Life Science Webinar Series Elegant protein- protein docking in Discovery Studio Francisco Hernandez-Guzman, Ph.D. November 20, 2007 Sr. Solutions Scientist fhernandez@accelrys.com
Agenda In silico protein-protein Docking Why? How? Discovery Studio & Pipeline Pilot Protein-protein Docking algorithms ZDOCK, RDOCK Clustering Added Benefits Visualization (GUI) Clustering, Parallelization Case study DEMO Conclusion 2
Why Protein-protein docking? Biological molecules in the body work together to elicit a response Need to understand protein-protein interactions Provide a solid hypothesis for protein interactions Experimental methods X-ray crystallography Difficult, slow, high degree of expertise Experimental bias Applications: Site directed mutagenesis, protein design Molecular detection/screening Affinity binding 3
How? Discovery Studio and Pipeline Pilot Protocols (Calculations) can be run in Pipeline Pilot or Discovery Studio 2.0 4
Accelrys Discovery Studio Discovery Studio WebPort WebPort (web (web access) access) Pipeline Pipeline Pilot Pilot (Pro or Lite ) (Pro or Lite ) ISV ISV Client Client (e.g., (e.g., Spotfire) Spotfire) Materials Materials Studio Studio Client Client Discovery Discovery Studio Studio Client Client Accord Accord Clients Clients Client Integration Layer S c i i T e g i i c P l l a t t f f o r r m Tool Integration Layer Data Access Layer Cmd-Line Isentris Chemistry Biology Materials Accord Accord IDBS Oracle ISIS Reporting Statistics ISV 5 Tools Databases
How? (cnt d) Procedure for Protein-protein docking: Protein preparation stage Docking Stage Rigid docking (ZDOCK) Clustering and Analysis Docked complex refinement and re-ranking (RDOCK) 6
Protein preparation stage Protein clean function Problem correction Naming Alternate conformation Incomplete residues Bond orders and connectivity Hydrogen Assignment Ionization based on pk (standard or predicted) Removal of irrelevant elements Waters, crystallization artifacts Forcefield based atom typing (RDOCK) Automatic assignment of topology and parameters Use of CHARMm Polar-H 7
Docking Stage Rigid docking (ZDOCK) FFT based initial stage rigid-body docking, efficient systematic search in rotational and translational space PSC pairwise shape complementarity scoring function include options for Blocking and Filtering Clustering and Analysis Uses an RMSD matrix to find largest number of neighbors Algorithm based on ClusPro (Comeau et al. 2004) and Lorenzen et al. 2007 Docked complex refinement and re-ranking (RDOCK) CHARMm-based procedure for refinement and reranking with electrostatic and ACE desolvation energy Li Li, Rong Chen, Zhiping Weng. Proteins 53:693-707 (2003) 8
ZDOCK - Rigid Body Docking using Fast Fourier Transform R FFT IFT Correlation L FFT Y X Surface Interior Binding Site 9
Grid-based Shape Complementarity 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 0 R GSC L GSC N N N N N N x= y= z= x= y= z= GSC(, l m,) n = Re R(,,) x y z L( x+ l, y+ m, z+ n) Im R(,,) x y z L( x+ l, y+ m, z+ n)
Grid-based Shape Complementarity 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i 9i R GSC L GSC N N N N N N x= y= z= x= y= z= GSC(, l m,) n = Re R(,,) x y z L( x+ l, y+ m, z+ n) Im R(,,) x y z L( x+ l, y+ m, z+ n)
Pairwise Shape Complementarity 2 3 3 3 2 2 3i 3i 3i 3i 3i 2 3 3i 9i 3i 3i 3i 2 +3i +3i 3 3i 9i 3i 5 2 +3i +3i +9i +9i +3i 3 3i 9i 3i 5 2 +3i +3i +9i +9i +3i 3 3i 9i 3i 3i 3i 2 +3i +3i 2 3i 3i 3i 3i 3i 2 2 3 3 3 2 2 R PSC N N N x= y= z= L PSC PSC(, l m, n) = Re R( x, y, z) L( x+ l, y+ m, z+ n)
Pairwise Shape Complementarity 2 3 3 3 2 2 3i 3i 3i 3i 3i 2 3 3i 9i 3i 3i 3i 2+6i +3i 2 +3i 3 3i 9i 3i 5+5i +3i 5 +3i 2+6i 2 +9i +9i +3i 3 3i 9i 3i 5+5i +3i 5 2+6i +3i 2 +9i +9i +3i 3 3i 9i 3i 3i 3i +3i 2+6i 2 +3i 2 3i 3i 3i 3i 3i 2 2 3 3 3 2 3 R PSC N N N x= y= z= L PSC PSC(, l m, n) = Re R( x, y, z) L( x+ l, y+ m, z+ n)
4 ZDOCK
5 RDOCK
Added Benefits: Visualization/Tools (GUI) Coarse grain parallelization Workstation Server 6 Server Server Server
Example: In silico Protein-protein docking Docking studies of α-lytic Protease with OMTKY3 & Eglin C Serine Protease catalytic triad His57 Asp02 Ser95 + OMTKY3 =? a-lytic protease (gbk) Currently no experimental 3D structures are available of the complexes (Oct 2007) Eglin C 7
OMTKY3 Eglin C 8
Docking of α-lytic Protease with OMTKY3 & Eglin C Method: ZDOCK 6 o rotational sampling grid (54000 poses sampled) - filtering residues: catalytic His57 (alp) and P Leu (inhibitors) RDOCK CHARMm 3-stage ABNR minimization: top 50 ZDOCK filtered poses Re-rank based on the RDOCK and ACE scoring functions Results: Top-ranked poses form clusters: reveal expected binding mode - P Leu as leading anchor residue in both complexes Small RMSD in binding loop region among top docked poses Side-chain movement in interface, backbone conformation unchanged Intermolecular h-bonds between binding loop active site 9
Docking of α-lytic Protease with OMTKY3 & Eglin C ALP-Eglin C # pose ALP-OMTKY3 # pose V43 T44 L45 D46 L47 C6 T7 L8 E9 Y20 20
Publication: Biochemistry. 2006; 45(38):342-348 2
Summary: Protein-protein docking example Correct binding mode identified as # predicted pose in both docking calculations Docking study predictions provide a quantitative energetic measure which supports the experimentally determined much stronger binding strength of Eglin C versus OMTKY3 for α-lytic Protease Desolvation interactions represent an important contributor to the overall stability of both complexes Free energy and desolvation energy successfully discriminate binding strength between both systems 22
23 DEMO!!!
Conclusion In silico protein docking can be used to derive sensible hypothesis about protein-protein interactions Integration to Discovery Studio allows for easier preparation and analysis of the data, as well as deployment of calculations Graphical utilities complement workflow by providing interactive analysis and manipulation tools for uncovering plausible protein-protein complexes 24
Acknowledgements Marc Faschnat Tina Yeh Lisa Yan Paul Flook Shikha O Brien Z-Lab (Prof. Zhiping Weng Boston University) 25
References: Chen, R., Li, L. & Weng, Z. (2003) ZDOCK: An Initial-stage Protein Docking Algorithm. Proteins. 52():80-7 Li, L., Chen, R. & Weng, Z. (2003) RDOCK: Refinement of Rigid-body Protein Docking Predictions. Proteins. 53:693-707. Wiehe K, Pierce B, Mintseris J, Tong W, Anderson R, Chen R, Weng Z (2005) ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5. Proteins. 60(2):207-23 Qasim MA, et al. (2006) Despite Having a Common P Leu, Eglin C Inhibits α-lytic Proteinase a Million-fold More Strongly than Does Turkey Ovomucoid Third Domain. Biochemistry. 45(38), 342-348 26