DepictStructBioinf

DepictStructBioinf allows researchers of the same protein domain to quickly aggregate knowledge, record findings in a relevant format, and compare hypotheses. By default, this package comes loaded with information about the APOBEC3 family of proteins.

Quick start (for Mac/Linux)

Ensure Pymol and Git are installed on your system, then in a terminal, run:

git clone https://github.com/j-wags/DepictStructBioinf.git
pip install biopython numpy mdanalysis
cd DepictStructBioinf
python depict.py -sf a3b_ctd
pymol visualize.pml

To see all annotations and structure families that can be loaded, run python depict.py -h

Depending on your system, the "pip" command may require a "sudo" at the beginning of the line.

Mac notes:

• The pip-affiliated python may be in /usr/local/bin/python instead of /usr/bin/python
• The Pymol executable may be called "MacPyMol" on the command line (instead of just "pymol"). An alternative way to open the visualize.pml file is by navigating to the DepictStructBioinf folder and double clicking.
• I've received reports that biopython and mdanalysis installations are giving errors on some platforms. I don't yet have a machine that can reproduce these errors. Creation of a virtualenv/miniconda may be an interim solution.

Project Cassettes

A "project cassette" is a directory containing:

aligned_structures

A directory containing all relevant protein structures to this project. Pymol will load structures directly from here, so be sure that any cleaning/3D alignment is already performed before the structures get here. For multi-chain proteins, I recommend splitting the chains into separate files and using a naming scheme like 3o02_A and 3o02_B

Annotations.py

Provides the dictionary "annotations". The core of each annotation is a text label, parent sequence (eg. a3b_ctd), and list of sequence positions. For example

annotations = {}
annotations['asp_314_in_a3b_ctd'] = {'parent':'a3b_ctd',
                                     'label':'Asp314 in A3Bctd',
                                     'posns':[i-192 for i in [314]], 
                                     'checkAA':'D',
                                     'help':'Aspartate which has been shown to be important for -1 base specificity.'
                                  }


annotations['zn_coordinating'] = {'parent':'a3g_ctd',
                                  'label':'Zinc-coordinating amino acids',
                                  'posns':[i-197 for i in [288,257,291]],
                                  'checkAA':'HCC',
                                  'help':'Zinc-coordinating amino acids. '
                                  }

The keys in this dictionary (ie. test1) are the names that will be presented to the user as annotation options when they type python depict.py -h.

The key-value pairs in the annotation dictionary are formatted as follows

• parent: The name of a sequence in the sequence alignment that this annotation belongs to.
• label: The label that will appear as floating text in the pymol visualization.
• posns: The sequence position(s) that this annotation refers to. Note: Indexing begins at 0, is for each domain (not the entire protein!) and ignores gaps.
• checkAA: The single-letter amino acid codes that SHOULD line up to your sequence. Used for internal checking (TODO: implement this as a regular test).
• help (optional): A help message for other users. This currently isn't used by the program.

Note - Negative indices in "posns" will be ignored, as pymol interprets negative numbers as the end of a range (eg. -27 is interpreted as 0-27).

Families.py

Provides the dictionary "families". Structure families can be helpful if you want to quickly load groups of proteins with common characteristics. For example

families = {}
families['a3a'] = ['4xxo_A','4xxo_B','2m65_A','5sww_AE','5sww_BF','5sww_CG','5sww_DH','5td5_AC']
families['dna_bound'] = ['5sww_AE','5sww_BF','5sww_CG','5sww_DH','5td5_AC','5k83_AH','5k83_CI','5k83_EJ']

The keys in this dictionary (ie. a3a) are presented to the user as choices under the "-sf" argument when the user runs "python depict.py -h".

SequenceAlignment.fasta

The sequence alignment in fasta format. This alignment must include all sequences referenced in Annotations.py, and sequences corresponding to structures that you will load. For structures to load, the sequence title in this file must be the structure name, excluding the path (assumed to be "project_casette/aligned_structures/") and exluding the suffix ".pdb"

For example:

a3a
MEASPASGPRHLMDPHIFTSNFNNG---IG---RHKTYLCYEVERLDNGTSVKMDQHRGF
LHNQ--------AKNLLCGFYGRHAELRFLDLVPSL-QLDPAQIYRVT--WFIS--WSPC
FSWGCAGEVRAFLQENTHVRLRIFAARIY-DY-DPLYKEALQMLRD----AGAQVSIMTY
DEFKH----CWDTFVDHQGC----PFQPWDGLDEHSQALSGRLRAILQNQGN--------
------
>a3b_ntd
-MNPQIRNPMERMYRDTFYDNFENEPILYG---RSYTWLCYEVKIKRGRSNLLWDT--GV
FRGQ------------VYFKPQYHAEMCFLSWFCGN-QLPAYKCFQIT--WFVS--WTPC
PD--CVAKLAEFLSEHPNVTLTISAARLY-YYWERDYRRALCRLSQ----AGARVTIMDY
EEFAY----CWENFVYNEGQ----QFMPWYKFDENYAFLHRTLKEILRYL----------
------
>2m65_A
MEASPASGPRHLMDPHIFTSNFNNG---IG---RHKTYLCYEVERLDNGTSVKMDQHRGF
LHNQAKN--------LLCGFYGRHAELRFLDLVPSL-QLDPAQIYRVT--WFIS--WSPC
FSWGCAGEVRAFLQENTHVRLRIFAARIY--DYDPLYKEALQMLRD----AGAQVSIMTY
DEFKH----CWDTFVDHQGC----PFQPWDGLDEHSQALSGRLRAILQNQGN--------
------
>4xxo_A
-------GPRHLMDPHIFTSNFNNG---IG---RHKTYLCYEVERLDS---VKMDQHRGF
LHNQAKN--------LLCGFYGRHAALRFLDLVPSL-QLDPAQIYRVT--WFIS--WSPC
FSWGCAGEVRAFLQENTHVRLRIFAARIY--DYDPLYKEALQMLRD----AGAQVSIMTY
DEFKH----CWDTFVDHQGA----PFQPWDGLDEHSQALSGRLRAILQN-----------
------
>4xxo_B
-------GPRHLMDPHIFTSNFNNG---IG---RHKTYLCYEVERLDN-TSVKMDQHRGF
LHNQAKN---------LLGFYGRHAALRFLDLVPSL-QLDPAQIYRVT--WFIS--WSPC
FSWGCAGEVRAFLQENTHVRLRIFAARIY--DYDPLYKEALQMLRD----AGAQVSIMTY
DEFKH----CWDTFVDHQGA----PFQPWDGLDEHSQALSGRLRAILQN-----------
------

##General notes

• Be very careful when extracting sequences from pdb files! Different structure-to-sequence programs will interpret gaps and variable-occupany residues differently (eg. ALYS and BLYS for placements of a lysine residue may be double counted in the sequence)
• Think carefully and use your judgement when dealing with systems involving homodimers or repeating/homologous domains.