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 10.3390/ijms20235966

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 []	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

PDB entries:	1cwp	MD engine:	Gromacs v4.5.5
Related data:	VIPERdb	Force-fields:	CHARMM27 all-atom CMAP [, ], TIP3P []
Pipeline input files:	config.zip	Solution:	H2O, Na, Cl
HPC center:	bmdhpc cluster, Insurgente cluster	Methods:	MD [, ], SMD [, ], Umbrella Sampling [, ], WHAM [, ], PMF [, ]

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

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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.)