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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
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