Structure/function studies of HIV proteins

HIV gp120 V3 loop modelling using de novo approaches

HIV protease-inhibitor binding energy prediction

Structure/function studies of gp120

• gp120 is missing loops (V1-3) in the experimental structure (1gc1)

• Re-build V3 loop in the context of the experimental structure

• Repeat for many different sequences for which phenotype is known

• Analyse ensembles of structures generated for patterns

• Correlate patterns to phenotype

Sequences modelled

R5-specifying sequences:

1V02X15 CTRPNNNTRKSIQVGPGKAIYTTGEIIGDLRQAHC1V10X106 ............P....R...A..G....I.K...1V15PX336 ....S....R..A....R.F.A.DQ....I.K...

2V02PLX01 CTRPNNNTRKSIPIGPGRAFYATGEIIGDIRQAHC2V07PLX71 ............T.R.........A...N......2V10PLX10 ............T...........Q..........2V16PLX01 .........R..T...........QV..N......2V23X22 ...........RHL.L.......DN..........

8v09x03 CTRPNNNTRKSI---NIGPGRAFYATGDIIGDIRQAHC8v11px07 .........R..---T......................8v13xb ............---H...........A..........8v17x06 ............---H...........E........Y.8v24x08 ............---H......S....E........Y.

9V03x01 CTRPNNNTRKSIHIGPGRAWYTTGEIIG-DIRQAHC9V09x05 ............QM.L............-.......9V20x14 ............QM.L....H.......-...R.Y.9V21x02 .A..G......VQM.L....H.......-.......

X4-specifying sequences:

CTRPNNNTRKSIQVGPGKAIYTTGEIIGDLRQAHC1V10X114 ....S....R..A....R...A.EK....I.K...1V15PX335 ....S....R..A....R.F.A.DK....I.K...1V19PX272 ....S....R..A....R.F.A.DK....I.K...

CTRPNNNTRKSIPIGPGRAFYATGEIIGDIRQAHC2V07PLX70 ............H...........K..........2V10PLX09 ............H..........EK...N......2V16PLX03 ............R......V...EK...N......2V23X24 .........RG.R......V...DK...N......

CTRPNNNTRKSI---NIGPGRAFYATGDIIGDIRQAHC8v19px04 ..........R.HIGH...........A......R.Y.8v20x04 ..........R.HIGH...........G......R.Y.8v24x17 ....S.....R.RIGH...........G......R.Y.

CTRPNNNTRKSIHIGPGRAWYTTGEIIG-DIRQAHC9V21x16 .....S..G...RM.L...RH..R....-...R.Y.9V22x07 .....RH.G...RM.L....H..R....-...K.Y.9V25x19 .....SH.G...RM.L....H..R....G...K.Y.9V25x20 .....RHAG...RM.M....H..R....D...K.YR

Semi-exhaustive segment-based foldingEFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK

generatefragments from database14-state , model

… …

minimisemonte carlo with simulated annealingconformational space annealing, GA

… …

filter all-atom pairwise interactions, bad contactscompactness, secondary structure

HIV gp120 loop modelled in the presence of neutralising antibody

HIV gp120 loop ensembles

Current summary of gp120 related work

• Able to generate ensembles of loops that cluster for different sequences

• Able to match conformations generated with predictions made for human proteins with some statistical significance

To do

• Need to use structure based alignments with other physical properties to correlate to sequences, and consequently the phenotype

• Not sure? “Ab binds to CD4 induced site on gp120”

• Blue sky: model interactions with models of receptors

Prediction of HIV-1 protease-inhibitor binding energies with MD

MD simulation time

Cor

rela

tion

coef

ficie

nt

ps0 0.2 0.4 0.6 0.8 1.0

1.0

0.5

with MD

without MD

Ekachai Jenwitheesuk

Molecular dynamics

• Force = -dU/dx (slope of potential U); acceleration, m a(t) = force

• All atoms are moving so forces between atoms are complicated functions of time

• Analytical solution for x(t) and v(t) is impossible; numerical solution is trivial

• Atoms move for very short times of 10-15 seconds or 0.001 picoseconds (ps)

x(t+t) = x(t) + v(t)t + [4a(t) – a(t-t)] t2/6

v(t+t) = v(t) + [2a(t+t)+5a(t)-a(t-t)] t/6

Ukinetic = ½ Σ mivi(t)2 = ½ n KBT

• Total energy (Upotential + Ukinetic) must not change with time

new position

old position

new velocity

old velocity

acceleration

acceleration

old velocity

n is number of coordinates (not atoms)

Current summary of protease-inhibitor related work

• Able to predict binding energies with very good correlations to experimentally determined energies

• Framework for modelling binding interactions that incorporates flexibility of both protein and substrate

To do/in progress

• Repeat for larger set of 100 protease-inhibitor complexes

• Relate binding energy to effectiveness of inhibitor

• Repeat for other proteins and inhibtors

• Incorporate into an HIV systems/population dynamics model