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Full-Text Articles in Physical Sciences and Mathematics
New Technologies For Glycomic Analysis: Toward A Systematic Understanding Of The Glycome, John Rakus, Lara Mahal
New Technologies For Glycomic Analysis: Toward A Systematic Understanding Of The Glycome, John Rakus, Lara Mahal
John F. Rakus
Carbohydrates are the most difficult class of biological molecules to study by high-throughput methods owing to the chemical similarities between the constituent monosaccharide building blocks, template-less biosynthesis, and the lack of clearly identifiable consensus sequences for the glycan modification of cohorts of glycoproteins. These molecules are crucial for a wide variety of cellular processes ranging from cell-cell communication to immunity, and they are altered in disease states such as cancer and inflammation. Thus, there has been a dedicated effort to develop glycan analysis into a high-throughput analytical field termed glycomics. Herein we highlight major advances in applying separation, mass spectrometry, …
Mir-30b/30d Regulation Of Galnac Transferases Enhances Invasion And Immunosuppression During Metastasis, Avital Gaziel-Sovran, Miguel Segura, Raffaella Di Micco, Mary Collins, Douglas Hanniford, Eleazar De Miera, John Rakus, John Dankert, Shulian Shang, Robert Kerbel, Nina Bhardwaj, Yongzhao Shao, Farbod Darvishian, Jiri Zavadil, Adrian Erlebacher, Lara Mahal, Iman Osman, Eva Hernando
Mir-30b/30d Regulation Of Galnac Transferases Enhances Invasion And Immunosuppression During Metastasis, Avital Gaziel-Sovran, Miguel Segura, Raffaella Di Micco, Mary Collins, Douglas Hanniford, Eleazar De Miera, John Rakus, John Dankert, Shulian Shang, Robert Kerbel, Nina Bhardwaj, Yongzhao Shao, Farbod Darvishian, Jiri Zavadil, Adrian Erlebacher, Lara Mahal, Iman Osman, Eva Hernando
John F. Rakus
To metastasize, a tumor cell must acquire abilities such as the capacity to colonize new tissue and evade immune surveillance. Recent evidence suggests that microRNAs can promote the evolution of malignant behaviors by regulating multiple targets. We performed a microRNA analysis of human melanoma, a highly invasive cancer, and found that miR-30b/30d upregulation correlates with stage, metastatic potential, shorter time to recurrence, and reduced overall survival. Ectopic expression of miR-30b/30d promoted the metastatic behavior of melanoma cells by directly targeting the GalNAc transferase GALNT7, resulted in increased synthesis of the immunosuppressive cytokine IL-10, and reduced immune cell activation and recruitment. …
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 …
Crystal Structure And Functional Assignment Of Yfau, A Metal Ion Dependent Class Ii Aldolase From Escherichia Coli K12, Dean Rea, Rebecca Hovington, John Rakus, John Gerlt, Vilmos Fu¨Lo¨P, Timothy Bugg, David Roper
Crystal Structure And Functional Assignment Of Yfau, A Metal Ion Dependent Class Ii Aldolase From Escherichia Coli K12, Dean Rea, Rebecca Hovington, John Rakus, John Gerlt, Vilmos Fu¨Lo¨P, Timothy Bugg, David Roper
John F. Rakus
One of the major challenges in the postgenomic era is the functional assignment of proteins using sequence- and structure-based predictive methods coupled with experimental validation. We have used these approaches to investigate the structure and function of theEscherichia coli K-12 protein YfaU, annotated as a putative 4-hydroxy-2-ketoheptane-1,7-dioate aldolase (HpcH) in the sequence databases. HpcH is the final enzyme in the degradation pathway of the aromatic compound homoprotocatechuate. We have determined the crystal structure of apo-YfaU and the Mg2+−pyruvate product complex. Despite greater sequence and structural similarity to HpcH, genomic context suggests YfaU is instead a 2-keto-3-deoxy sugar aldolase like the …
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 …