Prediction and refinement of complexes using coarse-grained and atomistic approaches in ATTRACT

Martin ZachariasTheoretical Biophysics T38Physics DepartmentTechnical University of Munich

The ATTRACT approach

• 31 LJ-atom types• Real charges

Multi-start systematic search by Energy Minimization

Multi-start systematic search by Energy Minimization

Score

distanceZacharias, Protein Sci. 2003,12;1271;Saladin et al., BMCStruct Biol 2009, 9:27; de Vries, Schindler, de Beauchene, Zacharias, Biophys. J. 2015,108:462.

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Multi-start systematic search by Energy Minimization

Multi-start systematic search by Energy Minimization

The ATTRACT approach

Multi-start systematic search by Energy Minimization

Multi-start systematic search by Energy Minimization

The ATTRACT approach

Multi-start systematic search by Energy Minimization

Multi-start systematic search by Energy Minimization

The ATTRACT approach

Multi-start systematic search by Energy Minimization

Multi-start systematic search by Energy Minimization

The ATTRACT approach

Systematic improvement of the scoring function

receptor

Score

distance

AimScoring optimization of near-native vs. alternative docking minima for a large set of training complexes

Target functionTop ranking of native solution

(large gap to incorrect solutions)

Step 1Generation of „high-ranked“

incorrect solutions

Step 2Optimization of pairwise

interactions with respect to target function

Step 3Test of scoring on separate

set of test complexes

Efficient inclusion of flexibility

Local flexibility:• Side chains and small loops

represented by several conformational copies

– Mean field representation

– Simultaneous optimization of docking geometry and side chain and loop structure

Global flexibility:• Inclusion of global soft collective

degrees of freedom from normal mode analysis– Accounting for most important

global motion using very few new variables (1-10)

Computationally very fast

May & Zacharias, BBA 2005; May & Zacharias, Proteins 2009;Bastard, Prevost & Zacharias, Proteins 2006

Docking with multiple loop copies

Softest global mode of Xylanase

Induced fit Docking using normal mode coordinates

• Illustration of a docking process including minimization in normal mode variables for an enzyme-inhibitor complex

New methods implemented in ATTRACT

de Beauchene, Plos Comput Biol, 2016; deVries et al., Biophys. J. 2015, 2016; Schindler et al., Proteins, 2014; Schindler et al., Structure, 2015; de Vries & Zacharias, Proteins, 2013; Setny et al., BMC Bioinfo., 2012; De Vries & Zacharias, PLosOne, 2012; Setny & Zacharias, NAR 2011

Multisubunit-Docking into CryoEM density starting from millions of start arrangements

ATTRACTProtein-Protein

Docking

Docking using GPU accleration

Web-Interfacewww.attract.ph.tum.de

Protein-DNA and Protein-RNA

docking

Protein-Peptide docking using pepATTRACT

Protein-Protein docking including

SAXS during docking

Single stranded RNA-Protein docking using combination of

RNA fragments

Refinement using iATTRACT

Refinement of predicted complexes

• Current procedure– Superposition of atomic resolution structures onto

coarse-grained models

– Energy minimization + Refinement at atomic resolution using Molecular Dynamic Simulations

• Problem:– Atomistic simulations are time consuming and often

don‘t move far from the start structure.

Refinement with iATTRACT• iATTRACT: combined energy minimization in rigid-body degrees of

freedom and atomistic motion at interface.

• Use of the normal mode concept implemented in ATTRACT: the motion of each interface atom is assigned one „mode“

• Motion of atoms at the interface is controlled by a structure-based force field with the unbound structure as reference.

• Atomistic interactions between proteins (OPLS force field)

Total energy

Refinement with iATTRACT

Schindler, de Vries, Zacharias Proteins, 2014, 83:248.

• iATTRACT allows relatively large translational and rotational displacements triggered by local adjustments at the interface.

• Test on 166 protein-protein complexes from benchmark 4.0

• Start: best 200 (in terms of iRMSD) rigid body docking solutions obtained using unbound partner structures

• Evaluation by interface root mean square deviation (iRMSD) and fraction of native contacts (fnat)

Refinement with iATTRACT

pdb1WDW

pdb2OUL

pdb2MTA

Docking refinement using iATTRACT

• Significant improvement of iRMSD and fnat after refinement – In some cases from an initial iRMSD of 6-8 Å to a final iRMSD of

~1 Å

• High probability to find structurally improved models for start structures with initial iRMSD < 5 Å.

Ranking after refinement using iATTRACT

• For a fraction of complexes a „funnel-like“ behavior of the scoring vs. iRMSD was observed.

• Only modest improvement in scoring near-native docking solutions

Prediction of Protein-Ligand complexes using Biasing-Replica-Exchange

• MD-simulations allow in principle for full flexibility.

• Limited timescale of search and trapping at the surface caused by non-optimal binding

• Trapping can be avoid using a special ambiguity restraint:

• The ambiguity restraint includes all heavy atoms on the surface of the two partners.

2ambiguityambiguity )()V(d refddk=

d

reference replica R0

d

replica R10

Illustration of the method

Test on simple system in vacuum• Receptor: two-Helix bundle

• Ligand: single helix• Partners kept semi-rigid (distance restraints between CA atoms in each partner)

~40 ps ~200 ps ~800 ps ~1500 ps

Test on simple system in vacuum• Receptor: two-Helix bundle

• Ligand: single helix• Partners kept semi-rigid (distance restraints between CA atoms in each partner)

~40 ps ~200 ps ~800 ps ~1500 ps

Refinement of unbound docking cases

• 20 start structures with 4 Å <RMSDlig < ~15 Å

• (a) Perform energy minimization

• (b) 12 MD simulations (short-range CA distance restraints in each partner and a center-of-mass restraint between partners)

• (c) H-REMD with repulsive potential and 12 replicas (otherwise same as MD)

Ligand RMSD (Å)

Ligand RMSD (Å)Ligand RMSD (Å)

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pdb1GCQ

pdb1PPEpdb2OOB

Results in CAPRI rounds 28-36Target best model fnat IRMSD[Å] category

59 5 0.18 3.8 acceptable quality (2*)60 5/6 1.0/0.94 0.44 high quality(2***,4**)

61 1 0.76 0.5 medium quality (5**)62 1 0.92 0.39 high quality (2***, 3**)63 1 0.81 0.49 high quality (2***, 3*)64 2 0.87 0.42 high quality (3***, 2**)65 2 0.27 3.7 incorrect66 1/1 0.5/0.75 1.3/2.1 acceptable (1*)67 5 0.88 0.8 medium quality (2**, 8*)95 3 0.5 3.3 acceptable quality (5*)96 3 0.15 2.96 acceptable quality (1*)97 8 0.05 12.2 incorrect98-99 - - - incorrect103 10 0.27 12.2 incorrect104 4 0.68 0.92 high quality (1***,9**) water (5++)105 3 0.66 1.2 medium quality (10**) water (7+++)107 - - - incorrect

Target 60-64: importin alpha in complex with peptides

experimental complex, target 63 predicted(***)

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-Alpha.Chang, C.-W., Counago, R.M., Williams, S.J., Boden, M., Kobe, B.(2013) Traffic 14: 1144

• Docking strategy:

• Docking using information from available complexes

• Atomistic refinement with restraint MD simulations

• (***) solutions for all except target61

Target 66: pria-helicase bound to ssb C-terminal tail peptide

Structural mechanisms of PriA-mediated DNA replication restart.Bhattacharyya et al. Proc Natl Acad Sci U S A. 111,1373 (2014).

• Systematic peptide-protein surface using pepATTRACT

• Refinement with iATTRACT and atomistic MD simulations

• More extended binding surface in predicted complexes.

experimental complex: yellow/bluepredicted(*) : orange/atom-coded

Target 67:Peptide in complex with WW3 domain/NEDD4

Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-Related Domain-Containing Protein-3 (ARRDC3).

Qi et al. J Biol. Chem. 289, 4743 (2014)

• Docking including exprimental data on binding site

• Molecular dynamics based refinement

Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome.McGinty, Henrici, Tan. Nature 514, 591 (2014)

• Docking using standard approach– Use restraint to keep active site in

enzyme near H3 tail ubiquination site

– Acidic patch at H2A/H2B interface

– differs from previous published model

Target 95:Ubiquitin-conjugating enzyme in complex with

nucleosome

Summary

• Several new features in ATTRACT docking package

• Rapid refinement using iATTRACT and/or Biasing potential replica exchange MD simulations

• Several successes in CAPRI challenge

• Extension of refinement to more realistic conditions

Acknowledgements

Group membersRainer BombliesIsaure de BeaucheneUwe EhrmannChristina FrostFlorian KandziaAlexander KnipsManuel LuitzKatja OstermeirGuiseppe La RosaAlexander SasseChristina SchindlerNadine SchwierzSjoerd de VriesFabian Zeller

Current Funding:DFG (RNA-Protein-Interaction)CIPSM, SFB-749 ;SFB1035,

SFB863

Collaboration of Protein-Protein docking

Chantal Prevost, Benjamin Boyer, Adrien Saladin, IBPC, Paris

Sebastien Fiorucci, University of Nice

CAPRI-DOCKING-TEAM:Christina Schindler, Sjoerd de Vries, Isaure de

Beauchene