Geometric arrangement algorithms for protein structure determination Jeff Martin Bruce Donald Laboratory http://www.cs.duke.edu/donaldlab/
Protein structure determination Protein structure determination Protein Synthesis
Protein structure determination Protein structure determination Protein Synthesis ANNTTGFTRIIKAAGYSWKGLRAAWINEAAF RQEGVAVLLAVVIACWLDVDAITRVLLISSV MLVMIVEILNSAIEAVVDRIGSEYHELSGRAK DMGSAAVLIAIIVAVITWCILLWSHFG Primary sequence
Protein structure determination Protein structure determination Protein Synthesis Protein Folding ANNTTGFTRIIKAAGYSWKGLRAAWINEAAF RQEGVAVLLAVVIACWLDVDAITRVLLISSV MLVMIVEILNSAIEAVVDRIGSEYHELSGRAK DMGSAAVLIAIIVAVITWCILLWSHFG Primary sequence
Protein structure determination Protein structure determination Protein Synthesis Protein Folding d ANNTTGFTRIIKAAGYSWKGLRAAWINEAAF RQEGVAVLLAVVIACWLDVDAITRVLLISSV MLVMIVEILNSAIEAVVDRIGSEYHELSGRAK DMGSAAVLIAIIVAVITWCILLWSHFG Primary sequence Experimental measurements
Why solve protein structures? Why solve protein structures? Structure determines function! Hence, studying structure helps understand function
How is protein function important? How is protein function important? MPER: HIV surface protein Disease mechanisms P Reardon, et al., (in preparation)
How is protein function important? How is protein function important? MPER: HIV surface protein Disease mechanisms P Reardon, et al., (in preparation) VRC01: HIV antibody T Zhou, I Georgiev, et al., Science, 2010
How is protein function important? How is protein function important? MPER: HIV surface protein Disease mechanisms P Reardon, et al., (in preparation) VRC01: HIV antibody T Zhou, I Georgiev, et al., Science, 2010 GrsA PheA: helps manufacture antibiotics New drugs CY Chen, I Georgiev, et al., PNAS, 2009
One protein function: a molecular assembly line One protein function: a molecular assembly line The domains have specific tasks, but how do they work? Protein Antibiotic
One protein function: a molecular assembly line One protein function: a molecular assembly line Solving the structure for a domain shows us how it works. Protein Antibiotic
One protein function: a molecular assembly line One protein function: a molecular assembly line If we modify a domain, the protein could perform a new function. Protein Antibiotic
Protein redesign relies on protein structure Protein redesign relies on protein structure Redesign! Switched specificity from Phenylalanine to Leucine! Predicted binding model for Leucine Prehaps we can engineer molecules to make new drugs? Cheng-Yu Chen, Ivelin Georgiev, Amy C. Anderson, Bruce R. Donald, Computational structure-based redesign of enzyme activity, PNAS 2009
Experimental methods Experimental methods d For atomic-precision protein structure determination Nuclear Magnetic Resonance X-ray Crystallography spectroscopy (NMR) Duke NMR Center Crystals of Insulin NMR is often preferred because measurements are in solution state.
How are structures traditionally solved by NMR? How are structures traditionally solved by NMR? Experimental Restraints • 13 C α chemical shi fts 13 C β chemical shifts • • 13 C O chemical shifts 1 H α chemical shifts • • 1 H N chemical shifts • 3 J HNH α couplings • 1 H- 15 N RDCs • 15 N R 2 • Nitroxide spin-label PREs • ATCUN PREs • NOEs • O 2 -induced 13 C paramagnetic shifts • Tryptophan indole solvent accessibility
Geometric restraints on protein structure Geometric restraints on protein structure Experimental Restraints • 13 C α chemical shi fts 13 C β chemical shifts • • 13 C O chemical shifts 1 H α chemical shifts • • 1 H N chemical shifts • 3 J HNH α couplings • 1 H- 15 N RDCs • 15 N R 2 Restraints on distance: • Nitroxide spin-label PREs • Nuclear Overhauser • ATCUN PREs Effect (NOE) • NOEs • O 2 -induced 13 C paramagnetic shifts • Paramagnetic Relaxation • Tryptophan indole solvent accessibility Enhancement (PRE)
Geometric restraints on protein structure Geometric restraints on protein structure Experimental Restraints Restraints on orientation: • 13 C α chemical shi fts 13 C β chemical shifts • • Residual Dipolar • 13 C O chemical shifts Couplings (RDCs) 1 H α chemical shifts • • 1 H N chemical shifts • 3 J HNH α couplings • 1 H- 15 N RDCs • 15 N R 2 • Nitroxide spin-label PREs • ATCUN PREs • NOEs • O 2 -induced 13 C paramagnetic shifts • Tryptophan indole solvent accessibility
Geometric restraints on protein structure Geometric restraints on protein structure Experimental Restraints Restraints on orientation: • 13 C α chemical shi fts 13 C β chemical shifts • • Residual Dipolar • 13 C O chemical shifts Couplings (RDCs) 1 H α chemical shifts • • 1 H N chemical shifts • 3 J HNH α couplings • 1 H- 15 N RDCs • 15 N R 2 • Nitroxide spin-label PREs • ATCUN PREs • NOEs • O 2 -induced 13 C paramagnetic shifts • Tryptophan indole solvent accessibility
How are structures traditionally solved by NMR? How are structures traditionally solved by NMR? Experimental Restraints • 13 C α chemical shi fts 13 C β chemical shifts • • 13 C O chemical shifts 1 H α chemical shifts • • 1 H N chemical shifts • 3 J HNH α couplings • 1 H- 15 N RDCs • 15 N R 2 Simulated Annealing: • Nitroxide spin-label PREs Molecular dynamics simulation • ATCUN PREs and energy minimization • NOEs • O 2 -induced 13 C paramagnetic shifts • Tryptophan indole solvent accessibility
Structure determination of protein complexes Structure determination of protein complexes traditionally uses simulated annealing as well
Simulated annealing is based on heuristics Simulated annealing is based on heuristics Stochastic search
Simulated annealing is based on heuristics Simulated annealing is based on heuristics Stochastic search Simulation & Minimization
Simulated annealing is based on heuristics Simulated annealing is based on heuristics Stochastic search Simulation & Minimization Convergence not guaranteed
Protein complexes are composed of subunits Protein complexes are composed of subunits Homodimers have 2 identical subunits Homo-oligomers have n identical subunits
Structure determination of protein complexes Structure determination of protein complexes using divide and conquer instead
Divide and conquer Divide and conquer de novo structure determination
Divide and conquer Divide and conquer de novo structure determination Oligomeric assembly
Related work in structure determination by solution NMR Related work in structure determination by solution NMR de novo determination Oligomeric assembly Heuristic Nilges, 1993 Wang, Lozano-Pérez, and Tidor, 1998 Nilges, 1995 Wang, Bansal, Jiang, and Prestegard, 2008 Nilges, et al., 1997 Meiler, et al., 2000 Fowler, et al., 2000 Tian, Valafar, and Prestegard, 2001 Herrmann, Güntert, and Wüthrich, 2002 Wedemeyer, Rohl, and Scheraga, 2002 Rieping, et al., 2007 Bardiaux, et al., 2009 Provable Chris Bailey-Kellogg, et al., 2000 Potluri, et al., 2006 Wang and Donald, 2004 Potluri, et al., 2007 * Wang, Mettu, and Donald, 2006 * Zeng, Tripathy, Zhou, and Donald, 2008 Martin, Yan, Bailey-Kellogg, Zeng, et al., 2009 Zhou, and Donald Zeng, Zhou, and Donald, 2011 Protein Science, 2011 Zeng, Roberts, Zhou, Donald, 2011 * Tripathy, Zeng, Zhou and Donald, 2011 Martin, Yan, Bailey-Kellogg, Zhou, and Donald * polynomial time algorithms J Comp Bio, 2011
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