Recycling Corner/Alpha Helix Generator

RIBOZOME - a Polypeptide Alpha Helix Generator script

Creates an alpha helix from a user input string.

Jmol script by Ron Mignery with help from Angel Herráez

Script for the Jmol application

The top-level function plico_gen_pp asks user for a peptide sequence in a pop-up.

The top-level function plico_gen_alpha accepts a sequence string as a parameter.

With this script you can generate a polypeptide alpha helix chain from a sequence string in 1-char amino-acid coding. You can optionally give it a chain label other than the default :A. You can also add to an existing chain, add new chains to an existing model or now create the chain in a new frame by prepending a '+' to the sequence string.

Chains start from the origin and extend along the Z-axis as they are built. If a chain with the same chain label as the new chain is at the origin, the new sequence is added to the old. If a chain with a different chain label is at the origin, all existing chains are shifted 20 angstroms to the right along the X axis until the origin is clear.

Ribozome is a member of the Plico suite of protein folding tools described here. It may be installed and accessed as a macro with the file:

Title=PLICO Generate Polypeptide
Script=script <path to your script folder>/ribozome.spt;plico_gen_pp

saved as ribozome.macro in your .jmol/macros directory as described in Macro.

Copy and paste the following into a text editor and save in your scripts directory as ribozome.spt.

#   RIBOZOME - Jmol script by Ron Mignery
#   v1.16 beta    7/13/2015 -minor edits
#
#   RIBOZOME takes a string message encoding an amino acid (aa) sequence
#   and generates a corresponding alpha helix one aa at a time from the
#   N terminus to the C terminus rotating the emerging helix as it goes.
#
#   The message is a string entered by the user at a prompt. [+A:...]
#   It may be typed in or pasted in and be of any length
#   If the message is prepended with "+" then the chain is created in a new
#   frame. Otherwise it is added to the current frame
#   If the message is prepended with <C>: (where C is any single letter)
#   then the chain is so labeled and separated from existing chains
#   if different from the first chain.
#
#   The IUPAC/IUBMB 1 letter code is used:
#   A=ALAnine B=GLutam?X* C=CYSteine D=ASPartate E=GLUtamate
#   F=PHEnylalanine G=GLYcine H=HIStidine I=IsoLEucine K=LYSine
#   L=LEUcine M=METhionine N=ASparagiNe O=PYrroLysine*** P=PROline
#   Q=GLutamiNe R=ARGinine S=SERine T=THReonine U=SElenoCysteine
#   V=VALine W=TRyPtophan X=UNKnown Y=TYRosine Z=ASpar?X**
#     *Either GLU or GLN: drawn as GLN with chi3 flipped
#    **Either ASP or ASN: drawn as ASN with chi3 flipped
#   ***Not supported: drawn as ALA

# The following constant values determine the pitch of the alpha helix
kPHI = -57    # Dihedral angle of N-CA bond (nominally -57)
kPSI = -47    # Dihedral angle of CA-C bond (nominally -47)
kOMEGA = 180    # Dihedral angle of the peptide bond (nomin ally 180)
kPEPTIDE_ANGLE = 120    # C-N-CA angle (nominally 120)
kPRO_BUMP = -10 # Psi angle change increment to N-3psi when N is Pro
gCHAIN = 'A'    # The chain id
gA = ""
gPdbAddHydrogens = false
gAppendNew = true
gNewFrame = false

# Lookup 3 letter code from 1 letter code
g3from1 = {"A":"ALA", "B":"GLX","C":"CYS", "D":"ASP","E":"GLU", "F":"PHE",
    "G":"GLY", "H":"HIS","I":"ILE", "K":"LYS","L":"LEU", "M":"MET",
    "N":"ASN", "O":"PYL","P":"PRO", "Q":"GLN","R":"ARG", "S":"SER",
    "T":"THR", "U":"SEC","V":"VAL", "W":"TRP","X":"UNK", "Y":"TYR", "Z":"ASX"}

# Generate PDB atom record
function gen_atom(e, aa, i, xyz) {
    gA =  format("ATOM  %5d %4s %3s ", gN, e, aa )
    gA +=  format("%s%4d    %8.3f", gCHAIN, i, xyz[1] )
    gA +=  format("%8.3f%8.3f\n", xyz[2], xyz[3] )
    gN++
    return gA
};

# Generate a PDB amino acid record set
function gen_aa(i, aa) {    # Writes globals gA and gN

    # From constructed AAs
    var N0 = [0.0, 0.0, 0.0]
    var CA = [ 0.200, 1.174, 0.911 ]
    var C  = [ -1.110, 1.668, 1.425 ]
    var O  = [ -1.320, 1.693, 2.62 ]
    var CB = [ 1.062, 2.1950, 0.230 ]

    var G1 = [ 2.359, 1.607, -0.344]
    var G2 = [ 1.363, 3.336, 1.157 ]
    var D1 = [ 3.222, 2.656, -1.048 ]
    var D2 = [ 3.143, 0.904, 0.725 ]
    var E1 = [ 3.645, 3.749, -0.167 ]
    var E2 = [ 2.491, 3.234, -2.249 ]
    var Z  = [ 4.474, 4.857, -0.565 ]
    var H1 = [ 4.090, 6.173, -0.166 ]
    var H2 = [ 5.565, 4.707, -1.229 ]

    var D1dn = [ 2.955, 2.229, -1.250 ]
    var D2dn = [ 2.859, 0.552, 0.102 ]

    var E1eq = [ 3.821, 3.528, -0.382 ]
    var E2eq = [ 3.337, 2.634, -2.293 ]

    var Gp = [ 2.008, 1.24, -0.46 ]
    var Dp = [ 1.022, 0.213, -1.031 ]

    var Gfy  = [ 2.368, 1.471, -0.0152 ]
    var D1fy = [ 3.346, 1.524, 0.921 ]
    var D2fy = [ 2.493, 0.516, -1.151 ]
    var E1fy = [ 4.513, 0.615, 0.8244 ]
    var E2fy = [ 3.528, -0.336, -1.206 ]
    var Zfy  = [ 4.588, -0.285, -0.168 ]
    var Hfy = [ 5.738, -1.245, -0.233 ]

    var Ghw  = [ 2.406, 1.626, -0.134 ]
    var D1hw = [3.498, 1.936, 0.675]
    var D2hw = [ 2.713, 0.901, -1.211 ]
    var E1hw = [ 4.160, 0.518, -1.178 ]
    var E2hw = [ 4.622, 1.160, 0.0816 ]
    var E3hw = [ 3.789, 2.523, 1.944 ]
    var Z2hw = [ 5.973, 1.177, 0.689 ]
    var Z3hw = [ 5.014, 2.550, 2.503 ]
    var H2hw = [ 6.153, 1.846, 1.844 ]

    #N1 = [ 2.069, -2.122, -0.554]

    # Build PDB atom records common to all AAs
    var a3 = g3from1[aa]
    if (a3 = "") {
        a3 = "UNK"
    }
    print format("+ %s%d/%d", a3, i, gSeq.count + gResno)
    gA = gen_atom(" N  ", a3, i, N0)
    gA += gen_atom(" CA ", a3, i, CA)
    gA += gen_atom(" C  ", a3, i, C)
    gA += gen_atom(" O  ", a3, i, O)
    if ((aa != 'G') && (aa != 'X')) {
        gA += gen_atom(" CB ", a3, i, CB)
    }

    # Now add AA specific atom records
    switch (aa) {
    case 'A' :
        break;
    case 'B' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD ", a3, i, D1)
        gA += gen_atom(" OE1", a3, i, E2eq)    # GLN with Es switched
        gA += gen_atom(" NE2", a3, i, E1eq)
        break;
    case 'C' :
        gA += gen_atom(" SG ", a3, i, G2)
        break;
    case 'D' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" OD1", a3, i, D1dn)
        gA += gen_atom(" OD2", a3, i, D2dn)
        break;
    case 'E' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD ", a3, i, D1)
        gA += gen_atom(" OE1", a3, i, E1eq)
        gA += gen_atom(" OE2", a3, i, E2eq)
        break;
    case 'F' :
        gA += gen_atom(" CG ", a3, i, Gfy)
        gA += gen_atom(" CD1", a3, i, D1fy)
        gA += gen_atom(" CD2", a3, i, D2fy)
        gA += gen_atom(" CE1", a3, i, E1fy)
        gA += gen_atom(" CE2", a3, i, E2fy)
        gA += gen_atom(" CZ ", a3, i, Zfy)
        break;
    case 'G' :
        break;
    case 'H' :
        gA += gen_atom(" CG ", a3, i, Ghw)
        gA += gen_atom(" ND1", a3, i, D1hw)
        gA += gen_atom(" CD2", a3, i, D2hw)
        gA += gen_atom(" CE1", a3, i, E2hw)
        gA += gen_atom(" NE2", a3, i, E1hw)
        break;
    case 'I' :
        gA += gen_atom(" CG1", a3, i, G1)
        gA += gen_atom(" CG2", a3, i, G2)
        gA += gen_atom(" CD1", a3, i, D1)
        break;
    case 'K' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD ", a3, i, D1)
        gA += gen_atom(" CE ", a3, i, E1)
        gA += gen_atom(" NZ ", a3, i, Z)
        break;
    case 'L' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD1", a3, i, D1)
        gA += gen_atom(" CD2", a3, i, D2)
        break;
    case 'M' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" SD ", a3, i, D1)
        gA += gen_atom(" CE ", a3, i, E1)
        break;
    case 'N' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" OD1", a3, i, D1dn)
        gA += gen_atom(" ND2", a3, i, D2dn)
        break;
    case 'P' :
        gA += gen_atom(" CG ", a3, i, GP)
        gA += gen_atom(" CD ", a3, i, DP)
        break;
    case 'Q' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD ", a3, i, D1)
        gA += gen_atom(" OE1", a3, i, E1eq)
        gA += gen_atom(" NE2", a3, i, E2eq)
        break;
    case 'R' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" CD ", a3, i, D1)
        gA += gen_atom(" NE ", a3, i, E1)
        gA += gen_atom(" CZ ", a3, i, Z)
        gA += gen_atom(" NH1", a3, i, H1)
        gA += gen_atom(" NH2", a3, i, H2)
        break;
    case 'S' :
        gA += gen_atom(" OG ", a3, i, G1)
        break;
    case 'T' :
        gA += gen_atom(" OG1", a3, i, G1)
        gA += gen_atom(" CG2", a3, i, G2)
        break;
    case 'U' :
        gA += gen_atom("SeG ", a3, i, G1)
        break;
    case 'V' :
        gA += gen_atom(" CG1", a3, i, G1)
        gA += gen_atom(" CG2", a3, i, G2)
        break;
    case 'W' :
        gA += gen_atom(" CG ", a3, i, Ghw)
        gA += gen_atom(" CD2", a3, i, D1hw)
        gA += gen_atom(" CD1", a3, i, D2hw)
        gA += gen_atom(" CE2", a3, i, E2hw)
        gA += gen_atom(" NE1", a3, i, E1hw)
        gA += gen_atom(" CE3", a3, i, E3hw)
        gA += gen_atom(" CZ2", a3, i, Z2hw)
        gA += gen_atom(" CZ3", a3, i, Z3hw)
        gA += gen_atom(" CH2", a3, i, H2hw)
        break;
    case 'X' :
        gA += gen_atom(" Xx ", a3, i, CB)
        break;
    case 'Y' :
        gA += gen_atom(" CG ", a3, i, Gfy)
        gA += gen_atom(" CD1", a3, i, D1fy)
        gA += gen_atom(" CD2", a3, i, D2fy)
        gA += gen_atom(" CE1", a3, i, E1fy)
        gA += gen_atom(" CE2", a3, i, E2fy)
        gA += gen_atom(" CZ ", a3, i, Zfy)
        gA += gen_atom(" OH ", a3, i, Hfy)
        break;
    case 'Z' :
        gA += gen_atom(" CG ", a3, i, G1)
        gA += gen_atom(" OD1", a3, i, D2dn)    # ASN with Ds switched
        gA += gen_atom(" ND2", a3, i, D1dn)
        break;
    default :
        break;
    }

    return gA
};

# Generate an alpha helix
function plico_gen_alpha(gSeq) {
    gPdbAddHydrogens = pdbAddHydrogens
    set pdbAddHydrogens false
    if (gPlicoRecord != "") {
        var g = format("show file \"%s\"", gPlicoRecord)
        var ls = script(g)
        if (ls.find("FileNotFoundException")) {
            ls = ""
        }
        ls += format("plico_gen_alpha(\"%s\");", gSeq)
        write var ls @gPlicoRecord
    }

    gSeq = gSeq%9999%0
    gNewFrame = false
    if (gSeq[1] == '+') {
        gNewFrame = true
        gSeq = gSeq[2][9999]
    }
    if (gSeq[2] == ':') {
        gCHAIN = gSeq[1]
        gSeq = gSeq[3][9999]
    }

    var f = (_frameID/1000000)
    var m = (_frameID%1000000)
    var c = gCHAIN
    gResno = 0    # global pre-existing AA count
    var pn = 1    # previous gN
    gAppendNew = appendNew
    gN = 1
    if (gNewFrame) {
        appendNew = true
    }
    else {
        appendNew = false

        # If not new
        if (m > 0) {

            # Get the largest atomno in frame
            gN = {(file=f) and (model=m)}.atomno.max

            # While there is an atom at the origin
            while (true) {
                var ai = {within(0.1, {0 0 0}) and (file=f) and (model=m)}
                if (ai.size > 0) {

                    # If on the same chain
                    if (ai[1].chain = c) {

                        # Delete OXT
                        delete {(atomName="OXT") and (file=f) and (model=m)
                            and (chain=c)}
                        gResno = ai.resno
                        pn = ai.atomno
                        break
                    }
                    # Else move all from the new chain rightward on X axis
                    else {
                        select {(file=f) and (model=m) and (chain!=c)}
                        translateselected {20, 0, 0 }
                        gN++
                    }
                }
                else {
                    break
                }
            } # endwhile
        }
    }

    # For each aa
    var nn = gN    # new N
    for (var i = 1; i <= gSeq.count; i++) {

        if ((m > 0) and not appendNew) {

            # Move polypeptide C to bond distance from new AA N
            select {(file=f) and (model=m) and (chain=c)}
            fix none
            translateselected {2.069, -2.122, -0.554 } #N1
        }

        # Gen AA
        gA = "data \"append aa\"\n"    # global PDB atom record
        gA += gen_aa(i + gResno, gSeq[i]);    # gN is updated in subroutine
        gA += "end \"append aa\""
        script inline @{gA}

        f = (_frameID/1000000)
        m = (_frameID%1000000)
        appendNew = false

        # If PRO ahead
        var pb = 0
        if ((gSeq.count - i) >= 2) {
            if (gSeq[i + 2] == 'P') {
                pb = kPRO_BUMP
            }
        }

        # If not first AA
        if (nn > 1) {

            # Gen axis on new N perpendicular to the plane
            # containing atoms nn, pn+2 and nn+1
            var aNn = {(atomno=nn) and (file=f) and (model=m) and (chain=c)}
            var aNn1 = {(atomno=@{nn+1}) and (file=f) and (model=m) and (chain=c)}
            var aPn1 = {(atomno=@{pn+1}) and (file=f) and (model=m) and (chain=c)}
            var aPn2 = {(atomno=@{pn+2}) and (file=f) and (model=m) and (chain=c)}
            var aPn3 = {(atomno=@{pn+3}) and (file=f) and (model=m) and (chain=c)}
            var v1=aPn2.xyz - aNn.xyz
            var v2=aNn1.xyz - aNn.xyz
            var axis = cross(v1, v2)

            # Center on atom previous C
            axis += aPn2.xyz

            # Rotate the polypeptide N on the new AA C to tetrahedral (nominally 110)
            select {(atomno < nn) and (file=f) and (model=m) and (chain=c)}
            fix {(atomno >= nn) and (file=f) and (model=m) and (chain=c)}
            rotateselected @axis @aNn @{kPEPTIDE_ANGLE - 65.5}

            # Make omega dihedral = kOMEGA (nominally 180)
            rotateselected @aPn2 @aNn @{kOMEGA - 154.7}

            # Make the new phi dihedral = kPHI (nominally -57)
            rotateselected @aNn @aNn1 @{kPHI - 2.5}

            # Make the old psi dihedral = kPSI (nominally -47)
            select {(atomno < nn) and (file=f) and (model=m) and (chain=c)
                and not aPn2 and not aPn3}
            rotateselected @aPn1 @aPn2 @{kPSI + 33.4 + pb}

            # Make the peptide bond
            connect @aNn @aPn2
        }

        # Step new and previous N
        pn = nn
        nn = gN

    } # endfor i

    # Add terminal O
    gA = "data \"append aa\"\n"    # global PDB atom record
    gA += gen_atom(" OXT", g3from1[gSeq[gResno+gSeq.count]],
        gResno+gSeq.count, [ -2.142, 2.057, 0.574])
    gA += "end \"append aa\""
    script inline @{gA}

    connect
    var xx = {(element="Xx") and (file=f) and (model=m) and (chain=c)}
    for (var i = 1; i <= xx.size; i++) {
          connect 1.8 {(atomindex=@{xx[i].atomIndex}) and (file=f)
            and (model=m) and (chain=c)}
    }

    # Clean up
    connect ([UNK].CA) ([UNK].Xx and within(group, _1) and (file=f)
        and (model=m) and (chain=c))
    select ((file=f) and (model=m))
    fix none
    print format("%d atoms generated", gN-1)
    appendNew = gAppendNew
    pdbAddHydrogens = gPdbAddHydrogens
}

function plico_gen_pp {
    echo Generating Alpha Helix

    # Get the sequence from the user
    gSeq = prompt("Enter AA sequence (<+A:>[A-Z]...)", "")%9999%0
    if ((gSeq != "NULL") and (gSeq.count > 0)) {
        print format ("Sequence=%s  phi=%d  psi=%d", gSeq, kPHI, kPSI)
        plico_gen_alpha(gSeq)
    }
}
# end of ribozome.spt

In a webpage

The main script is a small adaptation of the one above. Sequence input has been moved to the webpage. In addition, the helix parameters (which are fixed in the original script) may be changed in the page by a user. The model is generated and displayed in a Jmol object in the page (JmolApplet or JSmol HTML5 object).

The JSmol variant is not working yet. We need debugging the script, something in it fails to run properly in JSmol and no good helix is formed.

See it in action

Contributors

Remig, AngelHerraez