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Full-Text Articles in Physical Sciences and Mathematics
An Integrated Systems Approach To Deconstructing Glycosylation, L. Mahal, John Rakus, Kanoelani Pilobello, P. Agrawal
An Integrated Systems Approach To Deconstructing Glycosylation, L. Mahal, John Rakus, Kanoelani Pilobello, P. Agrawal
John F. Rakus
Glycosylation involves the post-translational addition of carbohydrates to protein molecules and is an intricate and indispensable biochemical process. Study of this complicated network of interactions is hindered by the lack of a coding template analogous to the genetic code, and by the vast structural complexity inherent to carbohydrate polymers. We use lectins (non-enzymatic carbohydrate-binding proteins of non-immunological origin) as microarray probes to identify carbohydrate features expressed on cellular surfaces. Specifically, we utilized lectin microarray technology to investigate the differences in carbohydrates expressed by the cell lines of the Nation Cancer Institute’s NCI-60 panel. Our investigation identified tissue-specific expression differences in …
Evolution Of Enzymatic Activities In The Enolase Superfamily: L-Rhamnonate Dehydratase, John Rakus, Alexander Fedorov, Elena Fedorov, Margaret Glasner, Brian Hubbard, Joseph Delli, Patricia Babbitt, Steven Almo, John Gerlt
Evolution Of Enzymatic Activities In The Enolase Superfamily: L-Rhamnonate Dehydratase, John Rakus, Alexander Fedorov, Elena Fedorov, Margaret Glasner, Brian Hubbard, Joseph Delli, Patricia Babbitt, Steven Almo, John Gerlt
John F. Rakus
The L-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: L-rhamnonate (6-deoxy-L-mannonate) has the “best” kinetic constants, with L-mannonate, L-lyxonate, and D-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg2+; the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy-L-rhamnonate …
Computation-Facilitated Assignment Of The Function In The Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis, John Rakus, Chakrapani Kalyanaraman, Alexander Fedorov, Elena Fedorov, Fiona Mills-Groninger, Rafael Toro, Jeffrey Bonanno, Kevin Bain, J. Sauder, Stephen Burley, Steven Almo, Matthew Jacobson, John Gerlt
Computation-Facilitated Assignment Of The Function In The Enolase Superfamily: A Regiochemically Distinct Galactarate Dehydratase From Oceanobacillus Iheyensis, John Rakus, Chakrapani Kalyanaraman, Alexander Fedorov, Elena Fedorov, Fiona Mills-Groninger, Rafael Toro, Jeffrey Bonanno, Kevin Bain, J. Sauder, Stephen Burley, Steven Almo, Matthew Jacobson, John Gerlt
John F. Rakus
The structure of an uncharacterized member of the enolase superfamily from Oceanobacillus iheyensis(GI 23100298, IMG locus tag Ob2843, PDB entry 2OQY) was determined by the New York SGX Research Center for Structural Genomics (NYSGXRC). The structure contained two Mg2+ ions located 10.4 A˚ from one another, with one located in the canonical position in the (β/R) 7 β-barrel domain (although the ligand at the end of the fifth β-strand is His, unprecedented in structurally characterized members of the superfamily); the second is located in a novel site within the capping domain. In silico docking of a library of mono- and …