molecular dynamics quantum chemistry - nvidia
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Unveiling the structure of the HIV-1 capsid
Juan R. Perilla http://www.ks.uiuc.edu
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign
Source: NIAID/NIH
HIV Replication Cycle - Overview
Structure of the HIV capsid
Capped fullerene cone
Pentamers introduce sharp declinations
Continuously changing curvature in the hexagonal lattice
Ganser, B. K. (1999). Science, 283, 80–83
Briggs, J. et al. (2006). Structure, 14, 15–20
Highly schematic model; beads are not proteins!
Pornillos, O. , Sønquist, et al. (2009). Cell, 137(7), 1282–92.
increase concentration
X-ray structure of CA Obtained Through Ingenious Preparation
Ganser-Pornillos, B. K. et al. (2007). Cell, 131(1), 70–9.
CA-hexameric planar lattice in crystal
NTD fills inside space of hexamers, CTD fills outside.
hexamer
hexameric center trimeric center
There are also dimeric symmetry centers!
Structure of Full Length CA NTDs and CTDs play different roles
C-terminal domain
N-terminal domain hexamer
Cryo-EM maps of the HIV Capsid
Cryo-EM micrograph of recombinant WT HIV-1 CA at 8 Angstrom
in vitro, 1 M NaCl
All-atoms MD of HIV-1 CA tube • 71 hexamers • 13 million atoms • 10 ns MDFF coupled to
density • 125 ns MD, • Blue waters NAMD
Early Science System
NAMD Benchmarks on the Early Science System (no-GPU)
MDFF Structural Refinement
hydrophobic interaction at trimeric interface, surr. by polar residues
a view into the trimeric interface, contacts between three helices_10
formation of peripheral hydrogen bonds
Modeling of Pentameric Oligomers CA-Pentamer
H H
P/H
H10 H10
H10
Compare: (1) H10 superimposed from HOH, (2) H10 from POH; clearly pentamer H10 moves a lot, H10(P)+H10(H)^2 become more compact than H10(H)^3
(1.3 M atoms) 1.5 µs simulation on Titan, GPU accelerated
Pentamer-of-Hexamers (POH)
Hexamer-of-Hexamers (HOH)
MD:HIV-1 CA pentamer-hexamer
• 1.3 million atoms • 1.5 µs MD • NAMD GPU-accelerated on
NVIDIA Fermi GPU
A204 I201
E213
K203
204C 204D 204L 204K 204Y WT
Infe
cti
vit
y (
% o
f W
T)
Co
re A
ss
ocia
ted
CA
(%
)
CA CTD
trimer interface
WT A204C
A204C assembles efficiently into cones
25
37
50
75 WT A204C WT A204C
mature CA6
A204C cross-links
only in mature virions
Ernest Yufenyu & Chris Aiken
100nm Gongpu Zhao
Analogy with fullerenes
Fitted structure High
strain region
The parameter ξ measures the deviation of the fullerene from a perfect sphere and the strength of its deformation. A perfect sphere corresponds to ξ=0, and an axially symmetric ellipsoid corresponds to ξ=1.
High correlation with experimental density
Spiral search on 2D-projection
3D-embedding DFT geometry optimization
Spiral search on 2D-projection
3D-embedding
DFT geometry optimization
Isomer search and geometry optimization
Fullerene model number
Co
rre
latio
n
252H
+12P
216H
+12P
212H
+12P
166H
+12P
All-atom MD simulation of mature HIV-1 capsid
• 216 hexamers +12 pentamers (13.4 M), • 64 million atoms total including solvent • 100 ns running NAMD on 4000 Cray-XE nodes, 128000 cores • 6 ns/day, all-atom
All-atom MD simulation of mature HIV-1 capsid
• 186 hexamers +12 pentamers (12 M), • 64 million atoms total • 100 ns running NAMD on NCSA Blue Waters 2000 to 3500 XK Nodes equipped with NVIDIA Tesla K20X • 9 to 12 ns/day
PDB Molecule of the month
www.pdb.org
Paper folding model
Courtesy of David Goodsell (Scripps)
Acknowledgments Peijun Zhang
Angela M. Gronenborn
Department of Structural Biology
Center for HIV Protein Interactions
University of Pittsburgh School of Medicine
Christopher Aiken
Department of Pathology,
Microbiology and Immunology
Vanderbilt University Medical Center
Acknowledgments
Theoretical and Computational Biophysics Group University of Illinois Urbana-Champaign
Jim Phillips NAMD
John Stone VMD
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Questions? Contact us
Devang Sachdev - NVIDIA
@DevangSachdev
Dr. Juan R. Perilla – UIUC
www.ks.uiuc.edu
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