ, Feng JA, Finkel SE, Landgraf R, Sigman D, Johnson RC. Structure of the E, coli Fis-DNA complex probed by protein conjugated with 1,10-phenanthroline Cu(I) complex. Proc Natl Acad Sci USA. 91:1994;1721-1725.
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Pan, C.Q.1
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Johnson, R.C.6
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28
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0027535528
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Mapping interactions between the catalytic domain of resolvase and its DNA substrate using cysteine-coupled EDTA-iron
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Mazzarelli JM, Ermacora MR, Fox RO, Grindley NDF. Mapping interactions between the catalytic domain of resolvase and its DNA substrate using cysteine-coupled EDTA-iron. Biochemistry. 32:1993;2779-2986.
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Mazzarelli, J.M.1
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29
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0031056544
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The two alpha subunits of Escherichia Coli RNA polymerase are asymetrically arranged and contact different halves of the DNA upstream element
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of special interest. The C-terminal regulatory domain (CTD) from the E. coli RNA polymerase α subunit was conjugated with an EDTA derivative. The resulting construct was used to investigate the interaction between the cAMP receptor protein (CRP) and the CTD when the protein complex was bound to DNA. Using the technique of affinity cleavage, the authors showed that the CTDs of two α subunits interact with two bound CRP dimers and that the architecture of the protein - DNA complex is controlled by the position of the CRP dimer on the DNA. Thus, protein-protein interactions appear to regulate key aspects of RNA polymerase function.
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Murakami K, Kimura M, Owens JT, Meares CF, Ishihama A. The two alpha subunits of Escherichia Coli RNA polymerase are asymetrically arranged and contact different halves of the DNA upstream element. of special interest Proc Natl Acad Sci USA. 94:1997;1709-1714 The C-terminal regulatory domain (CTD) from the E. coli RNA polymerase α subunit was conjugated with an EDTA derivative. The resulting construct was used to investigate the interaction between the cAMP receptor protein (CRP) and the CTD when the protein complex was bound to DNA. Using the technique of affinity cleavage, the authors showed that the CTDs of two α subunits interact with two bound CRP dimers and that the architecture of the protein - DNA complex is controlled by the position of the CRP dimer on the DNA. Thus, protein-protein interactions appear to regulate key aspects of RNA polymerase function.
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(1997)
Proc Natl Acad Sci USA
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Murakami, K.1
Kimura, M.2
Owens, J.T.3
Meares, C.F.4
Ishihama, A.5
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Corey DR, Schultz PG. Generation of a hybrid sequence specific single stranded deoxyribonuclease. Science. 238:1987;1401-1403.
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Corey DR, Pei D, Schultz PG. Generation of a catalytic sequence-specific hybrid DNase. Biochemistry. 28:1989;8277-8286.
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Corey DR, Pei D, Schultz PG. Sequence specific hydrolysis of duplex DNA by an oligonucleotide-directed nuclease. J Am Chem Soc. 111:1989;8523-8525.
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Pei D, Schuitz PG. Engineering protein specificity: gene manipulation with semisynthetic nucleases. J Am Chem Soc. 113:1991;9398-9400.
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Zuckermann RN, Schultz PG. A hybrid sequence-selective ribonuclease S. J Am Chem Soc. 110:1988;6592-6594.
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Zuckermann, R.N.1
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Rana TM, Meares CF. Specific cleavage of a protein by an attached iron chelate. J Am Chem Soc. 112:1990;2457-2458.
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Rana, T.M.1
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Rana TM, Meares CF. Iron chelate mediated proteolysis: protein structure dependence. J Am Chem Soc. 113:1991;1859-1861.
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Rana, T.M.1
Meares, C.F.2
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Mapping staphylococcal nuclease conformation using an EDTA-Fe derivative attached to genetically engineered cysteine residues
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Ermacora MR, Ledman DW, Hellinga HW, Hsu GW, Fox RO. Mapping staphylococcal nuclease conformation using an EDTA-Fe derivative attached to genetically engineered cysteine residues. Biochemistry. 33:1994;13625-13641.
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ErMacOra, M.R.1
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Hellinga, H.W.3
Hsu, G.W.4
Fox, R.O.5
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38
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0029115087
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Proximity mapping the surface of a membrane protein using an artificial protease: Demonstration that the quinone-binding domain of subunit I is near the N-terminal region of subunit II of cytochrome bd
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Ghaim JB, Greiner DP, Meares CF, Gennis Rb. Proximity mapping the surface of a membrane protein using an artificial protease: demonstration that the quinone-binding domain of subunit I is near the N-terminal region of subunit II of cytochrome bd. Biochemistry. 34:1995;11311-11315.
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Ghaim, J.B.1
Greiner, D.P.2
Meares, C.F.3
Gennis Rb4
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0029074762
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Helix packing of lactose permease in Escherichia coli studied by site-directed chemical cleavage
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Wu J, Perrin DM, Sigman DS, Kaback HR. Helix packing of lactose permease in Escherichia coli studied by site-directed chemical cleavage. Proc Natl Acad Sci USA. 92:1995;9186-9190.
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Wu, J.1
Perrin, D.M.2
Sigman, D.S.3
Kaback, H.R.4
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40
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0032562135
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Protease activity of 1,10-phenanthroline-copper(I). Targeted scission of the catalytic site of carbonic anhydrase
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of outstanding interest. Protein conjugates incorporating 1,10-phenanthroline moieties are useful constructs for protein affinity-cleavage experiments. Here, the mechanism of the cleavage reaction performed by a small molecule construct was investigated, showing that cleavage by this copper-based system proceeds by an oxidative pathway. N- and C-terminal sequencing and mass spectral analysis of the cleavage products indicate that the C-terminal cleavage products have free amino groups at their N termini, permitting analysis via Edman degradation. In contrast, the N-terminal fragments lack a free carboxyl group at their C termini, suggesting that scission occurs by hydrogen abstraction at Cα, followed by oxidative cleavage of the Cα-C(O) bond.
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Gallagher J, Zelenko O, Walts AD, Sigman DS. Protease activity of 1,10-phenanthroline-copper(I). Targeted scission of the catalytic site of carbonic anhydrase. of outstanding interest Biochemistry. 37:1998;2096-2104 Protein conjugates incorporating 1,10-phenanthroline moieties are useful constructs for protein affinity-cleavage experiments. Here, the mechanism of the cleavage reaction performed by a small molecule construct was investigated, showing that cleavage by this copper-based system proceeds by an oxidative pathway. N- and C-terminal sequencing and mass spectral analysis of the cleavage products indicate that the C-terminal cleavage products have free amino groups at their N termini, permitting analysis via Edman degradation. In contrast, the N-terminal fragments lack a free carboxyl group at their C termini, suggesting that scission occurs by hydrogen abstraction at Cα, followed by oxidative cleavage of the Cα-C(O) bond.
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Biochemistry
, vol.37
, pp. 2096-2104
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Gallagher, J.1
Zelenko, O.2
Walts, A.D.3
Sigman, D.S.4
-
41
-
-
0032477810
-
Dimeric association of Escherichia Coli RNA polymerase subunits, studied by cleavage of single cysteine alpha subunits conjugated to iron-(S)-1-[p-(bromoacetamido) benzyl]ethylenediaminetetraacetate
-
of outstanding interest. Using a series of four mutants of the E. coli RNA polymerase α subunit that each contain a single cysteine residue, four EDTA conjugates were prepared. It was necessary to prepare the constructs under denaturing conditions in order to obtain efficient conjugation. These modified proteins were used in affinity-cleavage experiments to show that the N-terminal assembly domain of one subunit is proximal to the linker region between the N- and C-terminal domains of the other subunit. In contrast to previous results with other EDTA-based conjugates, cleavage may occur in these examples via oxidative processes.
-
Miyake R, Murakami K, Owens JT, Greiner DP, Ozoline ON, Ishinama A, Moares CF. Dimeric association of Escherichia Coli RNA polymerase subunits, studied by cleavage of single cysteine alpha subunits conjugated to iron-(S)-1-[p-(bromoacetamido) benzyl]ethylenediaminetetraacetate. of outstanding interest Biochemistry. 37:1998;1344-1349 Using a series of four mutants of the E. coli RNA polymerase α subunit that each contain a single cysteine residue, four EDTA conjugates were prepared. It was necessary to prepare the constructs under denaturing conditions in order to obtain efficient conjugation. These modified proteins were used in affinity-cleavage experiments to show that the N-terminal assembly domain of one subunit is proximal to the linker region between the N- and C-terminal domains of the other subunit. In contrast to previous results with other EDTA-based conjugates, cleavage may occur in these examples via oxidative processes.
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(1998)
Biochemistry
, vol.37
, pp. 1344-1349
-
-
Miyake, R.1
Murakami, K.2
Owens, J.T.3
Greiner, D.P.4
Ozoline, O.N.5
Ishinama, A.6
Moares, C.F.7
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43
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0028252982
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Coenzyme-amino acid chimeras: New residues for the assembly of functional proteins
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Imperiali B, Roy RS. Coenzyme-amino acid chimeras: new residues for the assembly of functional proteins. J Am Chem Soc. 116:1994;12083-12084.
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Imperiali, B.1
Roy, R.S.2
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44
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0242701926
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Pyridoxamine-amino acid chimeras in semisynthetic aminotransferase mimics
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of outstanding interest. Two semisynthetic transaminases that incorporate a pyridoxamine cofactor into the C-peptide of RNase S are described. These conjugates were designed in order to examine whether elements from the catalytic apparatus of RNases could be recruited to accelerate pyridoxamine-catalyzed reactions. The rate accelerations and enantioselectivities obtained with these constructs suggest that the structure of the noncovalent RNase S protein - peptide complex plays an important role in modulating the properties of these pyridoxamine-containing catalysts.
-
Roy RS, Imperiali B. Pyridoxamine-amino acid chimeras in semisynthetic aminotransferase mimics. of outstanding interest Protein Sci. 10:1997;691-698 Two semisynthetic transaminases that incorporate a pyridoxamine cofactor into the C-peptide of RNase S are described. These conjugates were designed in order to examine whether elements from the catalytic apparatus of RNases could be recruited to accelerate pyridoxamine-catalyzed reactions. The rate accelerations and enantioselectivities obtained with these constructs suggest that the structure of the noncovalent RNase S protein - peptide complex plays an important role in modulating the properties of these pyridoxamine-containing catalysts.
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(1997)
Protein Sci
, vol.10
, pp. 691-698
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-
Roy, R.S.1
Imperiali, B.2
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45
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0028260307
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Lipid binding proteins: A family of fatty acid and retinoid transport proteins
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Banaszak L, Winter N, Xu Z, Bernlohr DA, Cowan S, Jones TA. Lipid binding proteins: a family of fatty acid and retinoid transport proteins. Adv Protein Chem. 45:1994;89-151.
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(1994)
Adv Protein Chem
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Banaszak, L.1
Winter, N.2
Xu, Z.3
Bernlohr, D.A.4
Cowan, S.5
Jones, T.A.6
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46
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0030573021
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The NMR solution structure of intestinal fatty acid binding protein complexed with palmitate: Application of a novel distance geometry algorithm
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Hoosdon ME, Ponder JW, Cistola DP. The NMR solution structure of intestinal fatty acid binding protein complexed with palmitate: application of a novel distance geometry algorithm. J Mol Biol. 264:1996;585-602.
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J Mol Biol
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Hoosdon, M.E.1
Ponder, J.W.2
Cistola, D.P.3
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47
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0029798560
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Enantioselective reductive amination of α-keto acids to α-amino acids by a pyridoxamine cofactor in a protein cavity
-
of special interest. ALBP - PX, an adipocyte lipid-binding protein conjugate that positions a disulfide-bound pyridoxamine cofactor within a sequestered protein cavity, reductively aminates a number of alkyl, aryl and sidechain functionalized α-keto acids to α-amino acids with enantioselectivities as high as 94% ee.
-
Kuang H, Brown ML, Davies RR, Young EC, Distefano MD. Enantioselective reductive amination of α-keto acids to α-amino acids by a pyridoxamine cofactor in a protein cavity. of special interest J Am Chem Soc. 118:1996;10702-10706 ALBP - PX, an adipocyte lipid-binding protein conjugate that positions a disulfide-bound pyridoxamine cofactor within a sequestered protein cavity, reductively aminates a number of alkyl, aryl and sidechain functionalized α-keto acids to α-amino acids with enantioselectivities as high as 94% ee.
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(1996)
J Am Chem Soc
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-
Kuang, H.1
Brown, M.L.2
Davies, R.R.3
Young, E.C.4
Distefano, M.D.5
-
48
-
-
0031777410
-
Structural characterization of two synthetic catalysts based on adipocyte lipid binding protein
-
of outstanding interest. The structures, determined by X-ray diffraction analysis, of two conjugates based on the adipocyte lipid binding protein are described. The X-ray models show the presence of the phenanthroline and pyridoxamine moieties within the protein cavity. They are useful for examining the origin of the chiral selectivities seen in the reactions catalyzed by these constructs. In both cases, these covalent adducts reduce the volume of the internal cavity and sterically limit substrate interactions as well as solvent access to potential intermediates in the reaction pathway.
-
Ory JJ, Mazhary A, Kuang H, Davies RR, Distelano MD, Banaszak LJ. Structural characterization of two synthetic catalysts based on adipocyte lipid binding protein. of outstanding interest Protein Eng. 11:1998;253-261 The structures, determined by X-ray diffraction analysis, of two conjugates based on the adipocyte lipid binding protein are described. The X-ray models show the presence of the phenanthroline and pyridoxamine moieties within the protein cavity. They are useful for examining the origin of the chiral selectivities seen in the reactions catalyzed by these constructs. In both cases, these covalent adducts reduce the volume of the internal cavity and sterically limit substrate interactions as well as solvent access to potential intermediates in the reaction pathway.
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(1998)
Protein Eng
, vol.11
, pp. 253-261
-
-
Ory, J.J.1
Mazhary, A.2
Kuang, H.3
Davies, R.R.4
Distelano, M.D.5
Banaszak, L.J.6
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49
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0030877055
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Modulation of the rate, enantioselectivity and substrate specificity of semisynthetic transaminases based on lipid binding proteins using site directed mutagenesis
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of special interest. A series of constructs in which the position of the pyridoxamine attachment within the intestinal fatty acid binding protein (IFABP) cavity was varied by site-directed mutagenesis are described. The IFABP-PX60 conjugate reacts at least 9.4-fold more rapidly than the original ALBP-PX conjugate, whereas IFABP-PX72 inverts the enantioselectivity of the reactions (compared to ALBP-PX) and IFABP-PX104 displays very selective substrate specificity. These results indicate that site-directed mutagenesis can be used to tune the rate, enantioselectivity and substrate specificity of semisynthetic transaminases that are based on fatty acid-binding proteins.
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Kuang H, Davies RR, Distefano MD. Modulation of the rate, enantioselectivity and substrate specificity of semisynthetic transaminases based on lipid binding proteins using site directed mutagenesis. of special interest Bioorg Med Chem Lett. 7:1997;2055-2060 A series of constructs in which the position of the pyridoxamine attachment within the intestinal fatty acid binding protein (IFABP) cavity was varied by site-directed mutagenesis are described. The IFABP-PX60 conjugate reacts at least 9.4-fold more rapidly than the original ALBP-PX conjugate, whereas IFABP-PX72 inverts the enantioselectivity of the reactions (compared to ALBP-PX) and IFABP-PX104 displays very selective substrate specificity. These results indicate that site-directed mutagenesis can be used to tune the rate, enantioselectivity and substrate specificity of semisynthetic transaminases that are based on fatty acid-binding proteins.
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(1997)
Bioorg Med Chem Lett
, vol.7
, pp. 2055-2060
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Kuang, H.1
Davies, R.R.2
Distefano, M.D.3
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50
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0032506976
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Catalytic enantioselective reductive amination in a host-guest system based on a protein cavity
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of outstanding interest. The properties of IFABP-PX60, a catalyst constructed by the covalent attachment of a pyridoxamine cofactor to a cysteine residue within the cavity of a mutant form of the intestinal fatty acid-binding protein (IFABP), are reported. Under single turnover conditions, IFABP-PX60 converts α-keto glutarate to glutamic acid 62-fold faster than free pyridoxamine. This conjugate catalytically performs this reaction with an efficiency at least 200-fold greater than the free cofactor; as many as 50 turnovers with an enantiomeric purity of 95% ee have been obtained. These results indicate that a host-guest system based on a fatty acid-binding protein can be used to generate a construct that mimics three key features of enzymatic catalysis: selectivity, rate enhancement and turnover.
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Kuang H, Distefano MD. Catalytic enantioselective reductive amination in a host-guest system based on a protein cavity. of outstanding interest J Am Chem Soc. 120:1998;1072-1073 The properties of IFABP-PX60, a catalyst constructed by the covalent attachment of a pyridoxamine cofactor to a cysteine residue within the cavity of a mutant form of the intestinal fatty acid-binding protein (IFABP), are reported. Under single turnover conditions, IFABP-PX60 converts α-keto glutarate to glutamic acid 62-fold faster than free pyridoxamine. This conjugate catalytically performs this reaction with an efficiency at least 200-fold greater than the free cofactor; as many as 50 turnovers with an enantiomeric purity of 95% ee have been obtained. These results indicate that a host-guest system based on a fatty acid-binding protein can be used to generate a construct that mimics three key features of enzymatic catalysis: selectivity, rate enhancement and turnover.
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(1998)
J Am Chem Soc
, vol.120
, pp. 1072-1073
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Kuang, H.1
Distefano, M.D.2
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51
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0032492675
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Effects of metal ions on the rates and enantioselectivities of reactions catalyzed by a series of semisynthetic transaminases created by site directed mutagenesis
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of special interest. The chemistry performed by intestinal fatty acid-binding protein (IFABP) conjugates under catalytic conditions and the effect on the reaction rate and enantioselectivity of added metal ions are both described. It appears that metal ions can be used to increase the rate of reactions catalyzed by semisynthetic transaminases, although the addition of metal ions can also retard the reaction rate. Furthermore, the presence of metal ions decreases reaction enantioselectivity.
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Qi D, Kuang H, Distefano MD. Effects of metal ions on the rates and enantioselectivities of reactions catalyzed by a series of semisynthetic transaminases created by site directed mutagenesis. of special interest Bioorg Med Chem Lett. 8:1998;875-880 The chemistry performed by intestinal fatty acid-binding protein (IFABP) conjugates under catalytic conditions and the effect on the reaction rate and enantioselectivity of added metal ions are both described. It appears that metal ions can be used to increase the rate of reactions catalyzed by semisynthetic transaminases, although the addition of metal ions can also retard the reaction rate. Furthermore, the presence of metal ions decreases reaction enantioselectivity.
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(1998)
Bioorg Med Chem Lett
, vol.8
, pp. 875-880
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Qi, D.1
Kuang, H.2
Distefano, M.D.3
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52
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0031439169
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A semisynthetic metalloenzyme based on a protein cavity that catalyzes the enantioselective hydrolysis of ester and amide substrates
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4-fold above the background rate. The kinetics of this amide hydrolysis reaction fit the Michaelis-Menten relationship that is characteristic of enzymatic processes.
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4-fold above the background rate. The kinetics of this amide hydrolysis reaction fit the Michaelis-Menten relationship that is characteristic of enzymatic processes.
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(1997)
J Am Chem Soc
, vol.119
, pp. 11643-11652
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Davies, R.R.1
Aidistefano, M.D.2
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53
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0026244229
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MOLSCRIPT; A program to produce both detailed and schematic plots of protein structure
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Kraulis PJ. MOLSCRIPT; a program to produce both detailed and schematic plots of protein structure. J Appl Crystallogr. 24:1991;946-950.
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(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
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Kraulis, P.J.1
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