Biomolecular Modelling and SimulationJulia M Goodfellow, Birkbeck College, University of London

The Chemical Interface:Simulation and BiodesignExample: Application of commonly used algorithm is that of molecular dynamics i.e. iterative solution of differential equations describing atomic motion.One bottleneck is cpu Second bottleneck is coordinated storage and analysis.

WrongRightWrongDisastrous

AMYLOIDPROTEIN MISFOLDING LEADS TO DISEASE Human Lysozyme 2 microglobulin Transthyretineye-lens crystallins p53 - cancer

Human LysozymeTwo domains: a and b. 130 residue enzyme Mutation causes repulsion between distal loop and b hairpin of b domain. Amyloid precursor has been suggested to be formed from destabilised b domain. H-bond networks change.D67H and I56T lead to non-neuropathic amyloidosis

Results agree with plots from native contacts plots whereby the number of native residue contacts decreases slightly faster in the mutant in all trajectories.Indication that mutant moves faster away from native structureRMSD shows that mutant unfolds slightly faster than wild type.Indication that more susceptible

Results: Unfolding rates

Clustering is used to identify favourable partially folded conformationsMost conformations have lost most of their secondary structure.Highly populated conformational states of the mutant and a few low populated of wild type have distorted domain The distortion is more evident in the area of the domain interface (Ile 56).Results: Clustering

GENERALISE PROBLEM1 ns simulation on 40,000 atom protein 20 days on typical single processorAiming for simulations of 10 trajectories of 10 ns = 100 ns UK community say 10 groups of 10 people each studying 5 related systems total days cpu = 20 x 100 x 100 x 5 = 1 x 106 days cpu = 3000 PCs for a year.1.5 Gb storage per 1 ns simulation = 70 terabytes storage per year.

PB electrostatics with conformational changeLowering of pH results in break up of tetramer and changes to the monomer structure for transthyretinWould like to be able to combine modelling of changes in conformation with changes in pH45,000 atoms with solventTyr 116Tyr116His88His90Glu92

Prototype GRIDcpu*diskarchiveCentre with strong link to particle physics community64 cpu64 cpu64 cpu64 cpuOther centresin future

GRID2 for Data Analysis Distributed data - often on tape i.e. not on lineOxfordBirkbeckBirminghamYorkSouthamptonNottinghamMetadata REST of WORLD

First StageMetadata - Define what has been done by whom is raw data available on line? make this information available to all Using Grid tools to allow sub-group (initially) to access raw data

Second stageDo we trust each others data?

Developing a kite mark for quality or resolution of data

What are we going to use to do this ?

Third StageDeveloping analysis tool box ( not reinventing the wheel).How are these to be used? Testing of Grid tools - where do we run the analysis? Do we move code to data or data to code? This may involve sharing of our servers for running programmes.

Where do we want to be?Sharing data with other modellers Integrating simulation data with other dataPresenting data so it can be used/accessed by non-modellersHaving all singing/all dancing databaseUsing any spare capacity within our group for number crunching

We shall never get people whose time is money to take much interest in atoms.Samuel Butler 1835-1902Funding:BBSRC, EPSRCWellcome TrustAICR

AcknowledgementsGeorge MoraitakisMark Sansom - OxfordDelphine Flatters Oliver Smart - BirminghamSpiros SkoulakisJonathan Essex - Southampton Isofina Pournara Leo Caves - YorkAndy Purkiss Charlie Naughton - NottinghamThomas MatthewsPaul Jeffrey (Oxford)David Boyd & Paul Durham (CLRC)

Electrostatic stability of wild type and mutant transthyretin oligomers90

90pH induced changesV30MT119M

CPU timings~17,000 atoms using Gromacs 2.0 - 8 processor Beowulf Cluster - 6 ns 12.5 days 27,000 atoms using AMBER 6 4 processor Beowulf Cluster - 3 ns 23 days

pK1/2 values monomerHis31 5.1His56 4.8His88 3.9His90 3.6

Glu54 2.1

Tyr116 9.3Glu92 0.3

His88 -5.3His90 -7.6

Tyr116 -1.7Glu92 -5.3

Tyr116 Glu92

pK1/2 values dimerTyr116His88His90Glu92

Free energiesD-M 16kcal/mol, T-M 43kcal/mol, pH 7-3.5D-M 13kcal/mol, T-M 35kcal/mol, pH 7-4 wt1 < wt2 mut_noa < mut_a

ConclusionsStability, Yes?Relative stability, No Important residues identified? Desolvation, DescreeningNeed for a method that allows for conformational flexibility.

Stability of -crystallins using molecular dynamicsAndy PurkissCrystallin X-ray crystal structure to 1.2 A two domain protein, each domain around 80 residues.Each domain has a pair of -sheets each formed from two greek key motifs.Short linker peptide with bend bringing domains together. A six residue hydrophobic domain interface. -crystallin features

High Temperature (500K) Simulation of crystallin0ns1nsWildtypeF56A Mutant

Water Insertion Protocol on crystallinCycle 1Cycle 1000WildtypeF56A Mutant

Cluster Analysis of Water insertion on C-terminal domain of Scrystallin

Cluster Analysis of Water insertion on C-terminal domain of crystallin

Distribution of the distance of Ile 56 from Helix B and Helix 310 (sitting each on the two opposite sides of the residue) from all the conformations sampled. Only in the mutant conformations we find that Ile 56 exhibits two alternative preferable distances from Helix B and from Helix 310 one near the distance of the crystal structure and one distant.

Results: Ile 56 positioning

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