- Designing Selectivity in Dirhodium Metallopeptide Catalysts for Protein Modification
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The ability to chemically alter proteins is important for broad areas of chemical biology, biophysics, and medicine. Chemical catalysts for protein modification, and particularly rhodium(II) conjugates, represent an important new approach to protein modification that develops novel functionalization approaches while shedding light on the development of selective chemistries in complex environments. Here, we elucidate the reaction parameters that allow selective catalysis and even discrimination among highly similar proteins. Furthermore, we show that quantifying modification allows the measurement of competitive ligand affinity, permitting straightforward measurement of protein-peptide interactions and inhibitors thereof. Taken as a whole, rhodium(II) conjugates replicate many features of enzymes in an entirely chemical construct.
- Martin, Samuel C.,Vohidov, Farrukh,Wang, Haopei,Knudsen, Sarah E.,Marzec, Alex A.,Ball, Zachary T.
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- The Mechanism of Escherichia coli Dethiobiotin Synthetase-the Closure of the ureido Ring of Dethiobiotin involves Formation of a Carbamic-phosphate Mixed Anhydride
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The final intermediate in the enzymatic synthesis of the ureido ring of D-dethiobiotin 1 from (7R,8S)-7,8-diaminononanoate 2 catalysed by E. coli dethiobiotin sunthetase is the phosphoric acid anhydride 4 of the carbamate 3.
- Baxter, Robert L.,Baxter, Helen C.
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- A Vinylogous Photocleavage Strategy Allows Direct Photocaging of Backbone Amide Structure
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Side-chain modifications that respond to external stimuli provide a convenient approach to control macromolecular structure and function. Responsive modification of backbone amide structure represents a direct and powerful alternative to impact folding and function. Here, we describe a new photocaging method using histidine-directed backbone modification to selectively modify peptides and proteins at the amide N-H bond. A new vinylogous photocleavage method allows photorelease of the backbone modification and, with it, restoration of function.
- Mangubat-Medina, Alicia E.,Martin, Samuel C.,Hanaya, Kengo,Ball, Zachary T.
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supporting information
p. 8401 - 8404
(2018/06/29)
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- Structural characterization of the mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase
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Mycobacterium tuberculosis (Mtb) depends on biotin synthesis for survival during infection. In the absence of biotin, disruption of the biotin biosynthesis pathway results in cell death rather than growth arrest, an unusual phenotype for an Mtb auxotroph. Humans lack the enzymes for biotin production, making the proteins of this essential Mtb pathway promising drug targets. To this end, we have determined the crystal structures of the second and third enzymes of the Mtb biotin biosynthetic pathway, 7,8-diaminopelargonic acid synthase (DAPAS) and dethiobiotin synthetase (DTBS), at respective resolutions of 2.2 and 1.85 A. Superimposition of the DAPAS structures bound either to the SAM analogue sinefungin or to 7-keto-8-aminopelargonic acid (KAPA) allowed us to map the putative binding site for the substrates and to propose a mechanism by which the enzyme accommodates their disparate structures. Comparison of the DTBS structures bound to the substrate 7,8-diaminopelargonic acid (DAPA) or to ADP and the product dethiobiotin (DTB) permitted derivation of an enzyme mechanism. There are significant differences between the Mtb enzymes and those of other organisms; the Bacillus subtilis DAPAS, presented here at a high resolution of 2.2 A, has active site variations and the Escherichia coli and Helicobacter pylori DTBS have alterations in their overall folds. We have begun to exploit the unique characteristics of the Mtb structures to design specific inhibitors against the biotin biosynthesis pathway in Mtb.
- Dey, Sanghamitra,Lane, James M.,Lee, Richard E.,Rubin, Eric J.,Sacchettini, James C.
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p. 6746 - 6760
(2011/04/26)
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- The design and synthesis of inhibitors of dethiobiotin synthetase as potential herbicides
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Dethiobiotin synthetase (DTBS; E.C. 6.6.6.6), the penultimate enzyme in the biosynthesis of the essential vitamin biotin, is a new potential target for novel herbicides. Inhibitors were designed based on mechanistic and structural information. The in-vitro activities of these potential inhibitors versus the bacterial enzyme are reported here. Mimics of 7,8- diaminopelargonic acid (DAPA) or the DAPA carbamate reaction intermediate were substrates or partial substrates for the enzyme. Synergistic binding with ATP was noted with compounds which contained an amino functionality. NMR studies and X-ray structures confirmed that the inhibitors could be phosphorylated by the enzyme. Several series of potential inhibitors were designed to take advantage of this partial substrate activity by generating potentially more tightly bound phosphorylated inhibitors in situ. Structure- activity relationships for these series based on both substrate and inhibitory activity are described herein. An X-ray structure for one of these inhibitors is also discussed. Although considerable potential for inhibitors of this type was demonstrated, none of the compounds reported showed sufficient herbicidal activity to be a commercial proposition.
- Rendina,Taylor,Gibson,Lorimer,Rayner,Lockett,Kranis,Wexler,Marcovici-Mizrahi,Nudelman,Nudelman,Marsilii,Chi,Wawrzak,Calabrese,Huang,Jia,Schneider,Lindqvist,Yang
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p. 236 - 247
(2007/10/03)
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- Synthesis and Biological Activity of 9-Mercaptodethiobiotin - a Putative Biotin Precursor in Escherichia coli
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A total synthesis of (+/-)-9-mercaptodethiobiotin 3 via the aldehyde 9 is described.Compound (+/-)-3 does not function as a biotin replacement factor for an E. coli mutant (SA291) lacking the entire biotin synthesis operon (bioABFCD-) but supports growth of an E. coli bioA mutant.Compound (+/-)-3 also supports growth of transformed cells of SA291 carrying a plasmid encoding the E. coli biotin synthase (bioB) gene indicating that the compound may be able to substitute for dethiobiotin 2 as a substrate for biotin synthase.
- Baxter, Robert L.,Camp, Dominic J.,Coutts, Andrew,Shaw, Nicholas
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p. 255 - 258
(2007/10/02)
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