Moloc offers the possibility to build peptides on a residue level
without having to bother about single atoms. The resulting C-alpha
structures can then be transferred directly to all atom models.
Let us build a model for Oxytocin (sequence CYIQNCPLG) which is cyclized
by a disulfide bond.
- Enter 'pca' (peptide modelling) fro the main menu.
- Click 'c' (C-alpha building) to be thrown into the
peptide builder menu.
- Click 'n' (open new entry) which produces a new
AA dipeptide.
- Click 'c' (change types of single residues) and
pick the first residue A1, to change it to cysteine C1 by a corresponding
selection. Change also A2 to Y2.
- Enter 'a' (build sequence, add, delete residues)
to add the rest of the sequence.
- Pick residue Y2 to indicate that you want to continue building
at that end of the chain.
- Select 's' secondary structure type for further
building. The menu header indicates the actual value.
- Continue by either selecting the following residues on the menu
bar or by clicking 'c' (chunk) to add the rest
of the sequence as a single junk entered by one letter code into
a string requester.
- Exit to go back to the peptide builder.
- Click 'b' (make, break bonds) an pick the two
cystein residues in sequence. The program asks whether you want to
inset a peptide bond (this for cyclic peptides) which you answer by
'no'.
Now the topology of your peptide is specified. Depending on your
choice of secondary structure for elongating the sequence the
conformation may need more or less adjustment to conform with
the cyclic condition. The peptide force field offers the possibility
to obtain a reasonable first order proposal for the conformation:
- Click 'o' (optimize Calf structure) to invoke
the peptide force field menu, which is arranged in close analogy
to the all-atom force field menu.
- Click 'o' (optimize) to perform an optimization.
- click ',' (peptide representation) an pick the structure
in order to obtain an indication how the peptide links between
adjacent C-alpha are oriented. (MIDDLE mouse picking removes this
display). This option can be selected in various places where one
works with C-alpha structures.
- Exit optimizer and C-alpha builder to return to the 'pca' menu.
- Click 'a' (generate full peptide) and pick the
C-alpha structure to generate the corresponding all-atom entry. Since
the S-S bond term in the C-alpha force field is a simple distance
term, the resulting conformation for the disulfide bridge may be
quite unrealistic. However, a short minimization with the all-atom
force field will quickly mend this possible defect.
Using Non-Natural Amino Acids
Moloc allows to build peptides containing non-natural amino acid
residues. These must be provided in file(s) witn neutral amino-
and acid groups. The names of these structures must start with a
letter and have at least three characters (preferably all letters).
- Read in the structures in menu option pca/h
before undertaking any building action or reading from file any
structures containing such residues. Moloc takes the first three
letters (upper-case) of the structure names as 3-letter code for
identification.
- Structures can be built on the Calf level by entering a sequence
in pca/c/m (starting) or in pca/c/a/c
to continue.
- Sequences can be given in single letter codes for natural residues
but for non-natural residues only 3-letter codes are available. To
distinguish those, they must be preceeded by a '-'
character! (e.g. 'a-aaaaa' is an alanine followed by a AAA-residue
and two alanines).
- When generating full structures (pca/a) Moloc
takes over the side-chain conformations from the templates.
- Calf structures can be stored and read back in .mca format.
- Full structures are preferably stored as .cif files. Storing in
.pdb format works but information on H-counts of non-natural side
chains is lost and may not be correctly reconstructed!
Homology Building
From a known protein structure a structural model for a homologous
protein can be built, provided a sequence alignment is given. The
alignment must be given in a file in which each line is interpreted
as single letter code sequence of the original protein or of the
homologous one, provided the line starts with either #1 or #2
respectively. All other lines are interpreted as comments. In case
of deletions or insertions, missing residues must be indicated by a
dot. For deletions the program simply connects the two ends of the
last and first residues present. Insertions are positioned near a
circle of appropriate size. It is understood that these regions are
subjected to subsequent energy minimization within the Calf force
field to generate acceptable geometries. The program automatically
generates a user set which contains the residues in the homologous
structure, which may be kept fixed under a subsequent minimization.
This set must be activated (definition of fixed residues) prior to
minimization.
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