A5016336553- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
- Biochemical and Molecular Research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- DNA and Nucleic Acid Chemistry
- Enzyme Production and Characterization
- MicroRNA in disease regulation
- S100 Proteins and Annexins
- Metabolomics and Mass Spectrometry Studies
- Gut microbiota and health
- Microbial bioremediation and biosurfactants
- Origins and Evolution of Life
- Amino Acid Enzymes and Metabolism
- Biochemical Acid Research Studies
- Cancer-related gene regulation
- Bacterial Genetics and Biotechnology
- Bioactive Compounds and Antitumor Agents
- Plant biochemistry and biosynthesis
- Neurogenesis and neuroplasticity mechanisms
- Pancreatic function and diabetes
- Diet, Metabolism, and Disease
- Porphyrin Metabolism and Disorders
Texas A&M University
2012-2025
University of California, San Francisco
2006-2010
QB3
2007-2009
Albert Einstein College of Medicine
2007-2009
University of Illinois Urbana-Champaign
2007-2008
Massachusetts Institute of Technology
2000-2005
New York University
2005
Whitehead Institute for Biomedical Research
2000-2005
Wellcome Sanger Institute
2005
University of North Carolina at Chapel Hill
2005
MicroRNAs (miRNAs) are small RNAs that regulate gene expression posttranscriptionally. To block all miRNA formation in zebrafish, we generated maternal-zygotic dicer (MZ ) mutants disrupt the Dicer ribonuclease III and double-stranded RNA-binding domains. Mutant embryos do not process precursor miRNAs into mature miRNAs, but injection of preprocessed restores silencing, indicating disrupted domains dispensable for later steps silencing. MZ undergo axis differentiate multiple cell types...
MicroRNAs (miRNAs) are an abundant class of ∼22-nucleotide (nt) noncoding RNAs, some which known to control the expression other genes at posttranscriptional level ([1–4][1]). We developed a computational procedure (MiRscan) identify miRNA ([5][2]) and apply it here
The RNA world hypothesis regarding the early evolution of life relies on premise that some sequences can catalyze replication. In support this conjecture, we describe here an molecule catalyzes type polymerization needed for ribozyme uses nucleoside triphosphates and coding information template to extend primer by successive addition up 14 nucleotides—more than a complete turn helix. Its activity is general in terms sequence length RNAs, provided 3′ terminus pairs with template. also quite...
Understanding the functions and evolution of specificity-determining residues is essential for improving strategies to predict design enzyme functions. Whether function an amino acid residue retained during depends on intramolecular epistasis, which occurs when same contributes different phenotypes in genetic backgrounds. This study examines relationship between epistasis functional divergence by investigating a conserved specificity determinant five homologs from N-succinylamino racemase...
The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by genome of Escherichia coli K-12. We screened library acid sugars discover enzyme displays promiscuous substrate specificity: (6-deoxy- l-mannonate) has "best" kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures RhamDs from both E. K-12 Salmonella typhimurium LT2 (95%...
Significance The rate at which proteins accumulate amino acid substitutions during evolution depends on the likelihood that mutations will disrupt structure or affect function. Many ability of to fold correctly, and previous studies showed burden imposed by misfolded in cells heavily influences evolutionary rates proteins. However, these could not examine influence function rates. work described here examines relationship between structural functional divergence a rapidly evolving protein...
The d-mannonate dehydratase (ManD) function was assigned to a group of orthologous proteins in the mechanistically diverse enolase superfamily by screening library acid sugars. Structures wild type ManD from Novosphingobium aromaticivorans were determined at pH 7.5 presence Mg2+ and also 2-keto-3-keto-d-gluconate dehydration product; structure catalytically active K271E mutant 5.5 substrate. As previously observed structures other members superfamily, contains two domains, an N-terminal α+β...
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies divergent evolution of enzyme function. Each the different reactions catalyzed by members initiated abstraction α-proton carboxylate substrate that coordinated to an essential Mg2+. muconate lactonizing (MLE) from Pseudomonas putida, member family catalyzes syn-cycloisomerization cis,cis-muconate (4S)-muconolactone in β-ketoadipate pathway, has provided critical insights into structural bases...
The class I ligase, a ribozyme previously isolated from random sequence, catalyzes reaction similar to RNA polymerization, positioning its 5'-nucleotide via Watson−Crick base pair, forming 3',5'-phosphodiester bond between and the substrate, releasing pyrophosphate. Like most ribozymes, it requires metal ions for structure catalysis. Here, we report ionic requirements of this self-ligating ribozyme. ligase at least five Mg2+ activity has [Mg2+]1/2 70−100 mM. It an unusual specificity Mg2+;...
To study the substrate specificity of enzymes, we use amidohydrolase and enolase superfamilies as model systems; members these share a common TIM barrel fold catalyze wide range chemical reactions. Here, describe collaboration between Enzyme Specificity Consortium (ENSPEC) New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize structural coverage superfamilies. Using sequence- structure-based protein comparisons, first selected 535 target proteins from variety...
Thermobifida fusca o-succinylbenzoate synthase (OSBS), a member of the enolase superfamily that catalyzes step in menaquinone biosynthesis, has an amino acid sequence is 22 and 28% identical with those two previously characterized OSBS enzymes from Escherichia coli Amycolatopsis sp. T-1-60, respectively. These values are considerably lower than typical levels identity among homologous proteins have same function. To determine how such divergent catalyze reaction, we determined structure T....
Understanding how enzyme specificity evolves will provide guiding principles for protein engineering and function prediction. The o-succinylbenzoate synthase (OSBS) family is an excellent model system elucidating these because it has many highly divergent amino acid sequences that are <20% identical, some members have evolved a second function. OSBS belongs to the enolase superfamily, of which use set conserved residues catalyze wide variety reactions. These only in family, so they not...
The o-succinylbenzoate synthase (OSBS) family is part of the functionally diverse enolase superfamily. Many proteins in one branch OSBS catalyze both and N-succinylamino acid racemization same active site. In some promiscuous NSAR/OSBS enzymes, NSAR activity biologically significant addition to or instead activity. Identifying important residues for each reaction could provide insight into how evolve new functions. We have made a series mutations Amycolatopsis sp. T-1-60 an site loop,...
In support of the idea that certain RNA molecules might be able to catalyze replication, a ribozyme was previously generated synthesizes short segments in reaction modeled after proteinaceous polymerases. Here, we describe substrate recognition by this polymerase ribozyme. Altering base or sugar moieties nucleoside triphosphate only moderately affects its utilization, provided alterations do not disrupt Watson−Crick pairing template. Correctly paired nucleotides have both lower Km and higher...
Studying the evolution of catalytically promiscuous enzymes like those from N-succinylamino acid racemase/o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some in this have only OSBS activity, while others catalyze and NSAR reactions. We characterized several NSAR/OSBS as a step toward determining structural basis for evolving activity. Three were promiscuous, most other enzymes. However, Alicyclobacillus acidocaldarius (AaOSBS)...