John.Yamauchi
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Experimental Biology Conference 2008 Postercasts
The Experimental Biology Conference is a multi-society, interdisciplinary, scientific meeting featuring plenary and award lectures, symposia, oral and poster sessions, career services, and exhibits...
Publications in PubMed
- Radi? Z, Manetsch R, Krasi?ski A, Raushel J, Yamauchi J, Garcia C, Kolb H, Sharpless KB, Taylor P. Molecular basis of interactions of cholinesterases with tight binding inhibitors. Chemico-biological interactions 2005 157-158. DOI:10.1016/j.cbi.2005.10.020.
Publications
2. Zoran Radic, Cindy Garcia, John Yamauchi, Daniel M. Quinn and Palmer Taylor, Conformational changes and catalytic triad reactivity in acetylcholinesterase monitored by intrinsic tryptophan and conjugated acrylodan fluorescence. Experimental Biology 2005, San Diego, CA, April 2 – 6, Abstract #230.14
3. Zoran Radic, John Yamauchi, Theresa Operana, Leo Pezzementi and Palmer Taylor, Conformational Changes in Substrate Bound Acetylcholinesterase Monitored by Intrinsic Tryptophan and Conjugated Acrylodan Fluorescence, USAMRICD Bioscience review 2004, Baltimore, MD, May 2004. Abstracts p.30
3. Zoran Radic, John Yamauchi, Theresa Operana, Leo Pezzementi and Palmer Taylor, Conformational Changes in Substrate Bound Acetylcholinesterase Monitored by Intrinsic Tryptophan and Conjugated Acrylodan Fluorescence, USAMRICD Bioscience review 2004, Baltimore, MD, May 2004. Abstracts p.30
History of Education and Employment
Education:
Molecular Pharmacology, Doctoral of Philosophy (2010) GPA 3.61
Biomedical Sciences Graduate Program and Skaggs School of Pharmacy and Pharmaceutical Sciences
Bioengineering (Biotechnology) B.S. (2006) GPA 3.59
University of California San Diego, Jacob’s School of Engineering
Relevant Experience:
Position: Graduate Student Researcher 05/2007-Present
Dr. Palmer Taylor, Dean of Skaggs School of Pharmacy and Pharmaceutical Sciences UCSD, CA (858)-534-4026
• Utilizing the Acetlycholine binding protein from snails, Aplysia Californica and Lymnae Stagnalis, as a structural surrogate for the nicotinic acetylcholine receptor.
• Steriochemical binding assays and crystallography with the binding proteins
• Compare binding constants of alpha7 and alpha4beta2 receptor with the binding protein with “click-chemistry” compounds
Position: Graduate Student Researcher (Lab Rotation) 01/2007-02/2007
Dr. J. Andrew McCammon HHMI, Department of Chemistry and Biochemistry UCSD, CA (858)-534-2905
• Conducted molecular dynamic simulations on various Alanine mutations of Interleukin-2 and observed the Chi1 and Chi2 rotational angles of GLU62
• Utilized AutoDock4 for the confirmation of published substrate inhibition values of Acetylcholinesterase by various substrates and inhibitors
Position: Graduate Student Researcher (Lab Rotation) 09/2006-12/2006
Dr. Tracy Handel, Skaggs School of Pharmacy and Pharmaceutical Sciences UCSD, CA (858)-822-6656
Purpose of project: Purify and obtain large amounts of reconstituted human chemokine receptor 2b (CCR2b)
• Transfected HEK293 cell lines with combinations of various purification tags on the C and N termini of CCR2b (chemokine receptor).
• Performed fluorescent calcium flux assays to determine the functionality of the recombinant receptor
• Purified membrane bound CCR2b using n-dodecyl beta-D-maltoside and nickel chromatography column
Position: Graduate Student Researcher (Lab Rotation) 07/2006-08/2006
Dr. Roger Tsien HHMI, Department of Pharmacology UCSD, CA (858)-534-4891
Purpose of project: Develop a non-invasive sensor for cancerous tissue
• Fabricated 15nm gold particles with oligonucleotides to induce aggregation as a method of detection
• Chemically fused a short cleavable peptide to two 3’ oligo ends, for a 5’ thiol linkage to gold particles to serve as a protecting mechanism against aggregation unless in presence of matrix metalloproteinases
• Characterized colorimetric and aggregative dependent properties (temp., salt conc., and surface density) to characterize the kinetics and stability of aggregates
Position: Research Assistant 06/2003-06/2006
Dr. Palmer Taylor, Department of Pharmacology UCSD, CA (858)-534-1366
Purpose of project: Characterize residues involved in inhibition of Acetylcholinesterase in the active site
• Generated mutants of Acetylcholinesterase in the active center gorge and Omega loop to inactivate and label mutant
• Observed fluorescent chromic shifts and intensity changes in Acrylodan labeled Acetylcholinesterase with changes in concentration of substrates/inhibitors to monitor conformational changes induced by ligands
• Characterized inhibition binding parameters (kobs, kon, koff, kd) of TFK+ on wild type and mutant species of Acetylcholinesterase to understand mechanism of stabilization in active site
Molecular Pharmacology, Doctoral of Philosophy (2010) GPA 3.61
Biomedical Sciences Graduate Program and Skaggs School of Pharmacy and Pharmaceutical Sciences
Bioengineering (Biotechnology) B.S. (2006) GPA 3.59
University of California San Diego, Jacob’s School of Engineering
Relevant Experience:
Position: Graduate Student Researcher 05/2007-Present
Dr. Palmer Taylor, Dean of Skaggs School of Pharmacy and Pharmaceutical Sciences UCSD, CA (858)-534-4026
• Utilizing the Acetlycholine binding protein from snails, Aplysia Californica and Lymnae Stagnalis, as a structural surrogate for the nicotinic acetylcholine receptor.
• Steriochemical binding assays and crystallography with the binding proteins
• Compare binding constants of alpha7 and alpha4beta2 receptor with the binding protein with “click-chemistry” compounds
Position: Graduate Student Researcher (Lab Rotation) 01/2007-02/2007
Dr. J. Andrew McCammon HHMI, Department of Chemistry and Biochemistry UCSD, CA (858)-534-2905
• Conducted molecular dynamic simulations on various Alanine mutations of Interleukin-2 and observed the Chi1 and Chi2 rotational angles of GLU62
• Utilized AutoDock4 for the confirmation of published substrate inhibition values of Acetylcholinesterase by various substrates and inhibitors
Position: Graduate Student Researcher (Lab Rotation) 09/2006-12/2006
Dr. Tracy Handel, Skaggs School of Pharmacy and Pharmaceutical Sciences UCSD, CA (858)-822-6656
Purpose of project: Purify and obtain large amounts of reconstituted human chemokine receptor 2b (CCR2b)
• Transfected HEK293 cell lines with combinations of various purification tags on the C and N termini of CCR2b (chemokine receptor).
• Performed fluorescent calcium flux assays to determine the functionality of the recombinant receptor
• Purified membrane bound CCR2b using n-dodecyl beta-D-maltoside and nickel chromatography column
Position: Graduate Student Researcher (Lab Rotation) 07/2006-08/2006
Dr. Roger Tsien HHMI, Department of Pharmacology UCSD, CA (858)-534-4891
Purpose of project: Develop a non-invasive sensor for cancerous tissue
• Fabricated 15nm gold particles with oligonucleotides to induce aggregation as a method of detection
• Chemically fused a short cleavable peptide to two 3’ oligo ends, for a 5’ thiol linkage to gold particles to serve as a protecting mechanism against aggregation unless in presence of matrix metalloproteinases
• Characterized colorimetric and aggregative dependent properties (temp., salt conc., and surface density) to characterize the kinetics and stability of aggregates
Position: Research Assistant 06/2003-06/2006
Dr. Palmer Taylor, Department of Pharmacology UCSD, CA (858)-534-1366
Purpose of project: Characterize residues involved in inhibition of Acetylcholinesterase in the active site
• Generated mutants of Acetylcholinesterase in the active center gorge and Omega loop to inactivate and label mutant
• Observed fluorescent chromic shifts and intensity changes in Acrylodan labeled Acetylcholinesterase with changes in concentration of substrates/inhibitors to monitor conformational changes induced by ligands
• Characterized inhibition binding parameters (kobs, kon, koff, kd) of TFK+ on wild type and mutant species of Acetylcholinesterase to understand mechanism of stabilization in active site