{"id":221,"date":"2019-03-08T00:08:09","date_gmt":"2019-03-08T00:08:09","guid":{"rendered":"https:\/\/ccsb.scripps.edu\/latticenucleoid\/?page_id=221"},"modified":"2019-05-06T13:25:50","modified_gmt":"2019-05-06T13:25:50","slug":"hivnucleoid","status":"publish","type":"page","link":"https:\/\/ccsb.scripps.edu\/latticenucleoid\/hivnucleoid\/","title":{"rendered":"HIV-1 Nucleoid"},"content":{"rendered":"

Lattice Models of HIV-1 Nucleoid Condensation<\/h3><\/h1><\/div>
<\/div><\/div><\/div><\/div><\/div>

Introduction<\/h3>\n

Four programs are included in this release, which together\u00a0model the mature HIV-1 nucleoid, using this five-step pipeline:
\n1) quasisymmetry.f<\/strong> — creates a lattice of points on a sphere that\u00a0correspond to the locations of gag proteins in the immature\u00a0HIV-1 virion
\n2) rnapath.f<\/strong> — performs a self-avoiding random walk on this lattice,\u00a0generating the path of two HIV-1 gRNA strands.
\n3) condense.f<\/strong> — in a short optimization run, is used to relax\u00a0the RNA path based on a 3 nt\/bead coarse-grain model.
\n4) makeconstraints.f<\/strong> — assigns the location of integrase and\u00a0nucleocapsid proteins, based on a list of experimental
\nlocalizations and choosing integrase sites that are in\u00a0proximity from step (3).
\n5) condense.f<\/strong> — condenses the nucleoid incorporating integrase and\u00a0nucleocapsid localizations and user-defined secondary structure\u00a0constraints.<\/p>\n

The result is a PDB-format file that may be read by most molecular\u00a0graphics programs. The PDB format is modified in the following ways:
\n–coordinates are in nanometers
\n–RNA strands have atom name “P” and residue name “RNA”
\n–integrase subunits have atom name “CA” and residue name “IN”
\n–nucleocapsid subunits have atom name “N”, and residue names
\n“NCO” for experimentally-observed positions and
\n“NCR” for randomly-placed positions
\nSuggested radii for visualization: RNA=0.5, NC=1.5, IN=2.5<\/p>\n

To create models:<\/p>\n

1) Compile the programs:
\ngfortran quasisymmetry.f -o quasisymmetry
\ngfortran rnapath.f -o rnapath
\ngfortran makeconstraints.f -o makeconstraints
\ngfortran condense.f -o condense<\/code><\/p>\n

2) The programs and pipeline require several input data files:
\nicos.mat<\/strong> — matrices for icosahedral symmetry
\nTlattice.pdb<\/strong> — coordinates for quasisymmetrical tiling
\ninpeaks.dat<\/strong> — experimental integrase binding sites
\nncpeaks.dat<\/strong> — experimental nucleocapsid binding sites
\n5UTR.const<\/strong> — constraint file for secondary structure in the 5’UTR<\/p>\n

3a) The programs may be run individually, reading input commands\u00a0from Unit 5, or from a command file, such as:
\n.\/condense < condense.inp > condense.log<\/code> (log file is optional)<\/p>\n

3b) The script file HIVnucleoid.script will run a full pipeline to generate\u00a0a nucleoid model with integrase tetramers.
\n.\/HIVnucleoid.script > HIVnucleoid.log<\/code> (log file is optional)
\nOn typical desktop hardware, this will require about 1\/2 hour.<\/p>\n

The script file HIVnucleoid_3types.script will run a pipeline to\u00a0generate three models: with tetramers, dimers, or no integrase.<\/p>\n

Please note that these programs were created to explore a specific\u00a0application, and are not designed for generalized use. They have\u00a0very little error checking, so large changes in input parameters\u00a0will be expected to lead to spurious results or program crashes.<\/p>\n<\/div>

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Downloads<\/h3>\n

Source code and input files are available at GitHub.<\/a><\/p>\n

Models from our first study are available at Zenodo<\/a>.<\/p>\n<\/div>

<\/div><\/div><\/div><\/div><\/div>

<\/i><\/i><\/span>quasisymmetry.f parameters<\/span><\/a><\/h4><\/div>
\n
quasisymmetry.pdb         # output file name\r\n7,1,2000,7.5              # H,K,number of gag hexamer positions, length of triangular edge\r\n1234                      # random seed<\/pre>\n
H,K are the indices that define the quasisymmetry. Values where H+K = ~8 are appropriate for HIV-1.<\/p>\n<\/div><\/div><\/div>
<\/i><\/i><\/span>rnapath.f parameters<\/span><\/a><\/h4><\/div>
\n
quasi_71.pdb     # input file name\r\nrnapath.pdb      # output file name\r\n21,3058          # number of points on each edge, number of beads per RNA chain\r\n1234             # random seed<\/pre>\n<\/div><\/div><\/div>
<\/i><\/i><\/span>makeconstraints.f parameters<\/span><\/a><\/h4><\/div>
\n
rnapath_relax.pdb     # input coordinate file\r\ninpeaks.dat           # input data file with integrase sites\r\nncpeaks.dat           # input data file with nucleocapsid sites\r\nnucleoid.const        # output constraint parameter file\r\n15.                   # max distance for crosslink (nm)\r\n0,35,100              # number of integrase dimers, integrase tetramers, and nucleocapsid\r\n1234                  # random seed<\/pre>\n<\/div><\/div><\/div>
<\/i><\/i><\/span>condense.f parameters<\/span><\/a><\/h4><\/div>
\n
rnapath.pdb         # input coordinate file (here, from rnapath.f)\r\n5UTR.const          # input constraint definition file\r\nNC.position         # input file for location of nucleocapsid\r\nrnapath_relax.pdb   # output coordinate file\r\n1 3058              # coordinate numbers in chain 1\r\n3059 6116           # coordinate numbers in chain 2\r\n-0.0001             # step size for (-0.0001) repulsion or (0.0005) attraction\r\n1,38.               # icellflag, if 1, constrain to cell radius\r\n10000               # number of steps\r\n1234                # random seed<\/pre>\n<\/div><\/div><\/div><\/div><\/div>
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