MDdb Science Gateway MDdb entry ID 690002
views
MDdb comments

Hot-spots and their contribution to the self-assembly of the viral capsid: in-silico prediction and analysis

Armando Díaz-Valle, José Marcos Falcón-González, Mauricio Carrillo-Tripp

Manuscript DOI: Preprint 10.1101/72302, Published NA

Date of Original MD DATA Submission: 31/07/2019 by Mauricio Carrillo-Tripp1
Date of last modification: 27/09/2019 Mauricio Carrillo-Tripp1

1 Biomolecular Diversity Laboratory, Centro de Investigación y de Estudios Avanzados Unidad Monterrey, Vía del Conocimiento 201, Parque PIIT, C.P. 66600, Apodaca, Nuevo León, México

ABSTRACT: In order to rationally design biopolymers that mimic biological functions, first, we need to elucidate the molecular mechanisms followed by nature. For example, the viral capsid is a macromolecular complex formed by self-assembled proteins which, in many cases, are biopolymers with an identical amino acid sequence. Specific protein-protein interactions drive the capsid self-assembly process, leading to several distinct protein interfaces. Following the hot-spot hypothesis, we propose a conservation-based methodology to identify those interface residues that are crucial elements on the self-assembly and thermodynamic stability of the capsid. We validate our predictions by computational free energy calculations using an atomic-scale molecular model of an icosahedral virus. Our results show that a single mutation in any of the hot-spots significantly perturbs the quaternary interaction, decreasing the absolute value of the binding free energy, without altering the tertiary structure. Our methodology can lead to a strategy to rationally modulate the capsid's thermodynamic properties.

SIMULATION DATA

MD Simulation
Visualize MD trajectory [Download MD coordinates and trajectory files]

Total Atoms

Protein chains

H2O

Na

Cl

T [K]

Box X,Y,Z [nm]

ns

ns/day

S01: WT monomer [coord] [traj]

214825

1

70695

136

132

310

129.5, 129.5, 129.5

50

2.1

S02: E176Q monomer [coord] [traj]

214825

1

70697

135

132

310

129.5, 129.5, 129.5

50

2.1

S03: R179Q monomer [coord] [traj]

214819

1

70695

137

132

310

129.5, 129.5, 129.5

50

2.1

S04: P188A monomer [coord] [traj]

214830

1

70698

136

132

310

129.5, 129.5, 129.5

50

2.1

S05: V189N monomer [coord] [traj]

214823

1

70695

136

132

310

129.5, 129.5, 129.5

50

2.1

S06: E77Q monomer [coord] [traj]

214839

1

70703

136

132

310

129.5, 129.5, 129.5

50

2.1

S07: F186A monomer [coord] [traj]

214829

1

70696

135

132

310

129.5, 129.5, 129.5

50

2.1

S08: WT dimer [coord] [traj]

269245

2

87987

174

166

310

223.9, 99.5, 124.5

2

2.6

S09: E176Q dimer [coord] [traj]

269163

2

87959

172

166

310

223.9, 99.5, 124.5

2

2.6

S10: R179Q dimer [coord] [traj]

269134

2

87954

176

166

310

223.9, 99.5, 124.5

2

2.6

S11: P188A dimer [coord] [traj]

269159

2

87961

174

166

310

223.9, 99.5, 124.5

2

2.6

S12: V189N dimer [coord] [traj]

269163

2

87961

174

166

310

223.9, 99.5, 124.5

2

2.6

S13: E77Q dimer [coord] [traj]

269159

2

87965

174

166

310

223.9, 99.5, 124.5

2

2.6

S14: F186A dimer [coord] [traj]

269157

2

87957

172

166

310

223.9, 99.5, 124.5

2

2.6

Simulation Protocol and Analysis

Monomers
# FOR EACH MUTANT j, MINIMIZE, EQUILIBRATE NVT AND NPT, AND DO MD
>grompp -f md.mdp -c mutant_j_npt.gro -t mutant_j_npt.cpt -p mutant_j_charmm.top -n index.ndx -o mutant_j.tpr
>mdrun -deffnm mutant_j
Dimers
# FOR EACH MUTANT j, MINIMIZE, EQUILIBRATE NVT AND NPT
# FOR EACH MUTANT j, SMD TO PULL DIMER APART ALONG THE REACTION COORDINATE
>grompp -f md_pull.mdp -c md_j_npt.gro -p ab_mutant_j_charmm.top -n index.ndx -t md_j_npt.cpt -o pull_j.tpr
>mdrun -s pull_j.tpr
# SEPARATE FRAMES TO CHOSE WINDOWS FOR UMBRELLA
>trjconv -s pull_j.tpr -f traj_j.xtc -o conf_j.gro -sep
# FOR EACH WINDOW i, MINIMIZE, EQUILIBRATE NVT AND NPT, AND DO UMBRELLA SAMPLING
>grompp -f md_umbrella.mdp -c npt_i_j.gro -t npt_i_j.cpt -p ab_mutant_j_charmm.top -n index.ndx -o umbrella_i_j.tpr
>mdrun -deffnm umbrella_i_j -pf pullf-umbrella_i_j.xvg -px pullx-umbrella_i_j.xvg
# USE WHAM TO GENERATE PMF
>g_wham -it tpr-files_j.dat -if pullf-files_j.dat -o -hist -unit kCal

Post-processing on trajectories uploaded

Monomers
(submited files)
# FOR EACH MUTANT j
# REMOVE WATER AND IONS, KEEP MOLECULES WHOLE
>echo 1 | trjconv -f mutant_j.xtc -s mutant_j.tpr -o mutant_j_noh2o_nojump.xtc -pbc nojump
# CENTER MOLECULE IN BOX
>echo 1 1 | trjconv -f mutant_j_noh2o_nojump.xtc -s mutant_j.tpr -o mutant_j_noh2o_center.xtc -center
# REMOVE ROTATIONS
>echo 1 1 | trjconv -f mutant_j_noh2o_center.xtc -s mutant_j.tpr -o mutant_j_noh2o_fit.xtc -fit rot+trans
# EXTRACT FIRST FRAME IN TRAJECTORY
>echo 1 | trjconv -f mutant_j_noh2o_fit.xtc -s mutant_j.tpr -o mutant_j_noh2o_fit_0000ns.pdb -dump 0
Dimers
(submited files)
# FOR EACH MUTANT j
# REMOVE WATER AND IONS, KEEP MOLECULES WHOLE
>echo 1 | trjconv -f mutant_j.xtc -s mutant_j.tpr -o mutant_j_noh2o_nojump.xtc -pbc nojump
# EXTRACT FIRST FRAME IN TRAJECTORY
>echo 1 | trjconv -f mutant_j_noh2o_nojump.xtc -s mutant_j.tpr -o mutant_j_noh2o_nojump_0000ns.pdb -dump 0
Use the following QRCode in printed media to link back to this metadata page: MDdb Science Gateway
This study was funded by: Consejo Nacional de Ciencia y Tecnología México (CONACYT grants number 132376 and CB2017-2018 A1-S-17041 to M.C.-T.)