Brittany Boykin Auburn University Department of Chemistry and Biochemistry Computational Seminar National Organization for the Professional Organization of Black Chemist and Chemical Engineers 2015 Annual Conference ID: 775290
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The role of H293 in Protein Arginine Methyltransferases 1 (PRMT1)
Brittany Boykin Auburn University Department of Chemistry and Biochemistry Computational Seminar National Organization for the Professional Organization of Black Chemist and Chemical Engineers 2015 Annual ConferenceOrlando, Florida24, September 2015
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Slide2Outline
Background
Overall Goal
Future Work
Acknowledgments
Q/A
Current Study
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Slide3Post-Translational Modification (PTMs)
Remarkably, there are 200+ types of PTM’s that include kinases, phosphatases, transferases
Walsh C. (2006) Posttranslational Modification of Proteins: Expanding Natures Inventory. Englewood, Colo.: Roberts and Co. Publishers. Xxi, 490 p. p.
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Slide4Arginine Methylation
FASEB J. 10, 471-480
(1996)
Methylation reactions involve methyl group transfers (AdoMet is the methyl donor and this reaction displays a Sn2 type geometry)
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Slide5Protein Arginine Methyltransferases (PRMTs)
Bedford, M. T., and Clarke, S. G. (2009) Protein Arginine Methylation in mammals: Who, What, and why. Mol Cell 33, 1-13
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Slide6Physiological roles of PRMTs
Journal of Biological Chemistry Vol. 289, NO. 13, pp. 9320-9327, March 28,
(2014)
PRMTs regulate proteins in cell processes and human diseases
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Slide7Target Diseases
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Slide8PRMT Human Isoforms
Cell. Mol. Life Sci.
2009 66:2109.
PRMT1
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Slide9Human Diseases: PRMT1’s Target
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Slide10Structure of PRMT1
Structure 2003 11: 509.
Dimerization - essential for SAM binding and enzymatic activity
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Slide11Active Site of PRMT1
Biochemistry
2011, 50, 3332-3345
J. Bio. Chem. Vol. 289, NO. 13, pp. 9320-9327 2014
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Slide12Overall Goal
Product Specificity
Org. Biomol. Chem., 2015, 13, 549-560
Control
Sterics
& Nucleophilicity
What use of the product depends on the local conditions?
We want to gain more insight by dissecting the active site of PRMT1 and identifying the significance of specific residues in regards to the substrate What orientation does the substrate display with the H293S mutation?
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Slide13Importance of H293
Salt-Bridge
Biochemistry
2011
April 26; 50(16): 3332-3345
This short bond plays a critical role in forming the two-helix boundary that impact cofactor and peptide binding
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Slide14Alternative Mechanism
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Slide15Current Research Objective
Objective Product Specificity of H293: Mutant H293S; How does the protein environment influence product specificity using aMD simulations and QM/MM calculationsAnalyzed systems:H293S-ArgH293S-MMA-ADMAH293S-MMA-SDMAWith the Ser in place of His:What orientation does the substrate displayDistribution of the His vs Ser
Question:Does H293 have more affect on the active site than proposed?
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Slide16Assisted Model Building With Energy Refinement (AMBER)
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Slide17Molecular Dynamics (MD)
F = ma
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Slide18(QM) | (MM)
Quantum Mechanical (QM)
Electronic Processes
Bonding Breaking/formationDFT/ Ab InitioPrimary subsystem (PS)
Molecular Mechanical (MM)Force-field based methodComputationally EfficientSecondary subsystem (SS)
Combined QM/MMChemical Reaction in macromolecules
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Slide19PRMT1 RMSF Analysis
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Slide20Preferred Methylation
SDMA
ADMA
ADMA
SDMA
H293S-MMANη2
H293S-MMANη1
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Slide21Future Work
To continue the QM/MM simulations for all mutant complexes: H293S-Arg, H293S-MMA-proADMA, and H293S-MMA-proSDMAContinue to compare to double mutant (H293S-M48F) and WT-enzymeTo compare to experimental results
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Slide22Acknowledgements
Alabama Super Computer Center Huntsville Alabama Collaborators: Dr. Joan Hevel (Utah State University)Orlando AcevedoMy Lab members Symon GathiakaNicole IppolitoRobel GhebreabBrian Doherty
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