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Molecular Control Engineering From Enzyme Design to Quantum Control. Raj Chakrabarti School of Chemical Engineering Purdue University. What is Molecular Control Engineering?. Control engineering : Manipulation of system dynamics through nonequilibrium
From Enzyme Design to Quantum Control
School of Chemical Engineering
Control of Biochemical
Optimization: Enzyme Design
Coherent Control of
Chemical Reaction Dynamics
How to design them?
What makes them optimal for catalysis, and how to improve?
Problem: hyperastronomical sequence space
Catalytic constraint: interatomic
distances rij < hbond dist
energy functions and solvation models
S-GB continuum solvation
10o resolution rotamer library (297 proteins)
Ghosh, A., Rapp, C.S. & Friesner, R.A. (1998)
J. Phys Chem. B102, 10983-10990.
Xiang, Z. and Honig, B. (2001) J. Mol. Biol.311: 421-430.
OPLS-AA molecular mechanics force field + Glidescore semiempirical binding affinity scoring function
Friesner, R.A, Banks, J.L., Murphy, R.B., Halgren, T.A. et al. (2004) J. Med. Chem. 47, 1739-1749.
Jacobson, M.P., Kaminski, G.A. Rapp, C.S. & Friesner, R.A. (2002) J. Phys. Chem. B106, 11673-11680.
ligand-binding sites and enzyme active sites
StreptavidinNative –10.04 kcal/mol
CO2- is covalent attachment site
9 / 10 residues predicted correctly in top 0.5 kcal/mol of sequences
Chakrabarti, R., Klibanov, A.M. and Friesner, R.A. Computational prediction of native protein ligand-binding and enzyme
active site sequences. PNAS, 2005.
detailed evolutionary information
Glucose-binding proteinNative –8.81 kcal/mol
Chakrabarti, R., Klibanov, A.M. and Friesner, R.A. PNAS, 2005.
and are associated with “evolutionary temperatures”
+ 1 kcal/mol
Number of residues correctly predicted
Max entropy distributions
~ single moment, evolutionary T
multiple moments, evolutionary T’s
High-resolution sequence optimization is robust across diverse functional families
to near-crystallographic resolution
Reviews on Computational Sequence Optimization and Designability of Enzymes
Nature Chemical Biology Volume 4 Number 5 May 2008:
“In a study by Chakrabarti et al. it was suggested that different enzyme active sites in natural proteins vary in their designability – that is, the number of sequences that are compatible with a specified structure and function.”
Chakrabarti R. Klibanov AM, Friesner RA. Sequence optimization and designability of enzyme active sites. Proc Natl Acad Sci USA 102:12035-12040, 2005
2008: GSK acquires
Sirtris Pharmaceuticals for
US $700 M
2010: Pfizer contests efficacy of drug leads from Sirtris experimental screening
2010: GSK terminates drug
development of several sirtuin activators
Sinclair DA. (2005) Mech. Ageing Dev. 126:987–1002
Brooks CL, Gu W. (2008) Cancer Cell 13:377–78
Brooks CL, Gu W. (2009) Nat. Rev. Cancer 9:123–28
Luo J, Nikolaev AY, Imai S, Chen D, Su F, et al. (2001) Cell 107:137–48
Vaziri H, Dessain SK, Eaton EN, Imai SI, Frye RA, et al. (2001) Cell 107:149–59
Michan S and Sinclair D (2007) Biochem J 404, 1-13.
Computational sequence optimization and experimental mutagenesis of Sirtuins
Example of screening focused library of sequence variants
3 permissible mutations identified by modeling at a target position
3 positions subject to mutagenesis
43 mutation combinations
= 64 sequence variations
Synthetic gene assembly and variant library construction via DNA synthesis
Biological selection of variant library
New enzymes -
Improved catalytic turnover
Altered substrate selectivity
Chakrabarti, R., De Jong, R., Cornish, V.C. and Friesner, R.A., unpublished results
Green: mutant; Orange: native; Yellow surface: acetyl-lysine Center: NAD+
E. Knoll, B. Ridder, and R. Chakrabarti, in preparation
Nobel Prize in Chemistry 1994; one of the most cited papers in Science (12757 citations in Science alone)
Produce millions of DNA molecules starting from one
Used every day in every Biochemistry and Molecular Biology lab ( Diagnosis, Genome Sequencing, Gene Expression, etc.)
March 2005: Roche Molecular Diagnostics PCR patents expire
2007: Celera Licenses and Roche negotiates for Chemical PCR
Single Strand – Primer Duplex
School of Chemical Engineering, Purdue University
Trinucleotide Repeat Diseases
Race for Diagnostic Methods: Standard PCR generally fails due to nonspecific amplification. First FDA-approved Fragile X test based on Chemical PCR
Chemical PCR: uses solvent engineering of PCR reaction media, to alter kinetic parameters of the reaction network and enable sequencing of untractable genomic DNA
R. Chakrabarti and C.E. Schutt, Nucleic Acids Res., 2001
R. Chakrabarti and C.E. Schutt, Gene 2002
R. Chakrabarti, in PCR Technology: Current Innovations, 2003
R. Chakrabarti and C.E. Schutt, Chemical PCR: Compositions for enhancing polynucleotide amplification reactions. US Patent 7.772.383, issued 8-10-10.
R. Chakrabarti and C.E. Schutt, Compositions and methods for improving polynucleotide amplification reactions using amides, sulfones and sulfoxides: II. US Patent 7.276,357, issued 10-2-07.
R.Chakrabarti and C.E. Schutt, US Patent 6,949,368, issued 9-27-05.
of Left, Forward + Left, Reverse + Right, Forward + Right, Reverse
Wild Type DNA
For N nucleotide template – 2N + 4 state equations
Typically N ~ 103
R. Chakrabarti et al. Optimal Control of Evolutionary Dynamics, Phys. Rev. Lett., 2008
K. Marimuthu and R. Chakrabarti, Optimally Controlled DNA amplification, in preparation
C. Brif, R. Chakrabarti and H. Rabitz, Control of Quantum Phenomena. Advances in Chemical Physics, 2011.
2011: An NSF funded quantum control experiment collaboration between
Purdue’s Andy Weiner (a founder of fs pulse shaping) and Chakrabarti Group
R. Chakrabarti, R. Wu and H. Rabitz, Quantum Multiobservable Control. Phys. Rev. A, 2008.
R. Chakrabarti, R. Wu and H. Rabitz, Quantum Pareto Optimal Control. Phys. Rev. A, 2008.
motion are needed to avoid undesired
directions necessary for steering system
toward target state
maximal selectivity, like coherent control
K. Moore, R. Chakrabarti, G. Riviello and H. Rabitz, Search Complexity and Resource Scaling for Quantum Control of Unitary Transformations. Phys. Rev. A, 2010
R. Wu, R. Chakrabarti and H. Rabitz, Critical Topology for Optimization on the Symplectic Group. J Opt. Theory, 2009
R. Chakrabarti and H. Rabitz, Quantum Control Landscapes, Int. Rev. Phys. Chem., 2007
R. Chakrabarti, Notions of Local Controllability and Optimal Feedforward Control for Quantum Systems. J. Physics A: Mathematical and Theoretical, 2011.
R. Chakrabarti and A. Ghosh. Optimal State Estimation of Controllable Quantum Dynamical Systems. Phys. Rev. A, in press, 2011.
Protein Design and Bionetwork Control
Princeton U Press Releases
New Journal of Physics, 2010; Advances in Chemical Physics, 2011
Invited Book, Taylor and Francis, 2012.